
_________ CCP-EM Job launch/home/tom/Code/devtools/install/bin/refmac5 ________



CCP-EM pipeline job 1 of 10 ___________________________________________________

__ Command ____________________________________________________________________
/home/tom/Code/devtools/install/bin/refmac5 xyzin /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1AKE_cha_molrep.pdb mapin /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc xyzout /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/1AKE_cha_molrep_start_rframe.pdb atomsf /home/tom/Code/devtools/checkout/refmac5.8/data/atomsf_electron.lib << eof
/home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/job_data/stdin_map2mtz.txt
eof
_______________________________________________________________________________
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<html> <!-- CCP4 HTML LOGFILE -->
<hr>
<!--SUMMARY_END--></FONT></B>
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<pre>
 
 ###############################################################
 ###############################################################
 ###############################################################
 ### CCP4 6.5.011: Refmac_5.8.0131 version 5.8.0131 : 06/08/15##
 ###############################################################
 User: unknown  Run date: 12/ 8/2015 Run time: 10:32:04 


 Please reference: Collaborative Computational Project, Number 4. 2011.
 "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242.
 as well as any specific reference in the program write-up.

<!--SUMMARY_END--></FONT></B>
 $TEXT:Reference1: $$ Main reference $$ 
   "REFMAC5 for the refinement of macromolecular crystal structures:"
   G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011) 
   Acta Crystallogr. D67, 355-367

 $$
 $SUMMARY :Reference1:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference2: $$ Secondary reference $$ 
   "Refinement of Macromolecular Structures by the  Maximum-Likelihood Method:"
   G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
   Acta Crystallogr. D53, 240-255
   EU  Validation contract: BIO2CT-92-0524

 $$
 $SUMMARY :Reference2:  $$ Refmac: $$
 :TEXT:Reference2: $$

 Data line--- mode sfcalc
 Data line--- source EM
 Data line--- sfcalc mrad 4.0
 Data line--- sfcalc shift
 Data line--- end
  Data line--- mode sfcalc
  Data line--- source EM
  Data line--- sfcalc mrad 4.0
  Data line--- sfcalc shift
  Data line--- END
===> Warning: Reflections file has not been defined
===> Warning: Switching to the idealisation mode

    ****                     Input and Default parameters#                      ****


Input coordinate file.  Logical name - XYZIN actual file name  - /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1AKE_cha_molrep.pdb
Output coordinate file. Logical name - XYZOUT actual file name - /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/1AKE_cha_molrep_start_rframe.pdb

  Refinement type                        : Idealisation
  Refinement type                        : NONE
  SF calculation from MAP: /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc
  SF calculation from CRD: /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1AKE_cha_molrep.pdb


    ****                           Makecif parameters                           ****

Dictionary files for restraints : /usr/local/sci_local/mx/ccp4-6.5/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /usr/local/sci_local/mx/ccp4-6.5/lib/data/monomers/ener_lib.cif
    Apart from amino acids and DNA/RNA all monomers will be checked to see if atom names and connectivity is correct
    Hydrogens will be restored in their riding positions
    Links between monomers will be checked. Only those links present in the coordinate file will be used
    Standard sugar links will be analysed and used
    For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
    Symmetry related links will be analysed and used
    Cis peptides will be found and used automatically




Monitoring style is "MEDIUM". Complete information will be printed out in the
first and last cycle. In all other cycles minimum information will be printed out
Sigma cutoffs for printing out outliers
If deviation of restraint parameter > alpha*sigma then information will be printed out
Distance outliers      10.000
Angle outliers         10.000
Torsion outliers       10.000
Chiral volume outliers 10.000
Plane outliers         10.000
Non-bonding outliers   10.000
---------------------------------------------------------------

 Input file :/home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/re
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.44
 _lib_update       30/05/14
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 11608
                with complete description    : 11608
  NUMBER OF MODIFICATIONS                    :    61
  NUMBER OF LINKS                            :    71
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )

FORMATTED      OLD     file opened on unit  45
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
Logical name: ATOMSF, Filename: /home/tom/Code/devtools/checkout/refmac5.8/data/atomsf_electron.lib
<!--SUMMARY_END--></FONT></B>

  Number of atoms    :    1656
  Number of residues :     214
  Number of chains   :       1
  I am reading library. Please wait.
                mon_lib.cif
  WARNING : CIS peptide bond is found, angle =     11.30
            ch:AA   res:  86  PHE              -->  87  PRO
  --------------------------------
  --- title of input coord file ---

  PDB_code:XXXX
  PDB_name:----
  PDB_date:XX-XXX-XX
  --------------------------------
  Number of chains                  :       1
  Total number of monomers          :     214
  Number of atoms                   :    3344
  Number of missing atoms           :       0
  Number of rebuilt atoms           :    1688
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0


 loop_
     _atom_type_symbol
     _atom_type_scat_Cromer_Mann_a1
     _atom_type_scat_Cromer_Mann_b1
     _atom_type_scat_Cromer_Mann_a2
     _atom_type_scat_Cromer_Mann_b2
     _atom_type_scat_Cromer_Mann_a3
     _atom_type_scat_Cromer_Mann_b3
     _atom_type_scat_Cromer_Mann_a4
     _atom_type_scat_Cromer_Mann_b4
     _atom_type_scat_Cromer_Mann_a5
     _atom_type_scat_Cromer_Mann_b5


  N      0.1022   0.2451   0.3219   1.7481   0.7982   6.1925   0.8197  17.3894   0.1715  48.1431
  C      0.0893   0.2465   0.2563   1.7100   0.7570   6.4094   1.0487  18.6113   0.3575  50.2523
  H      0.0116   0.5347   0.0400   3.5867   0.0657  12.3471   0.0191  18.9525   0.0398  38.6269
  S      0.2497   0.2681   0.5628   1.6711   1.3899   7.0267   2.1865  19.5377   0.7715  50.3888
  O      0.0974   0.2067   0.2921   1.3815   0.6910   4.6943   0.6990  12.7105   0.2039  32.4726


 Number of distances         :           0
 Number of angles            :           0
 Number of torsions          :           0
 Number of planes            :           0
 Number of chirals           :           0
 Number of intervals         :           0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
                        Standard  External       All
                Bonds:      3344         0      3344
               Angles:      6105         0      6105
              Chirals:       254         0       254
               Planes:       514         0       514
             Torsions:      1333         0      1333
            Intervals:         0         0         0
--------------------------------------------------------------------------------


  Number of harmonic restraints       =            0
  Number of atoms in special position =            0
 -----------------------------------------------------

 Map file here /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc

 Logical Name: /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc   Filename: /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc 

File name for input map file on unit  10 : /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc
file size 56320 ; logical name /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc



           Number of columns, rows, sections ...............   24   24   24
           Map mode ........................................    2
           Start and stop points on columns, rows, sections     0   23    0   23    0   23
           Grid sampling on x, y, z ........................   24   24   24
           Cell dimensions .................................   66.0000    66.0000    66.0000    90.0000    90.0000    90.0000
           Fast, medium, slow axes .........................    X    Y    Z
           Minimum density .................................     0.00000
           Maximum density .................................    43.92188
           Mean density ....................................     3.79930
           Rms deviation from mean density .................     9.01953
           Space-group .....................................    1
           Number of titles ................................    1


     Labels:                            
  MODIM M CCP4    Chimera 1.3.2570 Mon Sep  7 14:1                    ?    ?


 nsym 1           1
 res max nominal    5.50000000      res max used    5.51102161    
 Map manupilation mode = M
 reference map

 Logical Name: /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc   Filename: /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc 

File name for input map file on unit  10 : /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc
file size 56320 ; logical name /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc



           Number of columns, rows, sections ...............   24   24   24
           Map mode ........................................    2
           Start and stop points on columns, rows, sections     0   23    0   23    0   23
           Grid sampling on x, y, z ........................   24   24   24
           Cell dimensions .................................   66.0000    66.0000    66.0000    90.0000    90.0000    90.0000
           Fast, medium, slow axes .........................    X    Y    Z
           Minimum density .................................     0.00000
           Maximum density .................................    43.92188
           Mean density ....................................     3.79930
           Rms deviation from mean density .................     9.01953
           Space-group .....................................    1
           Number of titles ................................    1


     Labels:                            
  MODIM M CCP4    Chimera 1.3.2570 Mon Sep  7 14:1                    ?    ?


 Starting (nominal) resolution    9.07272771E-02   5.51102161    
 Number of all maps for SF calculation :           1
 Map file number 1 /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc
 File number            1 /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc
 nsym            1
 Start reading            0           0           0          23          23          23
 logname : MAPIN1 file name: 
 Number of maps            1
 Print stats of the original data to the file: orig_data_rescut.txt
 Number of resolution bins            9

    ****      Mean(|F|) and other statistics: Without accounting for mask       ****

 $TABLE: Mean(|F|) and other statistics
 $GRAPH: Mean(|F|), Mean(|F|^2), Mean(|F|^4) vs resolutions: 1,6,7,8
 $$
 2sin(th)/l 2sin(th)/l dmin dmax NREF Mn(|F|) Mn(|F|^2) Mn(|F|^4) Mn(A) Mn(B) Mn(A^2) Mn(B^2) cor(A,B)
 $$
   2.29558413E-04   3.82614089E-03   66.0014420       16.1666298             128   4583.77783       55708992.0       3.48502838E+16  -177.762680       14.8013153       48412660.0       7296326.00     -0.512377024    
   3.82614089E-03   7.42271356E-03   16.1666298       11.6069651             247   1149.11548       1735042.00       7.57135730E+12  -12.5792570       5.42083979       764395.875       970646.188       7.18705207E-02
   7.42271356E-03   1.10192858E-02   11.6069651       9.52627850             307   598.662720       478308.219       5.54877321E+11  -3.52150345      0.523956120       225560.031       252747.750      -5.62838018E-02
   1.10192858E-02   1.46158580E-02   9.52627850       8.27156830             369   294.713226       113671.953       2.85516329E+10  0.321767300       2.08096361       57696.1133       55975.7812      -4.54078019E-02
   1.46158580E-02   1.82124302E-02   8.27156830       7.40996313             421   159.269348       32721.8105       2.13478886E+09   3.63159704      0.670519710       15009.9717       17711.8340      -2.25084946E-02
   1.82124302E-02   2.18090024E-02   7.40996313       6.77145624             471   97.2547073       12346.8145       320414304.      -2.01833057      -1.10970914       5920.40625       6426.41406      0.110711686    
   2.18090024E-02   2.54055746E-02   6.77145624       6.27386951             529   61.7682724       5055.67139       58506360.0     -0.600897908     -0.430477321       2382.76660       2672.90356      0.151062295    
   2.54055746E-02   2.90021468E-02   6.27386951       5.87198448             543   42.2774429       2482.95288       15315608.0      0.426767021      0.537540793       1202.31934       1280.63416      0.165690675    
   2.90021468E-02   3.26087289E-02   5.87198448       5.53774643             546   30.4723988       1356.16553       6433904.00      0.951081574     -0.283423513       619.880737       736.286133       1.60751715E-02
 $$
 sharpening things:            0           1   0.00000000       0.00000000    

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: starting_map.mtz   Filename: starting_map.mtz 

 New limits for the box
           1           2           1
          21          20          21


 Box limits :
           1           2           1
          21          20          21
 New grid   :          22          20          22
 New cell   :   60.5000000       55.0000000       60.5000000       90.0000000       90.0000000       90.0000000    
 Shifts     :  -0.00000000      -2.75000000      -0.00000000    

 Testing in apply mask    1.52181013E-42          24          24          24   1.00000000    
        2523           1
 sharpening things:            0           1   0.00000000       0.00000000    

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: masked_fs.mtz   Filename: masked_fs.mtz 

  Time in seconds: CPU =         0.03
             Elapsed =           0.00

    ****           Things for loggraph, R factor and others vs cycle            ****


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS:<Rfactor> vs cycle :N:1,2,3:
:FOM vs cycle :N:1,4:
:-LL vs cycle :N:1,5:
:-LLfree vs cycle :N:1,6:
:Geometry vs cycle:N:1,7,8,9,10,11:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
 $$
 $TEXT:Result: $$ Final results $$
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
 Refmac_5.8.0131:  End of Refmac_5.8.0131  
Times: User:       6.1s System:    0.1s Elapsed:     0:06  
</pre>
</html>
<!--SUMMARY_END--></FONT></B>


CCP-EM job finished: Wednesday, 12. August 2015 10:32AM ______________________
_______________________________________________________________________________

_________ CCP-EM Job launch/home/tom/Code/devtools/install/bin/refmac5 ________



CCP-EM pipeline job 2 of 10 ___________________________________________________

__ Command ____________________________________________________________________
/home/tom/Code/devtools/install/bin/refmac5 xyzin /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/1AKE_cha_molrep_start_rframe.pdb hklin masked_fs.mtz xyzout /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/1AKE_cha_molrep_refine_rframe.pdb hklout /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/1AKE_cha_molrep_refine_rframe.mtz atomsf /home/tom/Code/devtools/checkout/refmac5.8/data/atomsf_electron.lib << eof
/home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/job_data/stdin_refine.txt
eof
_______________________________________________________________________________
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<html> <!-- CCP4 HTML LOGFILE -->
<hr>
<!--SUMMARY_END--></FONT></B>
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<pre>
 
 ###############################################################
 ###############################################################
 ###############################################################
 ### CCP4 6.5.011: Refmac_5.8.0131 version 5.8.0131 : 06/08/15##
 ###############################################################
 User: unknown  Run date: 12/ 8/2015 Run time: 10:32:10 


 Please reference: Collaborative Computational Project, Number 4. 2011.
 "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242.
 as well as any specific reference in the program write-up.

<!--SUMMARY_END--></FONT></B>
 $TEXT:Reference1: $$ Main reference $$ 
   "REFMAC5 for the refinement of macromolecular crystal structures:"
   G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011) 
   Acta Crystallogr. D67, 355-367

 $$
 $SUMMARY :Reference1:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference2: $$ Secondary reference $$ 
   "Refinement of Macromolecular Structures by the  Maximum-Likelihood Method:"
   G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
   Acta Crystallogr. D53, 240-255
   EU  Validation contract: BIO2CT-92-0524

 $$
 $SUMMARY :Reference2:  $$ Refmac: $$
 :TEXT:Reference2: $$

 Data line--- labin FP=Fout0 PHIB=Pout0
 Data line--- solvent no
 Data line--- source EM
 Data line--- mapc vector
 Data line--- REFI sharpen -50.0
 Data line--- BFACtor SET 40.0
 Data line--- ncycles 10
 Data line--- weight auto 10
 Data line--- RESO 10.0
 Data line--- ridge dist sigma 0.02
 Data line--- end
  Data line--- labin FP=Fout0 PHIB=Pout0
  Data line--- solvent no
  Data line--- source EM
  Data line--- mapc vector
  Data line--- REFI sharpen -50.0
  Data line--- BFACtor SET 40.0
  Data line--- ncycles 10
  Data line--- weight auto 10
  Data line--- RESO 10.0
  Data line--- ridge dist sigma 0.02
  Data line--- END

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN   Filename: masked_fs.mtz 

===> Warning: Figure of merit of phases has not been assigned
===> Warning: They will be assumed to be equal to 1.0

    ****                     Input and Default parameters#                      ****


Input coordinate file.  Logical name - XYZIN actual file name  - /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/1AKE_cha_molrep_start_rframe.pdb
Output coordinate file. Logical name - XYZOUT actual file name - /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/1AKE_cha_molrep_refine_rframe.pdb
Input reflection file.  Logical name - HKLIN actual file name  - masked_fs.mtz
Output reflection file. Logical name - HKLOUT actual file name - /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/1AKE_cha_molrep_refine_rframe.mtz

Cell from mtz :    60.500    55.000    60.500    90.000    90.000    90.000
Space group from mtz: number -    1; name - P 1

  Refinement type                        : Restrained

Initial B values of all atoms will be set to     40.000


    ****                           Makecif parameters                           ****

Dictionary files for restraints : /usr/local/sci_local/mx/ccp4-6.5/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /usr/local/sci_local/mx/ccp4-6.5/lib/data/monomers/ener_lib.cif
    Apart from amino acids and DNA/RNA all monomers will be checked to see if atom names and connectivity is correct
    Hydrogens will be restored in their riding positions
    Links between monomers will be checked. Only those links present in the coordinate file will be used
    Standard sugar links will be analysed and used
    For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
    Symmetry related links will be analysed and used
    Cis peptides will be found and used automatically


  Residual                               : Phase modified Maximum Likelihood for Fs
 Phase Blurred by  Scale*Exp(-B s**2)    :    1.00    0.00

    ****                    Least-square scaling parameters                     ****

Overall scale
Overall B value
Overall anisotropic B with tr(B) = 0.0


    ****                 Map sharpening parameters and methods                  ****

No map sharpening will be performed

  Method of minimisation                 : Sparse Matrix
  Experimental sigmas used for weighting
  Number of Bins and width:    20       0.0005
  Refinement of individual isotropic Bfactors
  Refinement resln        :    60.5000  9.9998
  Estimated number of reflections :        823
  Auto weighting. An attempt
  Refinement cycles       :    10
  Scaling type                           :
          Bulk solvent using using Babinet principle

  Estimation of D/Sigma in resolution bins
  using  working set of reflns with experimental sigmas
  Input phases not used in SigmaA estimation

  Scaling and SigmaA resln:    60.5000  9.9998

  Damping factors:     1.0000  1.0000


    ****                    Geometry restraints and weights                     ****


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

 Planar groups (all and main chain)
          WEIGHT= 1.00 1.00

 Chiral centers
          Weight= 1.00

 NON-BONDED CONTACTS
          Overall weight                          =  1.00
          Sigma for simple VDW                    =  0.20
          Sigma for VDW trhough torsion angle     =  0.20
          Sigma for HBOND                         =  0.20
          Sigma for metal-ion                     =  0.20
          Sigma for DUMMY and other atom          =  0.30
          Distance for donor-accepetor = vdw1+vdw2+(-0.30)
          Distance for acceptor - H    = vdw1+     ( 0.10)
          VDW distance through torsion = vdw1+vdw2+(-0.30)
          Distance for DUMMY-others    = vdw1+vdw2+(-0.70)

 TORSION ANGLES
          Weight= 1.00

 THERMAL FACTORS
          Weight= 1.00
     Main chain bond (1-2 neighbour)          1.5A**2
     Main chain angle (1-3 neighbour)         2.0A**2
     Side chain bond                          3.0A**2
     Side chain angle                         4.5A**2

 RESTRAINTS AGAINST EXCESSIVE SHIFTS
     Positional parameters                   0.00A
     Thermal parameters                      0.00A
     Occupancy parameters                    0.00

 RADIUS OF CONFIDENCE
     Positional parameters 0.00A
     Thermal parameters    0.00A**2
     Occupancy parameters  0.00

Restraints on changes of interatomic distances is appplied

    ****                    Distance shift penlty parameters                    ****

     Sigma:           0.0200
     Maximum distance 4.2000

Monitoring style is "MEDIUM". Complete information will be printed out in the
first and last cycle. In all other cycles minimum information will be printed out
Sigma cutoffs for printing out outliers
If deviation of restraint parameter > alpha*sigma then information will be printed out
Distance outliers      10.000
Angle outliers         10.000
Torsion outliers       10.000
Chiral volume outliers 10.000
Plane outliers         10.000
Non-bonding outliers   10.000
B value  outliers      10.000
---------------------------------------------------------------

 Input file :/home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/re
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.44
 _lib_update       30/05/14
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 11608
                with complete description    : 11608
  NUMBER OF MODIFICATIONS                    :    61
  NUMBER OF LINKS                            :    71
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )

FORMATTED      OLD     file opened on unit  45
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
Logical name: ATOMSF, Filename: /home/tom/Code/devtools/checkout/refmac5.8/data/atomsf_electron.lib
<!--SUMMARY_END--></FONT></B>

  Number of atoms    :    1656
  Number of residues :     214
  Number of chains   :       1
  I am reading library. Please wait.
                mon_lib.cif
  --------------------------------
  --- title of input coord file ---

  PDB_code:XXXX
  PDB_name:----
  PDB_date:12-AUG-15
  --------------------------------
  Number of chains                  :       1
  Total number of monomers          :     214
  Number of atoms                   :    3344
  Number of missing atoms           :       0
  Number of rebuilt atoms           :    1688
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0


 loop_
     _atom_type_symbol
     _atom_type_scat_Cromer_Mann_a1
     _atom_type_scat_Cromer_Mann_b1
     _atom_type_scat_Cromer_Mann_a2
     _atom_type_scat_Cromer_Mann_b2
     _atom_type_scat_Cromer_Mann_a3
     _atom_type_scat_Cromer_Mann_b3
     _atom_type_scat_Cromer_Mann_a4
     _atom_type_scat_Cromer_Mann_b4
     _atom_type_scat_Cromer_Mann_a5
     _atom_type_scat_Cromer_Mann_b5


  N      0.1022   0.2451   0.3219   1.7481   0.7982   6.1925   0.8197  17.3894   0.1715  48.1431
  C      0.0893   0.2465   0.2563   1.7100   0.7570   6.4094   1.0487  18.6113   0.3575  50.2523
  H      0.0116   0.5347   0.0400   3.5867   0.0657  12.3471   0.0191  18.9525   0.0398  38.6269
  S      0.2497   0.2681   0.5628   1.6711   1.3899   7.0267   2.1865  19.5377   0.7715  50.3888
  O      0.0974   0.2067   0.2921   1.3815   0.6910   4.6943   0.6990  12.7105   0.2039  32.4726


 Number of distances         :           0
 Number of angles            :           0
 Number of torsions          :           0
 Number of planes            :           0
 Number of chirals           :           0
 Number of intervals         :           0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
                        Standard  External       All
                Bonds:      3344         0      3344
               Angles:      6104         0      6104
              Chirals:       254         0       254
               Planes:       513         0       513
             Torsions:      1333         0      1333
            Intervals:         0         0         0
--------------------------------------------------------------------------------


  Number of harmonic restraints       =            0
  Number of atoms in special position =            0
 -----------------------------------------------------


    ****                           Info from mtz file                           ****

FreeR flag                         -999
Number of "free" reflections          0
Number of   all  reflections        421
 Warning ==>The number of free reflections with flag         -999  is zero
 Warning ==> Switching off use of free R
--------------------------------------------------------------------------------
 Number of reflections in file       2523
 Number of reflections read            421


######  TLS Group Definitions ######



     CGMAT cycle number =      1

 Limits of asymmetric unit      : 1.00 1.00 1.00
 Grid spacing to be used        :    56   54   56
 Maximuum H,K,L                 :     7    6    7
 Minimum acceptable grid spacing:    37   34   37
 File opened           20
 Weight matrix    6.51758397E-04
 Actual weight    10.0000000      is applied to the X-ray term
Norm of X_ray positional gradient                6.08
Norm of Geom. positional gradient                70.4
Norm of X_ray B-factor gradient                  2.70
Norm of Geom. B-factor gradient                  0.00
Product of X_ray and Geom posit. gradients      0.220E+05
 Cosine of angle between them                       0.005
Product of X_ray and Geom B-fact gradients       0.00
 Cosine of angle between them                       0.000


Residuals: XRAY=    -0.1556E+06 GEOM=     0.1064E+05 TOTAL=    -0.1449E+06
 function value   -144939.562    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1680     0.018     0.019
Bond distances: others                         1664     0.000     0.020
Bond angles  : refined atoms                   2263     2.946     1.988
Bond angles  : others                          3841     3.655     3.000
Torsion angles, period  1. refined              213     4.975     5.000
Torsion angles, period  2. refined               75    39.116    24.533
Torsion angles, period  3. refined              313    15.459    15.000
Torsion angles, period  4. refined               13    13.916    15.000
Chiral centres: refined atoms                   254     0.122     0.200
Planar groups: refined atoms                   1887     0.011     0.021
Planar groups: others                           344     0.012     0.020
VDW repulsions: refined_atoms                   618     0.224     0.200
VDW repulsions.others                          2916     0.237     0.200
VDW; torsion: refined_atoms                    1606     0.183     0.200
VDW; torsion.others                            2030     0.107     0.200
HBOND: refined_atoms                             28     0.063     0.200
M. chain bond B values: refined atoms           855     0.000     4.000
M. chain bond B values: others                  854     0.000     4.000
M. chain angle B values: refined atoms         1067     0.000     6.000
M. chain angle B values: others                1068     0.000     6.000
S. chain bond B values: refined atoms           825     0.000     4.000
S. chain bond B values: others                  825     0.000     4.000
S. chain angle B values: refined atoms         1196     0.000     6.000
S. chain angle B values: others                1196     0.000     6.000
Long range B values: refined atoms             6918     0.000    37.714
Long range B values: others                    6915     0.000    37.713
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =  250.767, B  = 445.132
Overall anisotropic scale factors
   B11 =  2.12 B22 =  0.79 B33 = -2.91 B12 = -1.02 B13 =  2.35 B23 = -2.61
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1. M(Rfactor) v. resln :N:1,6,7:
:Cycle    1. M(Fobs) and M(Fc) v. resln :N:1,4,5:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used $$
$$
 0.001       9 100.00  1549.5  1538.7  0.01  0.01
 0.001       6 100.00   475.5   470.5  0.04  0.04
 0.001      21 100.00   276.6   287.2  0.06  0.06
 0.002       6 100.00   267.9   272.8  0.03  0.03
 0.002      18 100.00   238.5   238.4  0.03  0.03
 0.003      17 100.00   205.7   209.7  0.05  0.05
 0.003      16 100.00   157.5   153.7  0.04  0.04
 0.004      24 100.00   107.2   105.0  0.07  0.07
 0.004      14 100.00   121.9   118.3  0.05  0.05
 0.005      22 100.00   113.0   111.0  0.06  0.06
 0.005      21 100.00    91.0    88.9  0.07  0.07
 0.006      32 100.00    87.3    85.2  0.07  0.07
 0.006      16 100.00    87.5    82.9  0.06  0.06
 0.007      22 100.00    85.7    86.3  0.06  0.06
 0.007      32 100.00    63.0    64.2  0.11  0.11
 0.008      28 100.00    66.8    68.0  0.08  0.08
 0.008      41 100.00    63.6    65.5  0.08  0.08
 0.009      14 100.00    45.4    46.3  0.12  0.12
 0.009      20 100.00    45.0    48.2  0.10  0.10
 0.010      42 100.00    39.1    40.0  0.15  0.15
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle    1. FSC and  Fom(<cos(DelPhi)>-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCwork CorrFofcWork$$
 $$
  0.0005      9   1.000      0   0.000      9   1.000  0.999  0.9999  0.9998
  0.0010      6   1.000      0   0.000      6   1.000  0.998  0.9950  0.9838
  0.0015     21   0.999      0   0.000     21   0.999  0.996  0.9981  0.9934
  0.0020      6   0.999      0   0.000      6   0.999  0.995  0.9984  0.9973
  0.0025     18   0.998      0   0.000     18   0.998  0.993  0.9984  0.9978
  0.0029     17   0.998      0   0.000     17   0.998  0.992  0.9978  0.9946
  0.0034     16   0.998      0   0.000     16   0.998  0.991  0.9970  0.9906
  0.0039     24   0.996      0   0.000     24   0.996  0.990  0.9949  0.9877
  0.0044     14   0.996      0   0.000     14   0.996  0.990  0.9965  0.9921
  0.0049     22   0.996      0   0.000     22   0.996  0.989  0.9954  0.9909
  0.0054     21   0.996      0   0.000     21   0.996  0.988  0.9941  0.9864
  0.0059     32   0.995      0   0.000     32   0.995  0.988  0.9946  0.9921
  0.0064     16   0.996      0   0.000     16   0.996  0.987  0.9944  0.9921
  0.0068     22   0.996      0   0.000     22   0.996  0.986  0.9946  0.9886
  0.0073     32   0.994      0   0.000     32   0.994  0.985  0.9888  0.9775
  0.0078     28   0.995      0   0.000     28   0.995  0.985  0.9925  0.9820
  0.0083     41   0.995      0   0.000     41   0.995  0.984  0.9918  0.9795
  0.0088     14   0.993      0   0.000     14   0.993  0.984  0.9830  0.9663
  0.0093     20   0.994      0   0.000     20   0.994  0.983  0.9916  0.9861
  0.0098     42   0.993      0   0.000     42   0.993  0.983  0.9792  0.9461
 $$
Resolution limits                    =     60.500    10.000
Number of used reflections           =        421
Percentage observed                  =   100.0000
Percentage of free reflections       =     0.0000
Overall R factor                     =     0.0495
Average Fourier shell correlation    =     0.9925
Overall weighted R factor            =     0.0495
Overall weighted R2 factor           =     0.0336
Average correlation coefficient      =     0.9831
Overall correlation coefficient      =     0.9993
Overall figure of merit              =     0.9956
ML based su of positional parameters =     1.2745
ML based su of thermal parameters    =   221.4872
-----------------------------------------------------------------------------
 Trying gamma equal    0.00000000    
 Trying gamma equal    5.00000007E-02
 Gamma decreased to    3.99999991E-02


 fvalues    12293.9121       10643.1914       61422.0547       133582.312    


     CGMAT cycle number =      2

 File opened           20
 Weight matrix    5.39198285E-04
 Actual weight    10.0000000      is applied to the X-ray term


 function value   -149639.281    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1680     0.015     0.019
Bond distances: others                         1664     0.007     0.020
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =  250.722, B  = 404.039
Overall anisotropic scale factors
   B11 =  2.09 B22 =  0.67 B33 = -2.76 B12 = -0.79 B13 =  2.32 B23 = -2.39
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.0485
Average Fourier shell correlation    =     0.9928
Average correlation coefficient      =     0.9838
Overall figure of merit              =     0.9957
-----------------------------------------------------------------------------
 Trying gamma equal    3.99999991E-02
 Gamma decreased to    3.09090894E-02


 fvalues    6336.56494       6072.24316       12731.0098       69437.8906    


     CGMAT cycle number =      3

 File opened           20
 Weight matrix    4.45975427E-04
 Actual weight    10.0000000      is applied to the X-ray term


 function value   -150414.047    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1680     0.014     0.019
Bond distances: others                         1664     0.002     0.020
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =  250.666, B  = 363.054
Overall anisotropic scale factors
   B11 =  1.85 B22 =  0.81 B33 = -2.66 B12 = -0.91 B13 =  2.41 B23 = -2.08
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.0476
Average Fourier shell correlation    =     0.9931
Average correlation coefficient      =     0.9845
Overall figure of merit              =     0.9958
-----------------------------------------------------------------------------
 Trying gamma equal    3.09090894E-02
 Gamma decreased to    2.26446278E-02


 fvalues    1378.69800       5431.79346      -10100.9785       19218.7734    


     CGMAT cycle number =      4

 File opened           20
 Weight matrix    3.90269503E-04
 Actual weight    10.0000000      is applied to the X-ray term


 function value   -150894.641    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1680     0.014     0.019
Bond distances: others                         1664     0.002     0.020
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =  250.618, B  = 338.430
Overall anisotropic scale factors
   B11 =  1.79 B22 =  0.77 B33 = -2.56 B12 = -1.13 B13 =  2.57 B23 = -1.79
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.0465
Average Fourier shell correlation    =     0.9934
Average correlation coefficient      =     0.9853
Overall figure of merit              =     0.9959
-----------------------------------------------------------------------------
 Trying gamma equal    2.26446278E-02
 Gamma decreased to    1.51314801E-02


 fvalues   -918.706360       5098.02588      -27027.6406      -4089.03760    


     CGMAT cycle number =      5

 File opened           20
 Weight matrix    3.48169153E-04
 Actual weight    10.0000000      is applied to the X-ray term


 function value   -151304.109    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1680     0.014     0.019
Bond distances: others                         1664     0.003     0.020
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =  250.910, B  = 318.738
Overall anisotropic scale factors
   B11 =  1.75 B22 =  0.73 B33 = -2.48 B12 = -1.30 B13 =  2.69 B23 = -1.80
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.0454
Average Fourier shell correlation    =     0.9937
Average correlation coefficient      =     0.9860
Overall figure of merit              =     0.9960
-----------------------------------------------------------------------------
 Trying gamma equal    1.51314801E-02
 Gamma decreased to    8.30134563E-03


 fvalues   -2451.02344       4854.99170      -41095.2969      -19655.2422    


     CGMAT cycle number =      6

 File opened           20
 Weight matrix    3.13204044E-04
 Actual weight    10.0000000      is applied to the X-ray term


 function value   -151679.641    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1680     0.013     0.019
Bond distances: others                         1664     0.002     0.020
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =  251.180, B  = 298.625
Overall anisotropic scale factors
   B11 =  1.90 B22 =  0.78 B33 = -2.69 B12 = -1.64 B13 =  2.95 B23 = -1.62
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.0443
Average Fourier shell correlation    =     0.9941
Average correlation coefficient      =     0.9868
Overall figure of merit              =     0.9961
-----------------------------------------------------------------------------
 Trying gamma equal    8.30134563E-03
 Gamma decreased to    2.09213281E-03


 fvalues   -3913.56641       4657.63379      -54489.4141      -34478.0312    


     CGMAT cycle number =      7

 File opened           20
 Weight matrix    2.86218303E-04
 Actual weight    10.0000000      is applied to the X-ray term


 function value   -152024.516    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1680     0.013     0.019
Bond distances: others                         1664     0.002     0.020
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =  250.965, B  = 276.117
Overall anisotropic scale factors
   B11 =  2.35 B22 =  0.38 B33 = -2.73 B12 = -1.84 B13 =  3.46 B23 = -1.25
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.0429
Average Fourier shell correlation    =     0.9944
Average correlation coefficient      =     0.9876
Overall figure of merit              =     0.9962
-----------------------------------------------------------------------------
 Trying gamma equal    2.09213281E-03
 Gamma decreased to    9.99999975E-05


 fvalues   -5471.51123       4504.87549      -68704.5469      -50210.2383    


     CGMAT cycle number =      8

 File opened           20
 Weight matrix    2.75981176E-04
 Actual weight    10.0000000      is applied to the X-ray term


 function value   -152394.750    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1680     0.013     0.019
Bond distances: others                         1664     0.004     0.020
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =  250.651, B  = 255.299
Overall anisotropic scale factors
   B11 =  3.52 B22 = -0.21 B33 = -3.31 B12 = -2.22 B13 =  3.49 B23 = -0.90
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.0411
Average Fourier shell correlation    =     0.9949
Average correlation coefficient      =     0.9885
Overall figure of merit              =     0.9964
-----------------------------------------------------------------------------
 Trying gamma equal    9.99999975E-05
 Trying gamma equal    2.57579032E-02
 Gamma decreased to    2.06263214E-02


 fvalues   -6425.15771       4405.27930      -77339.5469      -59846.2969    


     CGMAT cycle number =      9

 File opened           20
 Weight matrix    2.47664866E-04
 Actual weight    10.0000000      is applied to the X-ray term


 function value   -152632.656    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1680     0.012     0.019
Bond distances: others                         1664     0.002     0.020
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =  250.613, B  = 234.513
Overall anisotropic scale factors
   B11 =  3.64 B22 = -0.12 B33 = -3.52 B12 = -2.25 B13 =  3.72 B23 = -0.83
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.0403
Average Fourier shell correlation    =     0.9951
Average correlation coefficient      =     0.9889
Overall figure of merit              =     0.9965
-----------------------------------------------------------------------------
 Trying gamma equal    2.06263214E-02
 Gamma decreased to    1.59612484E-02


 fvalues   -7950.15039       4273.28027      -90818.8359      -75228.2188    


     CGMAT cycle number =     10

 Limits of asymmetric unit      : 1.00 1.00 1.00
 Grid spacing to be used        :    56   54   56
 Maximuum H,K,L                 :     7    6    7
 Minimum acceptable grid spacing:    37   34   37
 File opened           20
 Weight matrix    2.23485840E-04
 Actual weight    10.0000000      is applied to the X-ray term
Norm of X_ray positional gradient                7.16
Norm of Geom. positional gradient                13.7
Norm of X_ray B-factor gradient                  3.41
Norm of Geom. B-factor gradient                  0.00
Product of X_ray and Geom posit. gradients     -0.929E+05
 Cosine of angle between them                      -0.095
Product of X_ray and Geom B-fact gradients       0.00
 Cosine of angle between them                       0.000


Residuals: XRAY=    -0.1570E+06 GEOM=      4182.     TOTAL=    -0.1528E+06
 function value   -152846.906    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1680     0.012     0.019
Bond distances: others                         1664     0.002     0.020
Bond angles  : refined atoms                   2263     1.906     1.988
Bond angles  : others                          3841     1.030     3.000
Torsion angles, period  1. refined              213     5.384     5.000
Torsion angles, period  2. refined               75    38.998    24.533
Torsion angles, period  3. refined              313    15.403    15.000
Torsion angles, period  4. refined               13    13.380    15.000
Chiral centres: refined atoms                   254     0.092     0.200
Planar groups: refined atoms                   1887     0.006     0.021
Planar groups: others                           344     0.002     0.020
VDW repulsions: refined_atoms                   618     0.218     0.200
VDW repulsions.others                          3056     0.167     0.200
VDW; torsion: refined_atoms                    1582     0.174     0.200
VDW; torsion.others                            1978     0.082     0.200
HBOND: refined_atoms                             22     0.069     0.200
M. chain bond B values: refined atoms           855     0.000    22.000
M. chain bond B values: others                  854     0.000    22.000
M. chain angle B values: refined atoms         1067     0.000    33.000
M. chain angle B values: others                1068     0.000    33.000
S. chain bond B values: refined atoms           825     0.000    22.000
S. chain bond B values: others                  825     0.000    22.000
S. chain angle B values: refined atoms         1196     0.000    33.000
S. chain angle B values: others                1196     0.000    33.000
Long range B values: refined atoms             6925     0.000   207.470
Long range B values: others                    6922     0.000   207.463
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =  250.637, B  = 214.429
Overall anisotropic scale factors
   B11 =  3.64 B22 = -0.21 B33 = -3.42 B12 = -2.48 B13 =  3.91 B23 = -1.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10. M(Rfactor) v. resln :N:1,6,7:
:Cycle   10. M(Fobs) and M(Fc) v. resln :N:1,4,5:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used $$
$$
 0.001       9 100.00  1550.3  1542.7  0.01  0.01
 0.001       6 100.00   475.7   470.8  0.03  0.03
 0.001      21 100.00   276.7   284.7  0.04  0.04
 0.002       6 100.00   268.0   271.7  0.03  0.03
 0.002      18 100.00   238.7   238.4  0.02  0.02
 0.003      17 100.00   205.8   207.3  0.03  0.03
 0.003      16 100.00   157.6   154.6  0.04  0.04
 0.004      24 100.00   107.2   105.6  0.05  0.05
 0.004      14 100.00   122.0   118.8  0.04  0.04
 0.005      22 100.00   113.1   111.4  0.05  0.05
 0.005      21 100.00    91.0    90.3  0.05  0.05
 0.006      32 100.00    87.4    86.3  0.05  0.05
 0.006      16 100.00    87.5    85.0  0.04  0.04
 0.007      22 100.00    85.7    86.5  0.04  0.04
 0.007      32 100.00    63.0    64.6  0.08  0.08
 0.008      28 100.00    66.8    68.4  0.06  0.06
 0.008      41 100.00    63.6    65.6  0.07  0.07
 0.009      14 100.00    45.4    47.4  0.10  0.10
 0.009      20 100.00    45.0    48.1  0.08  0.08
 0.010      42 100.00    39.2    40.2  0.13  0.13
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle   10. FSC and  Fom(<cos(DelPhi)>-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCwork CorrFofcWork$$
 $$
  0.0005      9   1.000      0   0.000      9   1.000  0.999  1.0000  0.9999
  0.0010      6   1.000      0   0.000      6   1.000  0.997  0.9969  0.9902
  0.0015     21   0.999      0   0.000     21   0.999  0.995  0.9989  0.9964
  0.0020      6   0.999      0   0.000      6   0.999  0.993  0.9987  0.9977
  0.0025     18   0.999      0   0.000     18   0.999  0.992  0.9990  0.9988
  0.0029     17   0.998      0   0.000     17   0.998  0.991  0.9987  0.9971
  0.0034     16   0.998      0   0.000     16   0.998  0.990  0.9980  0.9939
  0.0039     24   0.997      0   0.000     24   0.997  0.989  0.9969  0.9939
  0.0044     14   0.997      0   0.000     14   0.997  0.988  0.9977  0.9953
  0.0049     22   0.997      0   0.000     22   0.997  0.987  0.9971  0.9939
  0.0054     21   0.997      0   0.000     21   0.997  0.986  0.9965  0.9929
  0.0059     32   0.996      0   0.000     32   0.996  0.985  0.9967  0.9952
  0.0064     16   0.997      0   0.000     16   0.997  0.984  0.9970  0.9974
  0.0068     22   0.997      0   0.000     22   0.997  0.984  0.9966  0.9941
  0.0073     32   0.995      0   0.000     32   0.995  0.983  0.9935  0.9885
  0.0078     28   0.996      0   0.000     28   0.996  0.982  0.9953  0.9894
  0.0083     41   0.996      0   0.000     41   0.996  0.982  0.9946  0.9866
  0.0088     14   0.995      0   0.000     14   0.995  0.981  0.9904  0.9814
  0.0093     20   0.995      0   0.000     20   0.995  0.980  0.9946  0.9906
  0.0098     42   0.994      0   0.000     42   0.994  0.980  0.9856  0.9602
 $$
Resolution limits                    =     60.500    10.000
Number of used reflections           =        421
Percentage observed                  =   100.0000
Percentage of free reflections       =     0.0000
Overall R factor                     =     0.0395
Average Fourier shell correlation    =     0.9952
Overall weighted R factor            =     0.0395
Overall weighted R2 factor           =     0.0261
Average correlation coefficient      =     0.9894
Overall correlation coefficient      =     0.9995
Overall figure of merit              =     0.9965
ML based su of positional parameters =     2.1758
ML based su of thermal parameters    =   390.7936
-----------------------------------------------------------------------------
 Trying gamma equal    1.59612484E-02
 Gamma decreased to    1.17202727E-02


 fvalues   -9246.40039       4182.21143      -102299.578      -88281.7891    


 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/1AKE_cha_molrep_refine_rframe.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1680     0.012     0.019
Bond distances: others                         1664     0.002     0.020
Bond angles  : refined atoms                   2263     1.874     1.988
Bond angles  : others                          3841     1.025     3.000
Torsion angles, period  1. refined              213     5.408     5.000
Torsion angles, period  2. refined               75    38.998    24.533
Torsion angles, period  3. refined              313    15.399    15.000
Torsion angles, period  4. refined               13    13.349    15.000
Chiral centres: refined atoms                   254     0.091     0.200
Planar groups: refined atoms                   1887     0.006     0.021
Planar groups: others                           344     0.002     0.020
VDW repulsions: refined_atoms                   616     0.218     0.200
VDW repulsions.others                          3068     0.165     0.200
VDW; torsion: refined_atoms                    1574     0.174     0.200
VDW; torsion.others                            1966     0.082     0.200
HBOND: refined_atoms                             22     0.069     0.200
M. chain bond B values: refined atoms           855     0.000    24.000
M. chain bond B values: others                  854     0.000    24.000
M. chain angle B values: refined atoms         1067     0.000    36.000
M. chain angle B values: others                1068     0.000    36.000
S. chain bond B values: refined atoms           825     1.508    23.988
S. chain bond B values: others                  825     1.508    23.988
S. chain angle B values: refined atoms         1196     1.937    35.982
S. chain angle B values: others                1196     1.937    35.982
Long range B values: refined atoms             6921     1.678   226.272
Long range B values: others                    6918     1.679   226.265
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =  250.638, B  = 194.340
Overall anisotropic scale factors
   B11 =  3.66 B22 = -0.07 B33 = -3.58 B12 = -2.36 B13 =  4.07 B23 = -1.11
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11. M(Rfactor) v. resln :N:1,6,7:
:Cycle   11. M(Fobs) and M(Fc) v. resln :N:1,4,5:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used $$
$$
 0.001       9 100.00  1550.3  1542.9  0.01  0.01
 0.001       6 100.00   475.7   470.8  0.03  0.03
 0.001      21 100.00   276.7   284.4  0.04  0.04
 0.002       6 100.00   268.0   271.6  0.03  0.03
 0.002      18 100.00   238.7   238.3  0.02  0.02
 0.003      17 100.00   205.8   207.0  0.03  0.03
 0.003      16 100.00   157.6   154.7  0.04  0.04
 0.004      24 100.00   107.2   105.6  0.05  0.05
 0.004      14 100.00   122.0   118.8  0.04  0.04
 0.005      22 100.00   113.1   111.5  0.05  0.05
 0.005      21 100.00    91.0    90.4  0.05  0.05
 0.006      32 100.00    87.4    86.3  0.05  0.05
 0.006      16 100.00    87.5    85.1  0.04  0.04
 0.007      22 100.00    85.7    86.5  0.04  0.04
 0.007      32 100.00    63.0    64.5  0.08  0.08
 0.008      28 100.00    66.8    68.4  0.06  0.06
 0.008      41 100.00    63.6    65.5  0.07  0.07
 0.009      14 100.00    45.4    47.4  0.10  0.10
 0.009      20 100.00    45.0    48.0  0.08  0.08
 0.010      42 100.00    39.2    40.2  0.13  0.13
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle   11. FSC and  Fom(<cos(DelPhi)>-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCwork CorrFofcWork$$
 $$
  0.0005      9   1.000      0   0.000      9   1.000  0.999  1.0000  0.9999
  0.0010      6   1.000      0   0.000      6   1.000  0.997  0.9970  0.9907
  0.0015     21   0.999      0   0.000     21   0.999  0.995  0.9989  0.9967
  0.0020      6   0.999      0   0.000      6   0.999  0.994  0.9987  0.9977
  0.0025     18   0.999      0   0.000     18   0.999  0.992  0.9991  0.9989
  0.0029     17   0.998      0   0.000     17   0.998  0.991  0.9987  0.9973
  0.0034     16   0.998      0   0.000     16   0.998  0.990  0.9981  0.9941
  0.0039     24   0.997      0   0.000     24   0.997  0.989  0.9971  0.9943
  0.0044     14   0.997      0   0.000     14   0.997  0.988  0.9978  0.9955
  0.0049     22   0.997      0   0.000     22   0.997  0.988  0.9973  0.9942
  0.0054     21   0.997      0   0.000     21   0.997  0.987  0.9967  0.9935
  0.0059     32   0.996      0   0.000     32   0.996  0.986  0.9969  0.9955
  0.0064     16   0.997      0   0.000     16   0.997  0.985  0.9971  0.9976
  0.0068     22   0.997      0   0.000     22   0.997  0.985  0.9967  0.9944
  0.0073     32   0.996      0   0.000     32   0.996  0.984  0.9938  0.9891
  0.0078     28   0.996      0   0.000     28   0.996  0.983  0.9955  0.9899
  0.0083     41   0.996      0   0.000     41   0.996  0.982  0.9949  0.9871
  0.0088     14   0.995      0   0.000     14   0.995  0.982  0.9908  0.9823
  0.0093     20   0.995      0   0.000     20   0.995  0.981  0.9947  0.9911
  0.0098     42   0.994      0   0.000     42   0.994  0.981  0.9861  0.9616
 $$
Resolution limits                    =     60.500    10.000
Number of used reflections           =        421
Percentage observed                  =   100.0000
Percentage of free reflections       =     0.0000
Overall R factor                     =     0.0385
Average Fourier shell correlation    =     0.9954
Overall weighted R factor            =     0.0385
Overall weighted R2 factor           =     0.0254
Average correlation coefficient      =     0.9899
Overall correlation coefficient      =     0.9996
Overall figure of merit              =     0.9966
ML based su of positional parameters =     2.1758
ML based su of thermal parameters    =   390.7936
-----------------------------------------------------------------------------
  Time in seconds: CPU =        21.08
             Elapsed =           0.00

    ****           Things for loggraph, R factor and others vs cycle            ****


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS:<Rfactor> vs cycle :N:1,2,3:
:FOM vs cycle :N:1,4:
:-LL vs cycle :N:1,5:
:-LLfree vs cycle :N:1,6:
:Geometry vs cycle:N:1,7,8,9,10,11:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.0495   0.0      0.996      -15558.       0.0   0.0185  0.997   2.946  1.568   0.122
       1   0.0485   0.0      0.996      -15571.       0.0   0.0153  0.790   2.557  1.294   0.105
       2   0.0476   0.0      0.996      -15585.       0.0   0.0145  0.742   2.376  1.183   0.101
       3   0.0465   0.0      0.996      -15599.       0.0   0.0140  0.712   2.256  1.112   0.098
       4   0.0454   0.0      0.996      -15616.       0.0   0.0135  0.688   2.165  1.060   0.097
       5   0.0443   0.0      0.996      -15634.       0.0   0.0132  0.667   2.092  1.019   0.095
       6   0.0429   0.0      0.996      -15653.       0.0   0.0129  0.650   2.032  0.985   0.094
       7   0.0411   0.0      0.996      -15680.       0.0   0.0126  0.637   1.983  0.957   0.094
       8   0.0403   0.0      0.996      -15691.       0.0   0.0122  0.617   1.942  0.934   0.092
       9   0.0395   0.0      0.997      -15703.       0.0   0.0120  0.602   1.906  0.914   0.092
      10   0.0385   0.0      0.997      -15717.       0.0   0.0117  0.590   1.874  0.896   0.091
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.0495   0.0385
     Rms BondLength    0.0185   0.0117
      Rms BondAngle    2.9462   1.8742
     Rms ChirVolume    0.1218   0.0908
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
 Refmac_5.8.0131:  End of Refmac_5.8.0131  
Times: User:      26.9s System:    0.2s Elapsed:     0:27  
</pre>
</html>
<!--SUMMARY_END--></FONT></B>


CCP-EM job finished: Wednesday, 12. August 2015 10:32AM ______________________
_______________________________________________________________________________

_________ CCP-EM Job launch/home/tom/Code/devtools/install/bin/refmac5 ________



CCP-EM pipeline job 3 of 10 ___________________________________________________

__ Command ____________________________________________________________________
/home/tom/Code/devtools/install/bin/refmac5 xyzin /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/1AKE_cha_molrep_refine_rframe.pdb xyzout /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/1AKE_cha_molrep_refine.pdb atomsf /home/tom/Code/devtools/checkout/refmac5.8/data/atomsf_electron.lib << eof
/home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/job_data/stdin_shift_refined.txt
eof
_______________________________________________________________________________
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<html> <!-- CCP4 HTML LOGFILE -->
<hr>
<!--SUMMARY_END--></FONT></B>
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<pre>
 
 ###############################################################
 ###############################################################
 ###############################################################
 ### CCP4 6.5.011: Refmac_5.8.0131 version 5.8.0131 : 06/08/15##
 ###############################################################
 User: unknown  Run date: 12/ 8/2015 Run time: 10:32:37 


 Please reference: Collaborative Computational Project, Number 4. 2011.
 "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242.
 as well as any specific reference in the program write-up.

<!--SUMMARY_END--></FONT></B>
 $TEXT:Reference1: $$ Main reference $$ 
   "REFMAC5 for the refinement of macromolecular crystal structures:"
   G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011) 
   Acta Crystallogr. D67, 355-367

 $$
 $SUMMARY :Reference1:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference2: $$ Secondary reference $$ 
   "Refinement of Macromolecular Structures by the  Maximum-Likelihood Method:"
   G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
   Acta Crystallogr. D53, 240-255
   EU  Validation contract: BIO2CT-92-0524

 $$
 $SUMMARY :Reference2:  $$ Refmac: $$
 :TEXT:Reference2: $$

 Data line--- labin FP=Fout0 PHIB=Pout0
 Data line---  pdbin cell       60.5000000       55.0000000       60.5000000       90.0000000       90.0000000       90.0000000    
 Data line---  pdbin shifts   -0.00000000      -2.75000000      -0.00000000    
 Data line---  pdbout cell      66.0000000       66.0000000       66.0000000       90.0000000       90.0000000       90.0000000    
 Data line---  pdbout shifts    0.00000000       2.75000000       0.00000000    
 Data line--- source EM
 Data line--- ncycle 0
 Data line--- end
  Data line--- labin FP=Fout0 PHIB=Pout0
  Data line--- pdbin cell       60.5000000       55.0000000       60.5000000       90.0000000       90.0000000       90.0000000
  Data line--- pdbin shifts   -0.00000000      -2.75000000      -0.00000000
  Data line--- pdbout cell      66.0000000       66.0000000       66.0000000       90.0000000       90.0000000       90.0000000
  Data line--- pdbout shifts    0.00000000       2.75000000       0.00000000
  Data line--- source EM
  Data line--- ncycle 0
  Data line--- END
===> Warning: Reflections file has not been defined
===> Warning: Switching to the idealisation mode

    ****                     Input and Default parameters#                      ****


Input coordinate file.  Logical name - XYZIN actual file name  - /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/1AKE_cha_molrep_refine_rframe.pdb
Output coordinate file. Logical name - XYZOUT actual file name - /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/1AKE_cha_molrep_refine.pdb

  Refinement type                        : Idealisation

    ****                           Makecif parameters                           ****

Dictionary files for restraints : /usr/local/sci_local/mx/ccp4-6.5/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /usr/local/sci_local/mx/ccp4-6.5/lib/data/monomers/ener_lib.cif
    Apart from amino acids and DNA/RNA all monomers will be checked to see if atom names and connectivity is correct
    Hydrogens will be restored in their riding positions
    Links between monomers will be checked. Only those links present in the coordinate file will be used
    Standard sugar links will be analysed and used
    For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
    Symmetry related links will be analysed and used
    Cis peptides will be found and used automatically


  Method of minimisation                 : Sparse Matrix

  Damping factors:     1.0000  1.0000


    ****                    Geometry restraints and weights                     ****


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

 Planar groups (all and main chain)
          WEIGHT= 1.00 1.00

 Chiral centers
          Weight= 1.00

 NON-BONDED CONTACTS
          Overall weight                          =  1.00
          Sigma for simple VDW                    =  0.20
          Sigma for VDW trhough torsion angle     =  0.20
          Sigma for HBOND                         =  0.20
          Sigma for metal-ion                     =  0.20
          Sigma for DUMMY and other atom          =  0.30
          Distance for donor-accepetor = vdw1+vdw2+(-0.30)
          Distance for acceptor - H    = vdw1+     ( 0.10)
          VDW distance through torsion = vdw1+vdw2+(-0.30)
          Distance for DUMMY-others    = vdw1+vdw2+(-0.70)

 TORSION ANGLES
          Weight= 1.00

 RESTRAINTS AGAINST EXCESSIVE SHIFTS
     Positional parameters                   0.00A
     Thermal parameters                      0.00A
     Occupancy parameters                    0.00

 RADIUS OF CONFIDENCE
     Positional parameters 0.00A
     Thermal parameters    0.00A**2
     Occupancy parameters  0.00

Monitoring style is "MEDIUM". Complete information will be printed out in the
first and last cycle. In all other cycles minimum information will be printed out
Sigma cutoffs for printing out outliers
If deviation of restraint parameter > alpha*sigma then information will be printed out
Distance outliers      10.000
Angle outliers         10.000
Torsion outliers       10.000
Chiral volume outliers 10.000
Plane outliers         10.000
Non-bonding outliers   10.000
---------------------------------------------------------------

 Input file :/home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/re
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.44
 _lib_update       30/05/14
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 11608
                with complete description    : 11608
  NUMBER OF MODIFICATIONS                    :    61
  NUMBER OF LINKS                            :    71
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )

FORMATTED      OLD     file opened on unit  45
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
Logical name: ATOMSF, Filename: /home/tom/Code/devtools/checkout/refmac5.8/data/atomsf_electron.lib
<!--SUMMARY_END--></FONT></B>

  Number of atoms    :    1656
  Number of residues :     214
  Number of chains   :       1
  I am reading library. Please wait.
                mon_lib.cif
  --------------------------------
  --- title of input coord file ---

  PDB_code:XXXX
  PDB_name:----
  PDB_date:12-AUG-15
  --------------------------------
  Number of chains                  :       1
  Total number of monomers          :     214
  Number of atoms                   :    3344
  Number of missing atoms           :       0
  Number of rebuilt atoms           :    1688
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0


 loop_
     _atom_type_symbol
     _atom_type_scat_Cromer_Mann_a1
     _atom_type_scat_Cromer_Mann_b1
     _atom_type_scat_Cromer_Mann_a2
     _atom_type_scat_Cromer_Mann_b2
     _atom_type_scat_Cromer_Mann_a3
     _atom_type_scat_Cromer_Mann_b3
     _atom_type_scat_Cromer_Mann_a4
     _atom_type_scat_Cromer_Mann_b4
     _atom_type_scat_Cromer_Mann_a5
     _atom_type_scat_Cromer_Mann_b5


  N      0.1022   0.2451   0.3219   1.7481   0.7982   6.1925   0.8197  17.3894   0.1715  48.1431
  C      0.0893   0.2465   0.2563   1.7100   0.7570   6.4094   1.0487  18.6113   0.3575  50.2523
  H      0.0116   0.5347   0.0400   3.5867   0.0657  12.3471   0.0191  18.9525   0.0398  38.6269
  S      0.2497   0.2681   0.5628   1.6711   1.3899   7.0267   2.1865  19.5377   0.7715  50.3888
  O      0.0974   0.2067   0.2921   1.3815   0.6910   4.6943   0.6990  12.7105   0.2039  32.4726


 Number of distances         :           0
 Number of angles            :           0
 Number of torsions          :           0
 Number of planes            :           0
 Number of chirals           :           0
 Number of intervals         :           0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
                        Standard  External       All
                Bonds:      3344         0      3344
               Angles:      6104         0      6104
              Chirals:       254         0       254
               Planes:       513         0       513
             Torsions:      1333         0      1333
            Intervals:         0         0         0
--------------------------------------------------------------------------------


  Number of harmonic restraints       =            0
  Number of atoms in special position =            0
 -----------------------------------------------------

  Time in seconds: CPU =         0.02
             Elapsed =           0.00

    ****           Things for loggraph, R factor and others vs cycle            ****


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS:<Rfactor> vs cycle :N:1,2,3:
:FOM vs cycle :N:1,4:
:-LL vs cycle :N:1,5:
:-LLfree vs cycle :N:1,6:
:Geometry vs cycle:N:1,7,8,9,10,11:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
 $$
 $TEXT:Result: $$ Final results $$
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
 Refmac_5.8.0131:  End of Refmac_5.8.0131  
Times: User:       6.1s System:    0.1s Elapsed:     0:06  
</pre>
</html>
<!--SUMMARY_END--></FONT></B>


CCP-EM job finished: Wednesday, 12. August 2015 10:32AM ______________________
_______________________________________________________________________________

_________ CCP-EM Job launch/usr/local/sci_local/mx/ccp4-6.5/bin/pdbset ________



CCP-EM pipeline job 4 of 10 ___________________________________________________

__ Command ____________________________________________________________________
/usr/local/sci_local/mx/ccp4-6.5/bin/pdbset xyzin /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/1AKE_cha_molrep_refine.pdb xyzout /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/1AKE_cha_molrep_refine_shaken.pdb atomsf /home/tom/Code/devtools/checkout/refmac5.8/data/atomsf_electron.lib << eof
/home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/job_data/stdin_shake.txt
eof
_______________________________________________________________________________
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<html> <!-- CCP4 HTML LOGFILE -->
<hr>
<!--SUMMARY_END--></FONT></B>
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<pre>
 
 ###############################################################
 ###############################################################
 ###############################################################
 ### CCP4 6.5.011: PDBSET           version 6.5.011 :         ##
 ###############################################################
 User: unknown  Run date: 12/ 8/2015 Run time: 10:32:43 


 Please reference: Collaborative Computational Project, Number 4. 2011.
 "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242.
 as well as any specific reference in the program write-up.

<!--SUMMARY_END--></FONT></B>

  Logical name: XYZIN  File name: /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/1AKE_cha_molrep_refine.pdb
  PDB file is being opened on unit 1 for INPUT.

  MATRICES DERIVED FROM CRYST1 CARD IN COORDINATE FILE


             RF                                  RO

    0.015  -0.000  -0.000  -0.000       66.000   0.000   0.000  -0.000
   -0.000   0.015  -0.000   0.000        0.000  66.000   0.000   0.000
    0.000  -0.000   0.015  -0.000        0.000   0.000  66.000  -0.000
   -0.000   0.000  -0.000   1.000       -0.000   0.000  -0.000   1.000

 Data line--- noise 0.5
 Data line--- solvent no

 Unknown keyword: SOLV

 Data line--- end

  Logical name: XYZOUT  File name: /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/1AKE_cha_molrep_refine_shaken.pdb
  PDB file is being opened on unit 2 for OUTPUT.

 Hydrogen atoms will be kept

Random shift introduced with maximum value:     0.5000

     1656  atoms copied


Random shift
       maximum: 0.5000
       atoms:     1656
       RMS:     0.2875


 Orthogonal Coordinate limits in output file:
                 Minimum   Maximum    Centre     Range
       On X :       8.52     54.04     31.28     45.52
       On Y :      11.66     53.28     32.47     41.62
       On Z :       9.27     54.54     31.91     45.27


 Fractional Coordinate limits in output file:
                 Minimum   Maximum    Centre     Range
       On X :       0.13      0.82      0.47      0.69
       On Y :       0.18      0.81      0.49      0.63
       On Z :       0.14      0.83      0.48      0.69


 Number of chains in input file =      1

   Original chain IDs:   A   


<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
 PDBSET:   === Normal completion PDBSET ===
Times: User:       0.0s System:    0.0s Elapsed:     0:00  
</pre>
</html>
<!--SUMMARY_END--></FONT></B>


CCP-EM job finished: Wednesday, 12. August 2015 10:32AM ______________________
_______________________________________________________________________________

_________ CCP-EM Job launch/home/tom/Code/devtools/install/bin/refmac5 ________



CCP-EM pipeline job 5 of 10 ___________________________________________________

__ Command ____________________________________________________________________
/home/tom/Code/devtools/install/bin/refmac5 xyzin /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/1AKE_cha_molrep_refine_shaken.pdb xyzout /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/1AKE_cha_molrep_refine_shaken_rframe.pdb mapin /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc mapref /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc atomsf /home/tom/Code/devtools/checkout/refmac5.8/data/atomsf_electron.lib << eof
/home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/job_data/stdin_map2mtz.txt
eof
_______________________________________________________________________________
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<html> <!-- CCP4 HTML LOGFILE -->
<hr>
<!--SUMMARY_END--></FONT></B>
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<pre>
 
 ###############################################################
 ###############################################################
 ###############################################################
 ### CCP4 6.5.011: Refmac_5.8.0131 version 5.8.0131 : 06/08/15##
 ###############################################################
 User: unknown  Run date: 12/ 8/2015 Run time: 10:32:43 


 Please reference: Collaborative Computational Project, Number 4. 2011.
 "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242.
 as well as any specific reference in the program write-up.

<!--SUMMARY_END--></FONT></B>
 $TEXT:Reference1: $$ Main reference $$ 
   "REFMAC5 for the refinement of macromolecular crystal structures:"
   G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011) 
   Acta Crystallogr. D67, 355-367

 $$
 $SUMMARY :Reference1:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference2: $$ Secondary reference $$ 
   "Refinement of Macromolecular Structures by the  Maximum-Likelihood Method:"
   G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
   Acta Crystallogr. D53, 240-255
   EU  Validation contract: BIO2CT-92-0524

 $$
 $SUMMARY :Reference2:  $$ Refmac: $$
 :TEXT:Reference2: $$

 Data line--- mode sfcalc
 Data line--- source EM
 Data line--- sfcalc mrad 4.0
 Data line--- sfcalc shift
 Data line--- end
  Data line--- mode sfcalc
  Data line--- source EM
  Data line--- sfcalc mrad 4.0
  Data line--- sfcalc shift
  Data line--- END
===> Warning: Reflections file has not been defined
===> Warning: Switching to the idealisation mode

    ****                     Input and Default parameters#                      ****


Input coordinate file.  Logical name - XYZIN actual file name  - /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/1AKE_cha_molrep_refine_shaken.pdb
Output coordinate file. Logical name - XYZOUT actual file name - /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/1AKE_cha_molrep_refine_shaken_rframe.pdb

  Refinement type                        : Idealisation
  Refinement type                        : NONE
  SF calculation from MAP: /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc
  SF calculation from CRD: /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/1AKE_cha_molrep_refine_shaken.pdb


    ****                           Makecif parameters                           ****

Dictionary files for restraints : /usr/local/sci_local/mx/ccp4-6.5/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /usr/local/sci_local/mx/ccp4-6.5/lib/data/monomers/ener_lib.cif
    Apart from amino acids and DNA/RNA all monomers will be checked to see if atom names and connectivity is correct
    Hydrogens will be restored in their riding positions
    Links between monomers will be checked. Only those links present in the coordinate file will be used
    Standard sugar links will be analysed and used
    For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
    Symmetry related links will be analysed and used
    Cis peptides will be found and used automatically




Monitoring style is "MEDIUM". Complete information will be printed out in the
first and last cycle. In all other cycles minimum information will be printed out
Sigma cutoffs for printing out outliers
If deviation of restraint parameter > alpha*sigma then information will be printed out
Distance outliers      10.000
Angle outliers         10.000
Torsion outliers       10.000
Chiral volume outliers 10.000
Plane outliers         10.000
Non-bonding outliers   10.000
---------------------------------------------------------------

 Input file :/home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/re
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.44
 _lib_update       30/05/14
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 11608
                with complete description    : 11608
  NUMBER OF MODIFICATIONS                    :    61
  NUMBER OF LINKS                            :    71
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )

FORMATTED      OLD     file opened on unit  45
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
Logical name: ATOMSF, Filename: /home/tom/Code/devtools/checkout/refmac5.8/data/atomsf_electron.lib
<!--SUMMARY_END--></FONT></B>

  Number of atoms    :    1656
  Number of residues :     214
  Number of chains   :       1
  I am reading library. Please wait.
                mon_lib.cif
  WARNING : CIS peptide bond is found, angle =     58.78
            ch:AA   res:  62  GLU              -->  63  LEU
  WARNING : CIS peptide bond is found, angle =     89.11
            ch:AA   res:  72  ILE              -->  73  ALA
      link will be created
  WARNING : CIS peptide bond is found, angle =     76.97
            ch:AA   res: 129  SER              --> 130  GLY
  WARNING : CIS peptide bond is found, angle =     59.61
            ch:AA   res: 167  ARG              --> 168  LEU
  WARNING : CIS peptide bond is found, angle =     38.11
            ch:AA   res: 195  LYS              --> 196  VAL
  --------------------------------
  --- title of input coord file ---

  PDB_code:XXXX
  PDB_name:----
  PDB_date:12-AUG-15
  --------------------------------
  Number of chains                  :       1
  Total number of monomers          :     214
  Number of atoms                   :    3344
  Number of missing atoms           :       0
  Number of rebuilt atoms           :    1688
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0


 loop_
     _atom_type_symbol
     _atom_type_scat_Cromer_Mann_a1
     _atom_type_scat_Cromer_Mann_b1
     _atom_type_scat_Cromer_Mann_a2
     _atom_type_scat_Cromer_Mann_b2
     _atom_type_scat_Cromer_Mann_a3
     _atom_type_scat_Cromer_Mann_b3
     _atom_type_scat_Cromer_Mann_a4
     _atom_type_scat_Cromer_Mann_b4
     _atom_type_scat_Cromer_Mann_a5
     _atom_type_scat_Cromer_Mann_b5


  N      0.1022   0.2451   0.3219   1.7481   0.7982   6.1925   0.8197  17.3894   0.1715  48.1431
  C      0.0893   0.2465   0.2563   1.7100   0.7570   6.4094   1.0487  18.6113   0.3575  50.2523
  H      0.0116   0.5347   0.0400   3.5867   0.0657  12.3471   0.0191  18.9525   0.0398  38.6269
  S      0.2497   0.2681   0.5628   1.6711   1.3899   7.0267   2.1865  19.5377   0.7715  50.3888
  O      0.0974   0.2067   0.2921   1.3815   0.6910   4.6943   0.6990  12.7105   0.2039  32.4726


 Number of distances         :           0
 Number of angles            :           0
 Number of torsions          :           0
 Number of planes            :           0
 Number of chirals           :           0
 Number of intervals         :           0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
                        Standard  External       All
                Bonds:      3292         0      3292
               Angles:      5896         0      5896
              Chirals:       254         0       254
               Planes:       409         0       409
             Torsions:      1177         0      1177
            Intervals:         0         0         0
--------------------------------------------------------------------------------


  Number of harmonic restraints       =            0
  Number of atoms in special position =            0
 -----------------------------------------------------

 Map file here /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc

 Logical Name: /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc   Filename: /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc 

File name for input map file on unit  10 : /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc
file size 56320 ; logical name /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc



           Number of columns, rows, sections ...............   24   24   24
           Map mode ........................................    2
           Start and stop points on columns, rows, sections     0   23    0   23    0   23
           Grid sampling on x, y, z ........................   24   24   24
           Cell dimensions .................................   66.0000    66.0000    66.0000    90.0000    90.0000    90.0000
           Fast, medium, slow axes .........................    X    Y    Z
           Minimum density .................................     0.00000
           Maximum density .................................    43.92188
           Mean density ....................................     3.79930
           Rms deviation from mean density .................     9.01953
           Space-group .....................................    1
           Number of titles ................................    1


     Labels:                            
  MODIM M CCP4    Chimera 1.3.2570 Mon Sep  7 14:1                    ?    ?


 nsym 1           1
 res max nominal    5.50000000      res max used    5.51102161    
 Map manupilation mode = M
 reference map

  Reference structure factors will be calculated from the map: /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc

 Logical Name: /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc   Filename: /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc 

File name for input map file on unit  10 : /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc
file size 56320 ; logical name /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc



           Number of columns, rows, sections ...............   24   24   24
           Map mode ........................................    2
           Start and stop points on columns, rows, sections     0   23    0   23    0   23
           Grid sampling on x, y, z ........................   24   24   24
           Cell dimensions .................................   66.0000    66.0000    66.0000    90.0000    90.0000    90.0000
           Fast, medium, slow axes .........................    X    Y    Z
           Minimum density .................................     0.00000
           Maximum density .................................    43.92188
           Mean density ....................................     3.79930
           Rms deviation from mean density .................     9.01953
           Space-group .....................................    1
           Number of titles ................................    1


     Labels:                            
  MODIM M CCP4    Chimera 1.3.2570 Mon Sep  7 14:1                    ?    ?


 nsym            1
 Start reading            0           0           0          23          23          23
 After map_reader_0           24          24          24           1           1
 After redalli
 Starting reso    9.07272771E-02   5.51102161    
 RelVol    20.7968750    
 Number of resolution bins            9

  The number of bins for reference SF :           9

 Logical Name: /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc   Filename: /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc 

File name for input map file on unit  10 : /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc
file size 56320 ; logical name /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc



           Number of columns, rows, sections ...............   24   24   24
           Map mode ........................................    2
           Start and stop points on columns, rows, sections     0   23    0   23    0   23
           Grid sampling on x, y, z ........................   24   24   24
           Cell dimensions .................................   66.0000    66.0000    66.0000    90.0000    90.0000    90.0000
           Fast, medium, slow axes .........................    X    Y    Z
           Minimum density .................................     0.00000
           Maximum density .................................    43.92188
           Mean density ....................................     3.79930
           Rms deviation from mean density .................     9.01953
           Space-group .....................................    1
           Number of titles ................................    1


     Labels:                            
  MODIM M CCP4    Chimera 1.3.2570 Mon Sep  7 14:1                    ?    ?


 Starting (nominal) resolution    9.07272771E-02   5.51102161    
 Number of all maps for SF calculation :           1
 Map file number 1 /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc
 File number            1 /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc
 nsym            1
 Start reading            0           0           0          23          23          23
 logname : MAPIN1 file name: 
 Number of maps            1

 Structure factors will be sharpened using reference map/curveR 

   Map maximum =    823.776184    
   Map minimum =   -83.4723816    
   Map mean    =   -5.52176316E-05
   Map rmsd    =    187.567963    

 Print stats of the original data to the file: orig_data_rescut.txt
 Number of resolution bins            9

    ****      Mean(|F|) and other statistics: Without accounting for mask       ****

 $TABLE: Mean(|F|) and other statistics
 $GRAPH: Mean(|F|), Mean(|F|^2), Mean(|F|^4) vs resolutions: 1,6,7,8
 $$
 2sin(th)/l 2sin(th)/l dmin dmax NREF Mn(|F|) Mn(|F|^2) Mn(|F|^4) Mn(A) Mn(B) Mn(A^2) Mn(B^2) cor(A,B)
 $$
   2.29558413E-04   3.82614089E-03   66.0014420       16.1666298             128   95328.2500       2.40946852E+10   6.51926839E+21  -3696.90869       307.820740       2.09389629E+10   3.15573555E+09 -0.512377143    
   3.82614089E-03   7.42271356E-03   16.1666298       11.6069651             247   23897.9883       750422208.       1.41633329E+18  -261.609009       112.736351       330608384.       419813984.       7.18705133E-02
   7.42271356E-03   1.10192858E-02   11.6069651       9.52627850             307   12450.3135       206873024.       1.03798047E+17  -73.2363052       10.8966894       97557008.0       109315952.      -5.62837981E-02
   1.10192858E-02   1.46158580E-02   9.52627850       8.27156830             369   6129.10352       49164156.0       5.34098511E+15   6.69177151       43.2775269       24954084.0       24210060.0      -4.54078652E-02
   1.46158580E-02   1.82124302E-02   8.27156830       7.40996313             421   3312.30225       14152484.0       3.99343543E+14   75.5258026       13.9446774       6491955.50       7660535.50      -2.25085244E-02
   1.82124302E-02   2.18090024E-02   7.40996313       6.77145624             471   2022.59546       5340126.00       5.99383574E+13  -41.9749718      -23.0784550       2560635.00       2779489.75      0.110711731    
   2.18090024E-02   2.54055746E-02   6.77145624       6.27386951             529   1284.58362       2186623.25       1.09444417E+13  -12.4967918      -8.95258045       1030568.06       1156055.25      0.151062414    
   2.54055746E-02   2.90021468E-02   6.27386951       5.87198448             543   879.239746       1073904.25       2.86502106E+12   8.87541771       11.1791744       520015.625       553887.938      0.165690720    
   2.90021468E-02   3.26087289E-02   5.87198448       5.53774643             546   633.729736       586554.312       1.20355317E+12   19.7794971      -5.89431477       268104.031       318450.719       1.60751659E-02
 $$
 sharpening things:            0           1   0.00000000       0.00000000    

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: starting_map.mtz   Filename: starting_map.mtz 

 New limits for the box
           1           2           1
          21          20          21


 Box limits :
           1           2           1
          21          20          21
 New grid   :          22          20          22
 New cell   :   60.5000000       55.0000000       60.5000000       90.0000000       90.0000000       90.0000000    
 Shifts     :  -0.00000000      -2.75000000      -0.00000000    

 Testing in apply mask    1.52181013E-42          24          24          24   1.00000000    
        2523           1
 sharpening things:            0           1   0.00000000       0.00000000    

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: masked_fs.mtz   Filename: masked_fs.mtz 

  Time in seconds: CPU =         0.04
             Elapsed =           0.00

    ****           Things for loggraph, R factor and others vs cycle            ****


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS:<Rfactor> vs cycle :N:1,2,3:
:FOM vs cycle :N:1,4:
:-LL vs cycle :N:1,5:
:-LLfree vs cycle :N:1,6:
:Geometry vs cycle:N:1,7,8,9,10,11:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
 $$
 $TEXT:Result: $$ Final results $$
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
 Refmac_5.8.0131:  End of Refmac_5.8.0131  
Times: User:       6.1s System:    0.1s Elapsed:     0:07  
</pre>
</html>
<!--SUMMARY_END--></FONT></B>


CCP-EM job finished: Wednesday, 12. August 2015 10:32AM ______________________
_______________________________________________________________________________

_________ CCP-EM Job launch/home/tom/Code/devtools/install/bin/refmac5 ________



CCP-EM pipeline job 6 of 10 ___________________________________________________

__ Command ____________________________________________________________________
/home/tom/Code/devtools/install/bin/refmac5 xyzin /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/1AKE_cha_molrep_refine_shaken_rframe.pdb hklin masked_fs.mtz xyzout /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/1AKE_cha_molrep_refine_shaken_refine_rframe.pdb hklout /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/1AKE_cha_molrep_refine_shaken_refine_rframe.mtz atomsf /home/tom/Code/devtools/checkout/refmac5.8/data/atomsf_electron.lib << eof
/home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/job_data/stdin_refine.txt
eof
_______________________________________________________________________________
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<html> <!-- CCP4 HTML LOGFILE -->
<hr>
<!--SUMMARY_END--></FONT></B>
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<pre>
 
 ###############################################################
 ###############################################################
 ###############################################################
 ### CCP4 6.5.011: Refmac_5.8.0131 version 5.8.0131 : 06/08/15##
 ###############################################################
 User: unknown  Run date: 12/ 8/2015 Run time: 10:32:50 


 Please reference: Collaborative Computational Project, Number 4. 2011.
 "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242.
 as well as any specific reference in the program write-up.

<!--SUMMARY_END--></FONT></B>
 $TEXT:Reference1: $$ Main reference $$ 
   "REFMAC5 for the refinement of macromolecular crystal structures:"
   G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011) 
   Acta Crystallogr. D67, 355-367

 $$
 $SUMMARY :Reference1:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference2: $$ Secondary reference $$ 
   "Refinement of Macromolecular Structures by the  Maximum-Likelihood Method:"
   G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
   Acta Crystallogr. D53, 240-255
   EU  Validation contract: BIO2CT-92-0524

 $$
 $SUMMARY :Reference2:  $$ Refmac: $$
 :TEXT:Reference2: $$

 Data line--- labin FP=Fout0 PHIB=Pout0
 Data line--- solvent no
 Data line--- source EM
 Data line--- mapc vector
 Data line--- REFI sharpen -50.0
 Data line--- BFACtor SET 40.0
 Data line--- ncycles 10
 Data line--- weight auto 10
 Data line--- RESO 10.0
 Data line--- ridge dist sigma 0.02
 Data line--- end
  Data line--- labin FP=Fout0 PHIB=Pout0
  Data line--- solvent no
  Data line--- source EM
  Data line--- mapc vector
  Data line--- REFI sharpen -50.0
  Data line--- BFACtor SET 40.0
  Data line--- ncycles 10
  Data line--- weight auto 10
  Data line--- RESO 10.0
  Data line--- ridge dist sigma 0.02
  Data line--- END

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN   Filename: masked_fs.mtz 

===> Warning: Figure of merit of phases has not been assigned
===> Warning: They will be assumed to be equal to 1.0

    ****                     Input and Default parameters#                      ****


Input coordinate file.  Logical name - XYZIN actual file name  - /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/1AKE_cha_molrep_refine_shaken_rframe.pdb
Output coordinate file. Logical name - XYZOUT actual file name - /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/1AKE_cha_molrep_refine_shaken_refine_rframe.pdb
Input reflection file.  Logical name - HKLIN actual file name  - masked_fs.mtz
Output reflection file. Logical name - HKLOUT actual file name - /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/1AKE_cha_molrep_refine_shaken_refine_rframe.mtz

Cell from mtz :    60.500    55.000    60.500    90.000    90.000    90.000
Space group from mtz: number -    1; name - P 1

  Refinement type                        : Restrained

Initial B values of all atoms will be set to     40.000


    ****                           Makecif parameters                           ****

Dictionary files for restraints : /usr/local/sci_local/mx/ccp4-6.5/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /usr/local/sci_local/mx/ccp4-6.5/lib/data/monomers/ener_lib.cif
    Apart from amino acids and DNA/RNA all monomers will be checked to see if atom names and connectivity is correct
    Hydrogens will be restored in their riding positions
    Links between monomers will be checked. Only those links present in the coordinate file will be used
    Standard sugar links will be analysed and used
    For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
    Symmetry related links will be analysed and used
    Cis peptides will be found and used automatically


  Residual                               : Phase modified Maximum Likelihood for Fs
 Phase Blurred by  Scale*Exp(-B s**2)    :    1.00    0.00

    ****                    Least-square scaling parameters                     ****

Overall scale
Overall B value
Overall anisotropic B with tr(B) = 0.0


    ****                 Map sharpening parameters and methods                  ****

No map sharpening will be performed

  Method of minimisation                 : Sparse Matrix
  Experimental sigmas used for weighting
  Number of Bins and width:    20       0.0005
  Refinement of individual isotropic Bfactors
  Refinement resln        :    60.5000  9.9998
  Estimated number of reflections :        823
  Auto weighting. An attempt
  Refinement cycles       :    10
  Scaling type                           :
          Bulk solvent using using Babinet principle

  Estimation of D/Sigma in resolution bins
  using  working set of reflns with experimental sigmas
  Input phases not used in SigmaA estimation

  Scaling and SigmaA resln:    60.5000  9.9998

  Damping factors:     1.0000  1.0000


    ****                    Geometry restraints and weights                     ****


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

 Planar groups (all and main chain)
          WEIGHT= 1.00 1.00

 Chiral centers
          Weight= 1.00

 NON-BONDED CONTACTS
          Overall weight                          =  1.00
          Sigma for simple VDW                    =  0.20
          Sigma for VDW trhough torsion angle     =  0.20
          Sigma for HBOND                         =  0.20
          Sigma for metal-ion                     =  0.20
          Sigma for DUMMY and other atom          =  0.30
          Distance for donor-accepetor = vdw1+vdw2+(-0.30)
          Distance for acceptor - H    = vdw1+     ( 0.10)
          VDW distance through torsion = vdw1+vdw2+(-0.30)
          Distance for DUMMY-others    = vdw1+vdw2+(-0.70)

 TORSION ANGLES
          Weight= 1.00

 THERMAL FACTORS
          Weight= 1.00
     Main chain bond (1-2 neighbour)          1.5A**2
     Main chain angle (1-3 neighbour)         2.0A**2
     Side chain bond                          3.0A**2
     Side chain angle                         4.5A**2

 RESTRAINTS AGAINST EXCESSIVE SHIFTS
     Positional parameters                   0.00A
     Thermal parameters                      0.00A
     Occupancy parameters                    0.00

 RADIUS OF CONFIDENCE
     Positional parameters 0.00A
     Thermal parameters    0.00A**2
     Occupancy parameters  0.00

Restraints on changes of interatomic distances is appplied

    ****                    Distance shift penlty parameters                    ****

     Sigma:           0.0200
     Maximum distance 4.2000

Monitoring style is "MEDIUM". Complete information will be printed out in the
first and last cycle. In all other cycles minimum information will be printed out
Sigma cutoffs for printing out outliers
If deviation of restraint parameter > alpha*sigma then information will be printed out
Distance outliers      10.000
Angle outliers         10.000
Torsion outliers       10.000
Chiral volume outliers 10.000
Plane outliers         10.000
Non-bonding outliers   10.000
B value  outliers      10.000
---------------------------------------------------------------

 Input file :/home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/re
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.44
 _lib_update       30/05/14
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 11608
                with complete description    : 11608
  NUMBER OF MODIFICATIONS                    :    61
  NUMBER OF LINKS                            :    71
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )

FORMATTED      OLD     file opened on unit  45
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
Logical name: ATOMSF, Filename: /home/tom/Code/devtools/checkout/refmac5.8/data/atomsf_electron.lib
<!--SUMMARY_END--></FONT></B>

  Number of atoms    :    1656
  Number of residues :     214
  Number of chains   :       1
  I am reading library. Please wait.
                mon_lib.cif
      link will be created
  --------------------------------
  --- title of input coord file ---

  PDB_code:XXXX
  PDB_name:----
  PDB_date:12-AUG-15
  --------------------------------
  Number of chains                  :       1
  Total number of monomers          :     214
  Number of atoms                   :    3344
  Number of missing atoms           :       0
  Number of rebuilt atoms           :    1688
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0


 loop_
     _atom_type_symbol
     _atom_type_scat_Cromer_Mann_a1
     _atom_type_scat_Cromer_Mann_b1
     _atom_type_scat_Cromer_Mann_a2
     _atom_type_scat_Cromer_Mann_b2
     _atom_type_scat_Cromer_Mann_a3
     _atom_type_scat_Cromer_Mann_b3
     _atom_type_scat_Cromer_Mann_a4
     _atom_type_scat_Cromer_Mann_b4
     _atom_type_scat_Cromer_Mann_a5
     _atom_type_scat_Cromer_Mann_b5


  N      0.1022   0.2451   0.3219   1.7481   0.7982   6.1925   0.8197  17.3894   0.1715  48.1431
  C      0.0893   0.2465   0.2563   1.7100   0.7570   6.4094   1.0487  18.6113   0.3575  50.2523
  H      0.0116   0.5347   0.0400   3.5867   0.0657  12.3471   0.0191  18.9525   0.0398  38.6269
  S      0.2497   0.2681   0.5628   1.6711   1.3899   7.0267   2.1865  19.5377   0.7715  50.3888
  O      0.0974   0.2067   0.2921   1.3815   0.6910   4.6943   0.6990  12.7105   0.2039  32.4726


 Number of distances         :           0
 Number of angles            :           0
 Number of torsions          :           0
 Number of planes            :           0
 Number of chirals           :           0
 Number of intervals         :           0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
                        Standard  External       All
                Bonds:      3292         0      3292
               Angles:      5896         0      5896
              Chirals:       254         0       254
               Planes:       409         0       409
             Torsions:      1177         0      1177
            Intervals:         0         0         0
--------------------------------------------------------------------------------


  Number of harmonic restraints       =            0
  Number of atoms in special position =            0
 -----------------------------------------------------


    ****                           Info from mtz file                           ****

FreeR flag                         -999
Number of "free" reflections          0
Number of   all  reflections        421
 Warning ==>The number of free reflections with flag         -999  is zero
 Warning ==> Switching off use of free R
--------------------------------------------------------------------------------
 Number of reflections in file       2523
 Number of reflections read            421


######  TLS Group Definitions ######



     CGMAT cycle number =      1

    ****                         Bond distance outliers                         ****

Bond distance deviations from the ideal >10.000Sigma will be monitored

A      1 MET N   . - A      1 MET CA  . mod.= 1.784 id.= 1.491 dev= -0.293 sig.= 0.021
A      1 MET CA  . - A      1 MET CB  . mod.= 2.124 id.= 1.530 dev= -0.594 sig.= 0.020
A      1 MET CA  . - A      1 MET C   . mod.= 0.959 id.= 1.525 dev=  0.566 sig.= 0.020
A      1 MET SD  . - A      1 MET CE  . mod.= 2.016 id.= 1.791 dev= -0.225 sig.= 0.020
A      1 MET C   . - A      1 MET O   . mod.= 2.019 id.= 1.231 dev= -0.788 sig.= 0.020
A      2 ARG CA  . - A      2 ARG CB  . mod.= 2.165 id.= 1.530 dev= -0.635 sig.= 0.020
A      2 ARG CA  . - A      2 ARG C   . mod.= 1.741 id.= 1.525 dev= -0.216 sig.= 0.021
A      2 ARG CG  . - A      2 ARG CD  . mod.= 1.051 id.= 1.520 dev=  0.469 sig.= 0.020
A      2 ARG CD  . - A      2 ARG NE  . mod.= 2.432 id.= 1.460 dev= -0.972 sig.= 0.018
A      2 ARG NE  . - A      2 ARG CZ  . mod.= 1.036 id.= 1.329 dev=  0.293 sig.= 0.014
A      2 ARG CZ  . - A      2 ARG NH2 . mod.= 1.673 id.= 1.326 dev= -0.347 sig.= 0.018
A      3 ILE CA  . - A      3 ILE CB  . mod.= 2.019 id.= 1.540 dev= -0.479 sig.= 0.020
A      3 ILE CB  . - A      3 ILE CG1 . mod.= 2.535 id.= 1.530 dev= -1.005 sig.= 0.020
A      3 ILE C   . - A      3 ILE O   . mod.= 1.765 id.= 1.231 dev= -0.534 sig.= 0.020
A      3 ILE C   . - A      4 ILE N   . mod.= 1.549 id.= 1.329 dev= -0.220 sig.= 0.014
A      4 ILE N   . - A      4 ILE CA  . mod.= 1.246 id.= 1.458 dev=  0.212 sig.= 0.021
A      4 ILE CA  . - A      4 ILE CB  . mod.= 1.189 id.= 1.540 dev=  0.351 sig.= 0.020
A      4 ILE CA  . - A      4 ILE C   . mod.= 1.859 id.= 1.525 dev= -0.334 sig.= 0.020
A      4 ILE CB  . - A      4 ILE CG2 . mod.= 2.033 id.= 1.521 dev= -0.512 sig.= 0.020
A      4 ILE C   . - A      4 ILE O   . mod.= 0.633 id.= 1.231 dev=  0.598 sig.= 0.020
A      5 LEU CA  . - A      5 LEU CB  . mod.= 1.960 id.= 1.530 dev= -0.430 sig.= 0.020
A      5 LEU CA  . - A      5 LEU C   . mod.= 1.820 id.= 1.525 dev= -0.295 sig.= 0.021
A      5 LEU CG  . - A      5 LEU CD1 . mod.= 1.301 id.= 1.521 dev=  0.220 sig.= 0.020
A      5 LEU CG  . - A      5 LEU CD2 . mod.= 2.178 id.= 1.521 dev= -0.657 sig.= 0.020
A      5 LEU C   . - A      5 LEU O   . mod.= 1.853 id.= 1.231 dev= -0.622 sig.= 0.020
A      5 LEU C   . - A      6 LEU N   . mod.= 0.719 id.= 1.329 dev=  0.610 sig.= 0.014
A      6 LEU N   . - A      6 LEU CA  . mod.= 1.696 id.= 1.458 dev= -0.238 sig.= 0.021
A      6 LEU CA  . - A      6 LEU C   . mod.= 0.948 id.= 1.525 dev=  0.577 sig.= 0.021
A      6 LEU CB  . - A      6 LEU CG  . mod.= 1.849 id.= 1.530 dev= -0.319 sig.= 0.020
A      6 LEU C   . - A      7 GLY N   . mod.= 1.167 id.= 1.329 dev=  0.162 sig.= 0.014
A      7 GLY CA  . - A      7 GLY C   . mod.= 1.745 id.= 1.516 dev= -0.229 sig.= 0.018
A      7 GLY C   . - A      7 GLY O   . mod.= 1.655 id.= 1.231 dev= -0.424 sig.= 0.020
A      7 GLY C   . - A      8 ALA N   . mod.= 0.955 id.= 1.329 dev=  0.374 sig.= 0.014
A      8 ALA N   . - A      8 ALA CA  . mod.= 1.842 id.= 1.458 dev= -0.384 sig.= 0.021
A      8 ALA CA  . - A      8 ALA CB  . mod.= 2.106 id.= 1.521 dev= -0.585 sig.= 0.020
A      8 ALA CA  . - A      8 ALA C   . mod.= 0.968 id.= 1.525 dev=  0.557 sig.= 0.021
A      8 ALA C   . - A      8 ALA O   . mod.= 0.906 id.= 1.231 dev=  0.325 sig.= 0.020
A      9 PRO N   . - A      9 PRO CA  . mod.= 1.682 id.= 1.458 dev= -0.224 sig.= 0.021
A      9 PRO N   . - A      9 PRO CD  . mod.= 1.298 id.= 1.473 dev=  0.175 sig.= 0.014
A      9 PRO CB  . - A      9 PRO CG  . mod.= 1.809 id.= 1.492 dev= -0.317 sig.= 0.025
A      9 PRO CG  . - A      9 PRO CD  . mod.= 1.943 id.= 1.503 dev= -0.440 sig.= 0.022
A      9 PRO C   . - A      9 PRO O   . mod.= 1.648 id.= 1.231 dev= -0.417 sig.= 0.020
A      9 PRO C   . - A     10 GLY N   . mod.= 1.007 id.= 1.329 dev=  0.322 sig.= 0.014
A     10 GLY C   . - A     10 GLY O   . mod.= 1.516 id.= 1.231 dev= -0.285 sig.= 0.020
A     10 GLY C   . - A     11 ALA N   . mod.= 1.722 id.= 1.329 dev= -0.393 sig.= 0.014
A     11 ALA N   . - A     11 ALA CA  . mod.= 1.207 id.= 1.458 dev=  0.251 sig.= 0.021
A     11 ALA CA  . - A     11 ALA CB  . mod.= 2.320 id.= 1.521 dev= -0.799 sig.= 0.020
A     11 ALA C   . - A     11 ALA O   . mod.= 1.871 id.= 1.231 dev= -0.640 sig.= 0.020
A     12 GLY CA  . - A     12 GLY C   . mod.= 2.137 id.= 1.516 dev= -0.621 sig.= 0.018
A     13 LYS N   . - A     13 LYS CA  . mod.= 2.084 id.= 1.458 dev= -0.626 sig.= 0.021
A     13 LYS CA  . - A     13 LYS C   . mod.= 1.204 id.= 1.525 dev=  0.321 sig.= 0.021
A     13 LYS CG  . - A     13 LYS CD  . mod.= 2.049 id.= 1.520 dev= -0.529 sig.= 0.020
A     13 LYS CD  . - A     13 LYS CE  . mod.= 0.616 id.= 1.520 dev=  0.904 sig.= 0.020
A     13 LYS CE  . - A     13 LYS NZ  . mod.= 1.142 id.= 1.489 dev=  0.347 sig.= 0.020
A     13 LYS C   . - A     13 LYS O   . mod.= 1.730 id.= 1.231 dev= -0.499 sig.= 0.020
A     13 LYS C   . - A     14 GLY N   . mod.= 1.682 id.= 1.329 dev= -0.353 sig.= 0.014
A     14 GLY N   . - A     14 GLY CA  . mod.= 1.246 id.= 1.458 dev=  0.212 sig.= 0.021
A     14 GLY C   . - A     15 THR N   . mod.= 1.651 id.= 1.329 dev= -0.322 sig.= 0.014
A     15 THR CA  . - A     15 THR CB  . mod.= 1.919 id.= 1.540 dev= -0.379 sig.= 0.020
A     15 THR C   . - A     15 THR O   . mod.= 0.943 id.= 1.231 dev=  0.288 sig.= 0.020
A     15 THR C   . - A     16 GLN N   . mod.= 1.122 id.= 1.329 dev=  0.207 sig.= 0.014
A     16 GLN N   . - A     16 GLN CA  . mod.= 1.688 id.= 1.458 dev= -0.230 sig.= 0.021
A     16 GLN CB  . - A     16 GLN CG  . mod.= 1.951 id.= 1.520 dev= -0.431 sig.= 0.020
A     16 GLN CG  . - A     16 GLN CD  . mod.= 2.128 id.= 1.516 dev= -0.612 sig.= 0.020
A     16 GLN CD  . - A     16 GLN NE2 . mod.= 1.737 id.= 1.328 dev= -0.409 sig.= 0.021
A     16 GLN C   . - A     16 GLN O   . mod.= 0.775 id.= 1.231 dev=  0.456 sig.= 0.020
A     16 GLN C   . - A     17 ALA N   . mod.= 1.666 id.= 1.329 dev= -0.337 sig.= 0.014
A     17 ALA N   . - A     17 ALA CA  . mod.= 0.730 id.= 1.458 dev=  0.728 sig.= 0.021
A     17 ALA CA  . - A     17 ALA CB  . mod.= 2.044 id.= 1.521 dev= -0.523 sig.= 0.020
A     17 ALA C   . - A     17 ALA O   . mod.= 1.438 id.= 1.231 dev= -0.207 sig.= 0.020
A     18 GLN CA  . - A     18 GLN C   . mod.= 1.876 id.= 1.525 dev= -0.351 sig.= 0.021
A     18 GLN CB  . - A     18 GLN CG  . mod.= 1.853 id.= 1.520 dev= -0.333 sig.= 0.020
A     18 GLN CG  . - A     18 GLN CD  . mod.= 1.291 id.= 1.516 dev=  0.225 sig.= 0.020
A     18 GLN CD  . - A     18 GLN OE1 . mod.= 1.491 id.= 1.231 dev= -0.260 sig.= 0.019
A     18 GLN CD  . - A     18 GLN NE2 . mod.= 1.612 id.= 1.328 dev= -0.284 sig.= 0.021
A     18 GLN C   . - A     18 GLN O   . mod.= 0.792 id.= 1.231 dev=  0.439 sig.= 0.020
A     18 GLN C   . - A     19 PHE N   . mod.= 1.617 id.= 1.329 dev= -0.288 sig.= 0.014
A     19 PHE N   . - A     19 PHE CA  . mod.= 1.075 id.= 1.458 dev=  0.383 sig.= 0.021
A     19 PHE CB  . - A     19 PHE CG  . mod.= 1.890 id.= 1.502 dev= -0.388 sig.= 0.020
A     19 PHE CG  . - A     19 PHE CD2 . mod.= 2.152 id.= 1.384 dev= -0.768 sig.= 0.021
A     19 PHE CD1 . - A     19 PHE CE1 . mod.= 1.837 id.= 1.382 dev= -0.455 sig.= 0.020
A     19 PHE CZ  . - A     19 PHE CE2 . mod.= 1.622 id.= 1.382 dev= -0.240 sig.= 0.020
A     19 PHE CE2 . - A     19 PHE CD2 . mod.= 0.736 id.= 1.382 dev=  0.646 sig.= 0.020
A     19 PHE C   . - A     19 PHE O   . mod.= 1.454 id.= 1.231 dev= -0.223 sig.= 0.020
A     19 PHE C   . - A     20 ILE N   . mod.= 1.633 id.= 1.329 dev= -0.304 sig.= 0.014
A     20 ILE CA  . - A     20 ILE CB  . mod.= 1.877 id.= 1.540 dev= -0.337 sig.= 0.020
A     20 ILE CA  . - A     20 ILE C   . mod.= 1.921 id.= 1.525 dev= -0.396 sig.= 0.020
A     20 ILE CB  . - A     20 ILE CG2 . mod.= 1.797 id.= 1.521 dev= -0.276 sig.= 0.020
A     20 ILE C   . - A     20 ILE O   . mod.= 0.680 id.= 1.231 dev=  0.551 sig.= 0.020
A     21 MET N   . - A     21 MET CA  . mod.= 2.057 id.= 1.458 dev= -0.599 sig.= 0.021
A     21 MET CA  . - A     21 MET C   . mod.= 2.122 id.= 1.525 dev= -0.597 sig.= 0.020
A     21 MET CB  . - A     21 MET CG  . mod.= 2.306 id.= 1.520 dev= -0.786 sig.= 0.020
A     21 MET CG  . - A     21 MET SD  . mod.= 2.379 id.= 1.803 dev= -0.576 sig.= 0.020
A     21 MET C   . - A     21 MET O   . mod.= 1.525 id.= 1.231 dev= -0.294 sig.= 0.020
A     22 GLU N   . - A     22 GLU CA  . mod.= 0.732 id.= 1.458 dev=  0.726 sig.= 0.021
A     22 GLU CB  . - A     22 GLU CG  . mod.= 2.536 id.= 1.520 dev= -1.016 sig.= 0.020
A     22 GLU CG  . - A     22 GLU CD  . mod.= 1.199 id.= 1.516 dev=  0.317 sig.= 0.020
A     22 GLU CD  . - A     22 GLU OE1 . mod.= 1.633 id.= 1.249 dev= -0.384 sig.= 0.019
A     22 GLU CD  . - A     22 GLU OE2 . mod.= 1.737 id.= 1.249 dev= -0.488 sig.= 0.019
A     22 GLU C   . - A     22 GLU O   . mod.= 1.762 id.= 1.231 dev= -0.531 sig.= 0.020
A     22 GLU C   . - A     23 LYS N   . mod.= 1.640 id.= 1.329 dev= -0.311 sig.= 0.014
A     23 LYS CA  . - A     23 LYS CB  . mod.= 1.760 id.= 1.530 dev= -0.230 sig.= 0.020
A     23 LYS CA  . - A     23 LYS C   . mod.= 1.044 id.= 1.525 dev=  0.481 sig.= 0.021
A     23 LYS CD  . - A     23 LYS CE  . mod.= 1.255 id.= 1.520 dev=  0.265 sig.= 0.020
A     23 LYS C   . - A     23 LYS O   . mod.= 1.437 id.= 1.231 dev= -0.206 sig.= 0.020
A     24 TYR CA  . - A     24 TYR C   . mod.= 1.994 id.= 1.525 dev= -0.469 sig.= 0.021
A     24 TYR CB  . - A     24 TYR CG  . mod.= 1.033 id.= 1.512 dev=  0.479 sig.= 0.022
A     24 TYR CG  . - A     24 TYR CD2 . mod.= 1.726 id.= 1.389 dev= -0.337 sig.= 0.021
A     24 TYR CD1 . - A     24 TYR CE1 . mod.= 1.994 id.= 1.382 dev= -0.612 sig.= 0.020
A     24 TYR CZ  . - A     24 TYR OH  . mod.= 1.123 id.= 1.376 dev=  0.253 sig.= 0.021
A     24 TYR CZ  . - A     24 TYR CE2 . mod.= 2.015 id.= 1.378 dev= -0.637 sig.= 0.020
A     24 TYR CE2 . - A     24 TYR CD2 . mod.= 1.661 id.= 1.382 dev= -0.279 sig.= 0.020
A     24 TYR C   . - A     24 TYR O   . mod.= 1.843 id.= 1.231 dev= -0.612 sig.= 0.020
A     24 TYR C   . - A     25 GLY N   . mod.= 0.531 id.= 1.329 dev=  0.798 sig.= 0.014
A     25 GLY N   . - A     25 GLY CA  . mod.= 2.031 id.= 1.458 dev= -0.573 sig.= 0.021
A     25 GLY CA  . - A     25 GLY C   . mod.= 2.015 id.= 1.516 dev= -0.499 sig.= 0.018
A     25 GLY C   . - A     25 GLY O   . mod.= 0.705 id.= 1.231 dev=  0.526 sig.= 0.020
A     25 GLY C   . - A     26 ILE N   . mod.= 1.619 id.= 1.329 dev= -0.290 sig.= 0.014
A     26 ILE N   . - A     26 ILE CA  . mod.= 2.054 id.= 1.458 dev= -0.596 sig.= 0.021
A     26 ILE CA  . - A     26 ILE CB  . mod.= 2.107 id.= 1.540 dev= -0.567 sig.= 0.020
A     26 ILE CA  . - A     26 ILE C   . mod.= 1.979 id.= 1.525 dev= -0.454 sig.= 0.020
A     26 ILE CB  . - A     26 ILE CG1 . mod.= 1.111 id.= 1.530 dev=  0.419 sig.= 0.020
A     26 ILE C   . - A     26 ILE O   . mod.= 1.561 id.= 1.231 dev= -0.330 sig.= 0.020
A     26 ILE C   . - A     27 PRO N   . mod.= 0.887 id.= 1.341 dev=  0.454 sig.= 0.016
A     27 PRO N   . - A     27 PRO CD  . mod.= 1.881 id.= 1.473 dev= -0.408 sig.= 0.014
A     27 PRO CA  . - A     27 PRO C   . mod.= 2.040 id.= 1.525 dev= -0.515 sig.= 0.021
A     27 PRO CB  . - A     27 PRO CG  . mod.= 2.449 id.= 1.492 dev= -0.957 sig.= 0.025
A     27 PRO CG  . - A     27 PRO CD  . mod.= 1.262 id.= 1.503 dev=  0.241 sig.= 0.022
A     27 PRO C   . - A     27 PRO O   . mod.= 0.984 id.= 1.231 dev=  0.247 sig.= 0.020
A     27 PRO C   . - A     28 GLN N   . mod.= 1.121 id.= 1.329 dev=  0.208 sig.= 0.014
A     28 GLN N   . - A     28 GLN CA  . mod.= 2.198 id.= 1.458 dev= -0.740 sig.= 0.021
A     28 GLN CA  . - A     28 GLN CB  . mod.= 1.905 id.= 1.530 dev= -0.375 sig.= 0.020
A     28 GLN CA  . - A     28 GLN C   . mod.= 0.944 id.= 1.525 dev=  0.581 sig.= 0.021
A     28 GLN CB  . - A     28 GLN CG  . mod.= 1.925 id.= 1.520 dev= -0.405 sig.= 0.020
A     28 GLN CD  . - A     28 GLN OE1 . mod.= 1.732 id.= 1.231 dev= -0.501 sig.= 0.019
A     28 GLN CD  . - A     28 GLN NE2 . mod.= 1.961 id.= 1.328 dev= -0.633 sig.= 0.021
A     28 GLN C   . - A     29 ILE N   . mod.= 1.704 id.= 1.329 dev= -0.375 sig.= 0.014
A     29 ILE N   . - A     29 ILE CA  . mod.= 2.230 id.= 1.458 dev= -0.772 sig.= 0.021
A     29 ILE CA  . - A     29 ILE C   . mod.= 1.859 id.= 1.525 dev= -0.334 sig.= 0.020
A     29 ILE CB  . - A     29 ILE CG1 . mod.= 2.220 id.= 1.530 dev= -0.690 sig.= 0.020
A     29 ILE CG1 . - A     29 ILE CD1 . mod.= 1.039 id.= 1.513 dev=  0.474 sig.= 0.020
A     29 ILE C   . - A     29 ILE O   . mod.= 1.664 id.= 1.231 dev= -0.433 sig.= 0.020
A     29 ILE C   . - A     30 SER N   . mod.= 1.007 id.= 1.329 dev=  0.322 sig.= 0.014
A     30 SER N   . - A     30 SER CA  . mod.= 2.032 id.= 1.458 dev= -0.574 sig.= 0.021
A     30 SER CA  . - A     30 SER CB  . mod.= 1.782 id.= 1.530 dev= -0.252 sig.= 0.020
A     30 SER CA  . - A     30 SER C   . mod.= 0.559 id.= 1.525 dev=  0.966 sig.= 0.021
A     30 SER CB  . - A     30 SER OG  . mod.= 1.875 id.= 1.417 dev= -0.458 sig.= 0.020
A     31 THR N   . - A     31 THR CA  . mod.= 0.778 id.= 1.458 dev=  0.680 sig.= 0.021
A     31 THR CA  . - A     31 THR CB  . mod.= 2.001 id.= 1.540 dev= -0.461 sig.= 0.020
A     31 THR CA  . - A     31 THR C   . mod.= 1.313 id.= 1.525 dev=  0.212 sig.= 0.021
A     31 THR CB  . - A     31 THR OG1 . mod.= 1.676 id.= 1.433 dev= -0.243 sig.= 0.016
A     32 GLY N   . - A     32 GLY CA  . mod.= 2.075 id.= 1.458 dev= -0.617 sig.= 0.021
A     32 GLY C   . - A     33 ASP N   . mod.= 1.036 id.= 1.329 dev=  0.293 sig.= 0.014
A     33 ASP CA  . - A     33 ASP CB  . mod.= 1.912 id.= 1.530 dev= -0.382 sig.= 0.020
A     33 ASP CA  . - A     33 ASP C   . mod.= 0.809 id.= 1.525 dev=  0.716 sig.= 0.021
A     33 ASP CB  . - A     33 ASP CG  . mod.= 0.850 id.= 1.516 dev=  0.666 sig.= 0.025
A     33 ASP CG  . - A     33 ASP OD1 . mod.= 1.779 id.= 1.249 dev= -0.530 sig.= 0.019
A     33 ASP CG  . - A     33 ASP OD2 . mod.= 1.584 id.= 1.249 dev= -0.335 sig.= 0.019
A     33 ASP C   . - A     33 ASP O   . mod.= 1.587 id.= 1.231 dev= -0.356 sig.= 0.020
A     33 ASP C   . - A     34 MET N   . mod.= 1.481 id.= 1.329 dev= -0.152 sig.= 0.014
A     34 MET N   . - A     34 MET CA  . mod.= 1.920 id.= 1.458 dev= -0.462 sig.= 0.021
A     34 MET SD  . - A     34 MET CE  . mod.= 2.143 id.= 1.791 dev= -0.352 sig.= 0.020
A     34 MET C   . - A     34 MET O   . mod.= 1.720 id.= 1.231 dev= -0.489 sig.= 0.020
A     34 MET C   . - A     35 LEU N   . mod.= 1.559 id.= 1.329 dev= -0.230 sig.= 0.014
A     35 LEU N   . - A     35 LEU CA  . mod.= 1.776 id.= 1.458 dev= -0.318 sig.= 0.021
A     35 LEU CA  . - A     35 LEU CB  . mod.= 1.997 id.= 1.530 dev= -0.467 sig.= 0.020
A     35 LEU CA  . - A     35 LEU C   . mod.= 1.763 id.= 1.525 dev= -0.238 sig.= 0.021
A     35 LEU CB  . - A     35 LEU CG  . mod.= 2.253 id.= 1.530 dev= -0.723 sig.= 0.020
A     35 LEU CG  . - A     35 LEU CD2 . mod.= 2.212 id.= 1.521 dev= -0.691 sig.= 0.020
A     35 LEU C   . - A     36 ARG N   . mod.= 1.694 id.= 1.329 dev= -0.365 sig.= 0.014
A     36 ARG CA  . - A     36 ARG CB  . mod.= 0.996 id.= 1.530 dev=  0.534 sig.= 0.020
A     36 ARG CA  . - A     36 ARG C   . mod.= 2.319 id.= 1.525 dev= -0.794 sig.= 0.021
A     36 ARG CB  . - A     36 ARG CG  . mod.= 1.834 id.= 1.520 dev= -0.314 sig.= 0.020
A     36 ARG CD  . - A     36 ARG NE  . mod.= 0.731 id.= 1.460 dev=  0.729 sig.= 0.018
A     36 ARG NE  . - A     36 ARG CZ  . mod.= 1.919 id.= 1.329 dev= -0.590 sig.= 0.014
A     36 ARG CZ  . - A     36 ARG NH2 . mod.= 1.753 id.= 1.326 dev= -0.427 sig.= 0.018
A     36 ARG C   . - A     37 ALA N   . mod.= 0.552 id.= 1.329 dev=  0.777 sig.= 0.014
A     37 ALA N   . - A     37 ALA CA  . mod.= 2.151 id.= 1.458 dev= -0.693 sig.= 0.021
A     37 ALA C   . - A     38 ALA N   . mod.= 1.612 id.= 1.329 dev= -0.283 sig.= 0.014
A     38 ALA CA  . - A     38 ALA CB  . mod.= 1.812 id.= 1.521 dev= -0.291 sig.= 0.020
A     39 VAL N   . - A     39 VAL CA  . mod.= 0.660 id.= 1.458 dev=  0.798 sig.= 0.021
A     39 VAL CA  . - A     39 VAL C   . mod.= 1.094 id.= 1.525 dev=  0.431 sig.= 0.020
A     39 VAL CB  . - A     39 VAL CG1 . mod.= 1.770 id.= 1.521 dev= -0.249 sig.= 0.020
A     39 VAL CB  . - A     39 VAL CG2 . mod.= 1.966 id.= 1.521 dev= -0.445 sig.= 0.020
A     39 VAL C   . - A     39 VAL O   . mod.= 1.859 id.= 1.231 dev= -0.628 sig.= 0.020
A     39 VAL C   . - A     40 LYS N   . mod.= 0.940 id.= 1.329 dev=  0.389 sig.= 0.014
A     40 LYS N   . - A     40 LYS CA  . mod.= 2.073 id.= 1.458 dev= -0.615 sig.= 0.021
A     40 LYS CA  . - A     40 LYS C   . mod.= 1.801 id.= 1.525 dev= -0.276 sig.= 0.021
A     40 LYS CB  . - A     40 LYS CG  . mod.= 1.906 id.= 1.520 dev= -0.386 sig.= 0.020
A     40 LYS CD  . - A     40 LYS CE  . mod.= 0.971 id.= 1.520 dev=  0.549 sig.= 0.020
A     40 LYS CE  . - A     40 LYS NZ  . mod.= 1.984 id.= 1.489 dev= -0.495 sig.= 0.020
A     40 LYS C   . - A     40 LYS O   . mod.= 1.733 id.= 1.231 dev= -0.502 sig.= 0.020
A     41 SER CA  . - A     41 SER CB  . mod.= 1.852 id.= 1.530 dev= -0.322 sig.= 0.020
A     41 SER CB  . - A     41 SER OG  . mod.= 1.108 id.= 1.417 dev=  0.309 sig.= 0.020
A     41 SER C   . - A     41 SER O   . mod.= 0.931 id.= 1.231 dev=  0.300 sig.= 0.020
A     42 GLY N   . - A     42 GLY CA  . mod.= 1.910 id.= 1.458 dev= -0.452 sig.= 0.021
A     42 GLY C   . - A     42 GLY O   . mod.= 0.672 id.= 1.231 dev=  0.559 sig.= 0.020
A     43 SER N   . - A     43 SER CA  . mod.= 0.815 id.= 1.458 dev=  0.643 sig.= 0.021
A     43 SER CA  . - A     43 SER C   . mod.= 2.388 id.= 1.525 dev= -0.863 sig.= 0.021
A     43 SER C   . - A     44 GLU N   . mod.= 0.857 id.= 1.329 dev=  0.472 sig.= 0.014
A     44 GLU CA  . - A     44 GLU CB  . mod.= 2.164 id.= 1.530 dev= -0.634 sig.= 0.020
A     44 GLU CA  . - A     44 GLU C   . mod.= 1.253 id.= 1.525 dev=  0.272 sig.= 0.021
A     44 GLU CB  . - A     44 GLU CG  . mod.= 1.230 id.= 1.520 dev=  0.290 sig.= 0.020
A     44 GLU CG  . - A     44 GLU CD  . mod.= 2.272 id.= 1.516 dev= -0.756 sig.= 0.020
A     44 GLU CD  . - A     44 GLU OE1 . mod.= 1.747 id.= 1.249 dev= -0.498 sig.= 0.019
A     44 GLU C   . - A     44 GLU O   . mod.= 1.728 id.= 1.231 dev= -0.497 sig.= 0.020
A     44 GLU C   . - A     45 LEU N   . mod.= 1.150 id.= 1.329 dev=  0.179 sig.= 0.014
A     45 LEU N   . - A     45 LEU CA  . mod.= 1.121 id.= 1.458 dev=  0.337 sig.= 0.021
A     45 LEU CA  . - A     45 LEU CB  . mod.= 2.654 id.= 1.530 dev= -1.124 sig.= 0.020
A     45 LEU CG  . - A     45 LEU CD1 . mod.= 1.272 id.= 1.521 dev=  0.249 sig.= 0.020
A     45 LEU CG  . - A     45 LEU CD2 . mod.= 2.091 id.= 1.521 dev= -0.570 sig.= 0.020
A     46 GLY CA  . - A     46 GLY C   . mod.= 1.934 id.= 1.516 dev= -0.418 sig.= 0.018
A     46 GLY C   . - A     46 GLY O   . mod.= 1.980 id.= 1.231 dev= -0.749 sig.= 0.020
A     46 GLY C   . - A     47 LYS N   . mod.= 0.711 id.= 1.329 dev=  0.618 sig.= 0.014
A     47 LYS N   . - A     47 LYS CA  . mod.= 1.814 id.= 1.458 dev= -0.356 sig.= 0.021
A     47 LYS CA  . - A     47 LYS CB  . mod.= 1.748 id.= 1.530 dev= -0.218 sig.= 0.020
A     48 GLN N   . - A     48 GLN CA  . mod.= 1.701 id.= 1.458 dev= -0.243 sig.= 0.021
A     48 GLN CA  . - A     48 GLN CB  . mod.= 0.757 id.= 1.530 dev=  0.773 sig.= 0.020
A     48 GLN CA  . - A     48 GLN C   . mod.= 1.982 id.= 1.525 dev= -0.457 sig.= 0.021
A     48 GLN CB  . - A     48 GLN CG  . mod.= 2.099 id.= 1.520 dev= -0.579 sig.= 0.020
A     48 GLN CG  . - A     48 GLN CD  . mod.= 1.081 id.= 1.516 dev=  0.435 sig.= 0.020
A     48 GLN CD  . - A     48 GLN OE1 . mod.= 1.826 id.= 1.231 dev= -0.595 sig.= 0.019
A     48 GLN CD  . - A     48 GLN NE2 . mod.= 1.615 id.= 1.328 dev= -0.287 sig.= 0.021
A     49 ALA CA  . - A     49 ALA C   . mod.= 1.285 id.= 1.525 dev=  0.240 sig.= 0.021
A     49 ALA C   . - A     50 LYS N   . mod.= 1.151 id.= 1.329 dev=  0.178 sig.= 0.014
A     50 LYS N   . - A     50 LYS CA  . mod.= 2.049 id.= 1.458 dev= -0.591 sig.= 0.021
A     50 LYS CA  . - A     50 LYS CB  . mod.= 1.108 id.= 1.530 dev=  0.422 sig.= 0.020
A     50 LYS CA  . - A     50 LYS C   . mod.= 1.852 id.= 1.525 dev= -0.327 sig.= 0.021
A     50 LYS CB  . - A     50 LYS CG  . mod.= 1.730 id.= 1.520 dev= -0.210 sig.= 0.020
A     50 LYS CD  . - A     50 LYS CE  . mod.= 2.010 id.= 1.520 dev= -0.490 sig.= 0.020
A     50 LYS C   . - A     50 LYS O   . mod.= 1.638 id.= 1.231 dev= -0.407 sig.= 0.020
A     50 LYS C   . - A     51 ASP N   . mod.= 0.897 id.= 1.329 dev=  0.432 sig.= 0.014
A     51 ASP N   . - A     51 ASP CA  . mod.= 1.742 id.= 1.458 dev= -0.284 sig.= 0.021
A     51 ASP CA  . - A     51 ASP CB  . mod.= 0.767 id.= 1.530 dev=  0.763 sig.= 0.020
A     51 ASP CG  . - A     51 ASP OD1 . mod.= 2.020 id.= 1.249 dev= -0.771 sig.= 0.019
A     51 ASP CG  . - A     51 ASP OD2 . mod.= 1.477 id.= 1.249 dev= -0.228 sig.= 0.019
A     51 ASP C   . - A     52 ILE N   . mod.= 1.033 id.= 1.329 dev=  0.296 sig.= 0.014
A     52 ILE N   . - A     52 ILE CA  . mod.= 1.788 id.= 1.458 dev= -0.330 sig.= 0.021
A     52 ILE CA  . - A     52 ILE CB  . mod.= 0.952 id.= 1.540 dev=  0.588 sig.= 0.020
A     52 ILE CA  . - A     52 ILE C   . mod.= 2.344 id.= 1.525 dev= -0.819 sig.= 0.020
A     52 ILE CB  . - A     52 ILE CG1 . mod.= 1.754 id.= 1.530 dev= -0.224 sig.= 0.020
A     52 ILE C   . - A     53 MET N   . mod.= 0.904 id.= 1.329 dev=  0.425 sig.= 0.014
A     53 MET N   . - A     53 MET CA  . mod.= 1.953 id.= 1.458 dev= -0.495 sig.= 0.021
A     53 MET CA  . - A     53 MET C   . mod.= 1.912 id.= 1.525 dev= -0.387 sig.= 0.020
A     53 MET CG  . - A     53 MET SD  . mod.= 2.072 id.= 1.803 dev= -0.269 sig.= 0.020
A     53 MET SD  . - A     53 MET CE  . mod.= 2.796 id.= 1.791 dev= -1.005 sig.= 0.020
A     53 MET C   . - A     53 MET O   . mod.= 0.905 id.= 1.231 dev=  0.326 sig.= 0.020
A     53 MET C   . - A     54 ASP N   . mod.= 1.715 id.= 1.329 dev= -0.386 sig.= 0.014
A     54 ASP CA  . - A     54 ASP CB  . mod.= 1.922 id.= 1.530 dev= -0.392 sig.= 0.020
A     54 ASP CG  . - A     54 ASP OD1 . mod.= 1.706 id.= 1.249 dev= -0.457 sig.= 0.019
A     54 ASP C   . - A     54 ASP O   . mod.= 1.712 id.= 1.231 dev= -0.481 sig.= 0.020
A     54 ASP C   . - A     55 ALA N   . mod.= 1.574 id.= 1.329 dev= -0.245 sig.= 0.014
A     55 ALA CA  . - A     55 ALA C   . mod.= 1.807 id.= 1.525 dev= -0.282 sig.= 0.021
A     56 GLY N   . - A     56 GLY CA  . mod.= 0.945 id.= 1.458 dev=  0.513 sig.= 0.021
A     56 GLY C   . - A     56 GLY O   . mod.= 0.657 id.= 1.231 dev=  0.574 sig.= 0.020
A     57 LYS N   . - A     57 LYS CA  . mod.= 1.721 id.= 1.458 dev= -0.263 sig.= 0.021
A     57 LYS CA  . - A     57 LYS CB  . mod.= 1.937 id.= 1.530 dev= -0.407 sig.= 0.020
A     57 LYS CA  . - A     57 LYS C   . mod.= 1.116 id.= 1.525 dev=  0.409 sig.= 0.021
A     57 LYS CG  . - A     57 LYS CD  . mod.= 2.345 id.= 1.520 dev= -0.825 sig.= 0.020
A     57 LYS CE  . - A     57 LYS NZ  . mod.= 0.917 id.= 1.489 dev=  0.572 sig.= 0.020
A     57 LYS C   . - A     58 LEU N   . mod.= 1.637 id.= 1.329 dev= -0.308 sig.= 0.014
A     58 LEU CA  . - A     58 LEU CB  . mod.= 1.807 id.= 1.530 dev= -0.277 sig.= 0.020
A     58 LEU CA  . - A     58 LEU C   . mod.= 2.226 id.= 1.525 dev= -0.701 sig.= 0.021
A     58 LEU CG  . - A     58 LEU CD2 . mod.= 0.973 id.= 1.521 dev=  0.548 sig.= 0.020
A     58 LEU C   . - A     58 LEU O   . mod.= 0.990 id.= 1.231 dev=  0.241 sig.= 0.020
A     58 LEU C   . - A     59 VAL N   . mod.= 1.098 id.= 1.329 dev=  0.231 sig.= 0.014
A     59 VAL CA  . - A     59 VAL C   . mod.= 2.672 id.= 1.525 dev= -1.147 sig.= 0.020
A     59 VAL CB  . - A     59 VAL CG1 . mod.= 1.874 id.= 1.521 dev= -0.353 sig.= 0.020
A     60 THR N   . - A     60 THR CA  . mod.= 1.701 id.= 1.458 dev= -0.243 sig.= 0.021
A     60 THR CA  . - A     60 THR C   . mod.= 1.900 id.= 1.525 dev= -0.375 sig.= 0.021
A     60 THR CB  . - A     60 THR OG1 . mod.= 1.777 id.= 1.433 dev= -0.344 sig.= 0.016
A     60 THR C   . - A     60 THR O   . mod.= 0.998 id.= 1.231 dev=  0.233 sig.= 0.020
A     61 ASP N   . - A     61 ASP CA  . mod.= 0.732 id.= 1.458 dev=  0.726 sig.= 0.021
A     61 ASP CA  . - A     61 ASP C   . mod.= 1.281 id.= 1.525 dev=  0.244 sig.= 0.021
A     61 ASP CB  . - A     61 ASP CG  . mod.= 1.242 id.= 1.516 dev=  0.274 sig.= 0.025
A     61 ASP CG  . - A     61 ASP OD2 . mod.= 1.809 id.= 1.249 dev= -0.560 sig.= 0.019
A     61 ASP C   . - A     61 ASP O   . mod.= 2.187 id.= 1.231 dev= -0.956 sig.= 0.020
A     62 GLU CA  . - A     62 GLU CB  . mod.= 1.897 id.= 1.530 dev= -0.367 sig.= 0.020
A     62 GLU CA  . - A     62 GLU C   . mod.= 1.310 id.= 1.525 dev=  0.215 sig.= 0.021
A     62 GLU CB  . - A     62 GLU CG  . mod.= 2.021 id.= 1.520 dev= -0.501 sig.= 0.020
A     62 GLU CG  . - A     62 GLU CD  . mod.= 2.398 id.= 1.516 dev= -0.882 sig.= 0.020
A     62 GLU CD  . - A     62 GLU OE2 . mod.= 1.513 id.= 1.249 dev= -0.264 sig.= 0.019
A     62 GLU C   . - A     62 GLU O   . mod.= 1.712 id.= 1.231 dev= -0.481 sig.= 0.020
A     63 LEU N   . - A     63 LEU CA  . mod.= 1.987 id.= 1.458 dev= -0.529 sig.= 0.021
A     63 LEU CB  . - A     63 LEU CG  . mod.= 1.859 id.= 1.530 dev= -0.329 sig.= 0.020
A     63 LEU CG  . - A     63 LEU CD1 . mod.= 1.244 id.= 1.521 dev=  0.277 sig.= 0.020
A     64 VAL N   . - A     64 VAL CA  . mod.= 1.880 id.= 1.458 dev= -0.422 sig.= 0.021
A     64 VAL CA  . - A     64 VAL CB  . mod.= 1.894 id.= 1.540 dev= -0.354 sig.= 0.020
A     64 VAL CA  . - A     64 VAL C   . mod.= 1.136 id.= 1.525 dev=  0.389 sig.= 0.020
A     64 VAL CB  . - A     64 VAL CG1 . mod.= 1.790 id.= 1.521 dev= -0.269 sig.= 0.020
A     64 VAL CB  . - A     64 VAL CG2 . mod.= 2.214 id.= 1.521 dev= -0.693 sig.= 0.020
A     64 VAL C   . - A     64 VAL O   . mod.= 1.549 id.= 1.231 dev= -0.318 sig.= 0.020
A     65 ILE N   . - A     65 ILE CA  . mod.= 2.201 id.= 1.458 dev= -0.743 sig.= 0.021
A     65 ILE CA  . - A     65 ILE C   . mod.= 1.303 id.= 1.525 dev=  0.222 sig.= 0.020
A     65 ILE C   . - A     65 ILE O   . mod.= 1.860 id.= 1.231 dev= -0.629 sig.= 0.020
A     65 ILE C   . - A     66 ALA N   . mod.= 0.906 id.= 1.329 dev=  0.423 sig.= 0.014
A     66 ALA N   . - A     66 ALA CA  . mod.= 1.824 id.= 1.458 dev= -0.366 sig.= 0.021
A     66 ALA CA  . - A     66 ALA CB  . mod.= 0.652 id.= 1.521 dev=  0.869 sig.= 0.020
A     66 ALA C   . - A     66 ALA O   . mod.= 1.680 id.= 1.231 dev= -0.449 sig.= 0.020
A     66 ALA C   . - A     67 LEU N   . mod.= 1.721 id.= 1.329 dev= -0.392 sig.= 0.014
A     67 LEU CA  . - A     67 LEU CB  . mod.= 1.300 id.= 1.530 dev=  0.230 sig.= 0.020
A     67 LEU CG  . - A     67 LEU CD1 . mod.= 2.280 id.= 1.521 dev= -0.759 sig.= 0.020
A     67 LEU CG  . - A     67 LEU CD2 . mod.= 1.314 id.= 1.521 dev=  0.207 sig.= 0.020
A     68 VAL CA  . - A     68 VAL C   . mod.= 1.977 id.= 1.525 dev= -0.452 sig.= 0.020
A     68 VAL CB  . - A     68 VAL CG1 . mod.= 1.740 id.= 1.521 dev= -0.219 sig.= 0.020
A     68 VAL CB  . - A     68 VAL CG2 . mod.= 0.966 id.= 1.521 dev=  0.555 sig.= 0.020
A     68 VAL C   . - A     68 VAL O   . mod.= 0.799 id.= 1.231 dev=  0.432 sig.= 0.020
A     69 LYS N   . - A     69 LYS CA  . mod.= 2.043 id.= 1.458 dev= -0.585 sig.= 0.021
A     69 LYS CA  . - A     69 LYS CB  . mod.= 0.620 id.= 1.530 dev=  0.910 sig.= 0.020
A     69 LYS CA  . - A     69 LYS C   . mod.= 1.869 id.= 1.525 dev= -0.344 sig.= 0.021
A     69 LYS CB  . - A     69 LYS CG  . mod.= 1.304 id.= 1.520 dev=  0.216 sig.= 0.020
A     69 LYS CD  . - A     69 LYS CE  . mod.= 2.243 id.= 1.520 dev= -0.723 sig.= 0.020
A     69 LYS CE  . - A     69 LYS NZ  . mod.= 2.036 id.= 1.489 dev= -0.547 sig.= 0.020
A     69 LYS C   . - A     69 LYS O   . mod.= 1.021 id.= 1.231 dev=  0.210 sig.= 0.020
A     69 LYS C   . - A     70 GLU N   . mod.= 1.564 id.= 1.329 dev= -0.235 sig.= 0.014
A     70 GLU CA  . - A     70 GLU CB  . mod.= 1.934 id.= 1.530 dev= -0.404 sig.= 0.020
A     70 GLU CA  . - A     70 GLU C   . mod.= 1.263 id.= 1.525 dev=  0.262 sig.= 0.021
A     70 GLU CB  . - A     70 GLU CG  . mod.= 1.142 id.= 1.520 dev=  0.378 sig.= 0.020
A     70 GLU CG  . - A     70 GLU CD  . mod.= 2.170 id.= 1.516 dev= -0.654 sig.= 0.020
A     70 GLU CD  . - A     70 GLU OE1 . mod.= 0.777 id.= 1.249 dev=  0.472 sig.= 0.019
A     70 GLU C   . - A     71 ARG N   . mod.= 0.928 id.= 1.329 dev=  0.401 sig.= 0.014
A     71 ARG N   . - A     71 ARG CA  . mod.= 1.864 id.= 1.458 dev= -0.406 sig.= 0.021
A     71 ARG CA  . - A     71 ARG C   . mod.= 1.957 id.= 1.525 dev= -0.432 sig.= 0.021
A     71 ARG CG  . - A     71 ARG CD  . mod.= 1.811 id.= 1.520 dev= -0.291 sig.= 0.020
A     71 ARG CD  . - A     71 ARG NE  . mod.= 1.946 id.= 1.460 dev= -0.486 sig.= 0.018
A     71 ARG CZ  . - A     71 ARG NH1 . mod.= 1.888 id.= 1.326 dev= -0.562 sig.= 0.018
A     71 ARG C   . - A     72 ILE N   . mod.= 1.549 id.= 1.329 dev= -0.220 sig.= 0.014
A     72 ILE N   . - A     72 ILE CA  . mod.= 1.925 id.= 1.458 dev= -0.467 sig.= 0.021
A     72 ILE CA  . - A     72 ILE CB  . mod.= 1.835 id.= 1.540 dev= -0.295 sig.= 0.020
A     72 ILE CB  . - A     72 ILE CG1 . mod.= 1.736 id.= 1.530 dev= -0.206 sig.= 0.020
A     72 ILE CG1 . - A     72 ILE CD1 . mod.= 1.933 id.= 1.513 dev= -0.420 sig.= 0.020
A     72 ILE C   . - A     72 ILE O   . mod.= 1.509 id.= 1.231 dev= -0.278 sig.= 0.020
A     72 ILE C   . - A     73 ALA N   . mod.= 0.595 id.= 1.329 dev=  0.734 sig.= 0.014
A     73 ALA N   . - A     73 ALA CA  . mod.= 1.801 id.= 1.458 dev= -0.343 sig.= 0.021
A     73 ALA C   . - A     73 ALA O   . mod.= 1.448 id.= 1.231 dev= -0.217 sig.= 0.020
A     73 ALA C   . - A     74 GLN N   . mod.= 1.480 id.= 1.329 dev= -0.151 sig.= 0.014
A     74 GLN CA  . - A     74 GLN CB  . mod.= 1.828 id.= 1.530 dev= -0.298 sig.= 0.020
A     74 GLN CA  . - A     74 GLN C   . mod.= 2.596 id.= 1.525 dev= -1.071 sig.= 0.021
A     74 GLN CB  . - A     74 GLN CG  . mod.= 1.140 id.= 1.520 dev=  0.380 sig.= 0.020
A     74 GLN CG  . - A     74 GLN CD  . mod.= 1.724 id.= 1.516 dev= -0.208 sig.= 0.020
A     74 GLN CD  . - A     74 GLN NE2 . mod.= 1.003 id.= 1.328 dev=  0.325 sig.= 0.021
A     74 GLN C   . - A     74 GLN O   . mod.= 1.542 id.= 1.231 dev= -0.311 sig.= 0.020
A     74 GLN C   . - A     75 GLU N   . mod.= 0.879 id.= 1.329 dev=  0.450 sig.= 0.014
A     75 GLU N   . - A     75 GLU CA  . mod.= 1.749 id.= 1.458 dev= -0.291 sig.= 0.021
A     75 GLU CA  . - A     75 GLU CB  . mod.= 1.297 id.= 1.530 dev=  0.233 sig.= 0.020
A     75 GLU CA  . - A     75 GLU C   . mod.= 1.151 id.= 1.525 dev=  0.374 sig.= 0.021
A     75 GLU CB  . - A     75 GLU CG  . mod.= 1.318 id.= 1.520 dev=  0.202 sig.= 0.020
A     75 GLU CG  . - A     75 GLU CD  . mod.= 1.997 id.= 1.516 dev= -0.481 sig.= 0.020
A     75 GLU CD  . - A     75 GLU OE1 . mod.= 1.816 id.= 1.249 dev= -0.567 sig.= 0.019
A     75 GLU C   . - A     75 GLU O   . mod.= 2.134 id.= 1.231 dev= -0.903 sig.= 0.020
A     75 GLU C   . - A     76 ASP N   . mod.= 1.154 id.= 1.329 dev=  0.175 sig.= 0.014
A     76 ASP N   . - A     76 ASP CA  . mod.= 2.011 id.= 1.458 dev= -0.553 sig.= 0.021
A     76 ASP CA  . - A     76 ASP CB  . mod.= 1.800 id.= 1.530 dev= -0.270 sig.= 0.020
A     76 ASP CA  . - A     76 ASP C   . mod.= 1.150 id.= 1.525 dev=  0.375 sig.= 0.021
A     76 ASP CB  . - A     76 ASP CG  . mod.= 2.310 id.= 1.516 dev= -0.794 sig.= 0.025
A     76 ASP CG  . - A     76 ASP OD1 . mod.= 0.461 id.= 1.249 dev=  0.788 sig.= 0.019
A     76 ASP CG  . - A     76 ASP OD2 . mod.= 1.811 id.= 1.249 dev= -0.562 sig.= 0.019
A     76 ASP C   . - A     76 ASP O   . mod.= 0.836 id.= 1.231 dev=  0.395 sig.= 0.020
A     77 CYS N   . - A     77 CYS CA  . mod.= 2.166 id.= 1.458 dev= -0.708 sig.= 0.021
A     77 CYS CB  . - A     77 CYS SG  . mod.= 2.646 id.= 1.808 dev= -0.838 sig.= 0.020
A     78 ARG N   . - A     78 ARG CA  . mod.= 2.023 id.= 1.458 dev= -0.565 sig.= 0.021
A     78 ARG CB  . - A     78 ARG CG  . mod.= 1.194 id.= 1.520 dev=  0.326 sig.= 0.020
A     78 ARG CG  . - A     78 ARG CD  . mod.= 1.759 id.= 1.520 dev= -0.239 sig.= 0.020
A     78 ARG CD  . - A     78 ARG NE  . mod.= 2.157 id.= 1.460 dev= -0.697 sig.= 0.018
A     78 ARG NE  . - A     78 ARG CZ  . mod.= 1.728 id.= 1.329 dev= -0.399 sig.= 0.014
A     78 ARG CZ  . - A     78 ARG NH1 . mod.= 0.868 id.= 1.326 dev=  0.458 sig.= 0.018
A     78 ARG CZ  . - A     78 ARG NH2 . mod.= 1.873 id.= 1.326 dev= -0.547 sig.= 0.018
A     78 ARG C   . - A     78 ARG O   . mod.= 1.627 id.= 1.231 dev= -0.396 sig.= 0.020
A     79 ASN CA  . - A     79 ASN CB  . mod.= 1.779 id.= 1.530 dev= -0.249 sig.= 0.020
A     79 ASN CA  . - A     79 ASN C   . mod.= 2.168 id.= 1.525 dev= -0.643 sig.= 0.021
A     79 ASN CB  . - A     79 ASN CG  . mod.= 1.773 id.= 1.516 dev= -0.257 sig.= 0.020
A     79 ASN C   . - A     80 GLY N   . mod.= 0.814 id.= 1.329 dev=  0.515 sig.= 0.014
A     80 GLY N   . - A     80 GLY CA  . mod.= 2.072 id.= 1.458 dev= -0.614 sig.= 0.021
A     80 GLY C   . - A     80 GLY O   . mod.= 0.961 id.= 1.231 dev=  0.270 sig.= 0.020
A     81 PHE N   . - A     81 PHE CA  . mod.= 2.234 id.= 1.458 dev= -0.776 sig.= 0.021
A     81 PHE CB  . - A     81 PHE CG  . mod.= 2.243 id.= 1.502 dev= -0.741 sig.= 0.020
A     81 PHE CD1 . - A     81 PHE CE1 . mod.= 1.949 id.= 1.382 dev= -0.567 sig.= 0.020
A     81 PHE CE1 . - A     81 PHE CZ  . mod.= 0.877 id.= 1.382 dev=  0.505 sig.= 0.020
A     81 PHE CZ  . - A     81 PHE CE2 . mod.= 2.313 id.= 1.382 dev= -0.931 sig.= 0.020
A     81 PHE CE2 . - A     81 PHE CD2 . mod.= 1.592 id.= 1.382 dev= -0.210 sig.= 0.020
A     81 PHE C   . - A     81 PHE O   . mod.= 1.703 id.= 1.231 dev= -0.472 sig.= 0.020
A     82 LEU CA  . - A     82 LEU CB  . mod.= 1.938 id.= 1.530 dev= -0.408 sig.= 0.020
A     82 LEU CA  . - A     82 LEU C   . mod.= 2.248 id.= 1.525 dev= -0.723 sig.= 0.021
A     82 LEU CB  . - A     82 LEU CG  . mod.= 1.118 id.= 1.530 dev=  0.412 sig.= 0.020
A     82 LEU C   . - A     82 LEU O   . mod.= 1.786 id.= 1.231 dev= -0.555 sig.= 0.020
A     82 LEU C   . - A     83 LEU N   . mod.= 1.068 id.= 1.329 dev=  0.261 sig.= 0.014
A     83 LEU N   . - A     83 LEU CA  . mod.= 1.872 id.= 1.458 dev= -0.414 sig.= 0.021
A     83 LEU CA  . - A     83 LEU CB  . mod.= 1.760 id.= 1.530 dev= -0.230 sig.= 0.020
A     83 LEU CA  . - A     83 LEU C   . mod.= 1.921 id.= 1.525 dev= -0.396 sig.= 0.021
A     83 LEU CB  . - A     83 LEU CG  . mod.= 1.063 id.= 1.530 dev=  0.467 sig.= 0.020
A     83 LEU CG  . - A     83 LEU CD1 . mod.= 1.843 id.= 1.521 dev= -0.322 sig.= 0.020
A     84 ASP CA  . - A     84 ASP CB  . mod.= 1.731 id.= 1.530 dev= -0.201 sig.= 0.020
A     84 ASP CB  . - A     84 ASP CG  . mod.= 1.866 id.= 1.516 dev= -0.350 sig.= 0.025
A     84 ASP CG  . - A     84 ASP OD1 . mod.= 1.571 id.= 1.249 dev= -0.322 sig.= 0.019
A     84 ASP CG  . - A     84 ASP OD2 . mod.= 1.543 id.= 1.249 dev= -0.294 sig.= 0.019
A     85 GLY N   . - A     85 GLY CA  . mod.= 2.047 id.= 1.458 dev= -0.589 sig.= 0.021
A     85 GLY C   . - A     86 PHE N   . mod.= 1.532 id.= 1.329 dev= -0.203 sig.= 0.014
A     86 PHE CA  . - A     86 PHE CB  . mod.= 1.862 id.= 1.530 dev= -0.332 sig.= 0.020
A     86 PHE CG  . - A     86 PHE CD2 . mod.= 1.077 id.= 1.384 dev=  0.307 sig.= 0.021
A     86 PHE CD1 . - A     86 PHE CE1 . mod.= 1.726 id.= 1.382 dev= -0.344 sig.= 0.020
A     86 PHE CE1 . - A     86 PHE CZ  . mod.= 0.869 id.= 1.382 dev=  0.513 sig.= 0.020
A     86 PHE CZ  . - A     86 PHE CE2 . mod.= 1.898 id.= 1.382 dev= -0.516 sig.= 0.020
A     86 PHE CE2 . - A     86 PHE CD2 . mod.= 1.805 id.= 1.382 dev= -0.423 sig.= 0.020
A     86 PHE C   . - A     86 PHE O   . mod.= 0.740 id.= 1.231 dev=  0.491 sig.= 0.020
A     86 PHE C   . - A     87 PRO N   . mod.= 1.878 id.= 1.329 dev= -0.549 sig.= 0.014
A     87 PRO N   . - A     87 PRO CD  . mod.= 1.272 id.= 1.473 dev=  0.201 sig.= 0.014
A     87 PRO CA  . - A     87 PRO CB  . mod.= 2.260 id.= 1.530 dev= -0.730 sig.= 0.020
A     87 PRO C   . - A     87 PRO O   . mod.= 1.477 id.= 1.231 dev= -0.246 sig.= 0.020
A     87 PRO C   . - A     88 ARG N   . mod.= 1.107 id.= 1.329 dev=  0.222 sig.= 0.014
A     88 ARG N   . - A     88 ARG CA  . mod.= 1.163 id.= 1.458 dev=  0.295 sig.= 0.021
A     88 ARG CB  . - A     88 ARG CG  . mod.= 2.173 id.= 1.520 dev= -0.653 sig.= 0.020
A     88 ARG CG  . - A     88 ARG CD  . mod.= 1.903 id.= 1.520 dev= -0.383 sig.= 0.020
A     88 ARG NE  . - A     88 ARG CZ  . mod.= 1.492 id.= 1.329 dev= -0.163 sig.= 0.014
A     88 ARG CZ  . - A     88 ARG NH1 . mod.= 2.136 id.= 1.326 dev= -0.810 sig.= 0.018
A     88 ARG C   . - A     88 ARG O   . mod.= 1.970 id.= 1.231 dev= -0.739 sig.= 0.020
A     88 ARG C   . - A     89 THR N   . mod.= 1.568 id.= 1.329 dev= -0.239 sig.= 0.014
A     89 THR CA  . - A     89 THR C   . mod.= 1.296 id.= 1.525 dev=  0.229 sig.= 0.021
A     89 THR CB  . - A     89 THR OG1 . mod.= 1.598 id.= 1.433 dev= -0.165 sig.= 0.016
A     89 THR C   . - A     90 ILE N   . mod.= 0.988 id.= 1.329 dev=  0.341 sig.= 0.014
A     90 ILE N   . - A     90 ILE CA  . mod.= 2.049 id.= 1.458 dev= -0.591 sig.= 0.021
A     90 ILE CA  . - A     90 ILE CB  . mod.= 2.139 id.= 1.540 dev= -0.599 sig.= 0.020
A     90 ILE CB  . - A     90 ILE CG1 . mod.= 1.932 id.= 1.530 dev= -0.402 sig.= 0.020
A     90 ILE CB  . - A     90 ILE CG2 . mod.= 1.726 id.= 1.521 dev= -0.205 sig.= 0.020
A     90 ILE CG1 . - A     90 ILE CD1 . mod.= 2.151 id.= 1.513 dev= -0.638 sig.= 0.020
A     90 ILE C   . - A     90 ILE O   . mod.= 0.943 id.= 1.231 dev=  0.288 sig.= 0.020
A     90 ILE C   . - A     91 PRO N   . mod.= 1.610 id.= 1.341 dev= -0.269 sig.= 0.016
A     91 PRO N   . - A     91 PRO CA  . mod.= 1.809 id.= 1.458 dev= -0.351 sig.= 0.021
A     91 PRO CA  . - A     91 PRO CB  . mod.= 1.103 id.= 1.530 dev=  0.427 sig.= 0.020
A     91 PRO CB  . - A     91 PRO CG  . mod.= 1.901 id.= 1.492 dev= -0.409 sig.= 0.025
A     91 PRO CG  . - A     91 PRO CD  . mod.= 1.755 id.= 1.503 dev= -0.252 sig.= 0.022
A     91 PRO C   . - A     91 PRO O   . mod.= 1.692 id.= 1.231 dev= -0.461 sig.= 0.020
A     92 GLN N   . - A     92 GLN CA  . mod.= 1.097 id.= 1.458 dev=  0.361 sig.= 0.021
A     92 GLN CA  . - A     92 GLN CB  . mod.= 1.753 id.= 1.530 dev= -0.223 sig.= 0.020
A     92 GLN CA  . - A     92 GLN C   . mod.= 1.870 id.= 1.525 dev= -0.345 sig.= 0.021
A     92 GLN CB  . - A     92 GLN CG  . mod.= 2.621 id.= 1.520 dev= -1.101 sig.= 0.020
A     92 GLN CG  . - A     92 GLN CD  . mod.= 0.992 id.= 1.516 dev=  0.524 sig.= 0.020
A     92 GLN CD  . - A     92 GLN NE2 . mod.= 1.581 id.= 1.328 dev= -0.253 sig.= 0.021
A     92 GLN C   . - A     92 GLN O   . mod.= 1.800 id.= 1.231 dev= -0.569 sig.= 0.020
A     92 GLN C   . - A     93 ALA N   . mod.= 1.636 id.= 1.329 dev= -0.307 sig.= 0.014
A     93 ALA N   . - A     93 ALA CA  . mod.= 1.119 id.= 1.458 dev=  0.339 sig.= 0.021
A     93 ALA C   . - A     94 ASP N   . mod.= 1.155 id.= 1.329 dev=  0.174 sig.= 0.014
A     94 ASP N   . - A     94 ASP CA  . mod.= 1.957 id.= 1.458 dev= -0.499 sig.= 0.021
A     94 ASP CA  . - A     94 ASP CB  . mod.= 2.297 id.= 1.530 dev= -0.767 sig.= 0.020
A     94 ASP CA  . - A     94 ASP C   . mod.= 1.154 id.= 1.525 dev=  0.371 sig.= 0.021
A     94 ASP CG  . - A     94 ASP OD1 . mod.= 1.767 id.= 1.249 dev= -0.518 sig.= 0.019
A     94 ASP CG  . - A     94 ASP OD2 . mod.= 1.834 id.= 1.249 dev= -0.585 sig.= 0.019
A     94 ASP C   . - A     94 ASP O   . mod.= 0.565 id.= 1.231 dev=  0.666 sig.= 0.020
A     95 ALA N   . - A     95 ALA CA  . mod.= 2.206 id.= 1.458 dev= -0.748 sig.= 0.021
A     95 ALA CA  . - A     95 ALA CB  . mod.= 1.096 id.= 1.521 dev=  0.425 sig.= 0.020
A     95 ALA C   . - A     95 ALA O   . mod.= 1.860 id.= 1.231 dev= -0.629 sig.= 0.020
A     96 MET CA  . - A     96 MET CB  . mod.= 1.848 id.= 1.530 dev= -0.318 sig.= 0.020
A     96 MET CA  . - A     96 MET C   . mod.= 1.015 id.= 1.525 dev=  0.510 sig.= 0.020
A     96 MET CB  . - A     96 MET CG  . mod.= 0.713 id.= 1.520 dev=  0.807 sig.= 0.020
A     96 MET SD  . - A     96 MET CE  . mod.= 1.540 id.= 1.791 dev=  0.251 sig.= 0.020
A     96 MET C   . - A     96 MET O   . mod.= 1.938 id.= 1.231 dev= -0.707 sig.= 0.020
A     97 LYS N   . - A     97 LYS CA  . mod.= 2.072 id.= 1.458 dev= -0.614 sig.= 0.021
A     97 LYS CA  . - A     97 LYS C   . mod.= 1.778 id.= 1.525 dev= -0.253 sig.= 0.021
A     97 LYS CB  . - A     97 LYS CG  . mod.= 2.304 id.= 1.520 dev= -0.784 sig.= 0.020
A     97 LYS CD  . - A     97 LYS CE  . mod.= 1.116 id.= 1.520 dev=  0.404 sig.= 0.020
A     97 LYS CE  . - A     97 LYS NZ  . mod.= 1.182 id.= 1.489 dev=  0.307 sig.= 0.020
A     98 GLU CA  . - A     98 GLU CB  . mod.= 1.936 id.= 1.530 dev= -0.406 sig.= 0.020
A     98 GLU CA  . - A     98 GLU C   . mod.= 1.213 id.= 1.525 dev=  0.312 sig.= 0.021
A     98 GLU CB  . - A     98 GLU CG  . mod.= 1.286 id.= 1.520 dev=  0.234 sig.= 0.020
A     98 GLU CG  . - A     98 GLU CD  . mod.= 2.208 id.= 1.516 dev= -0.692 sig.= 0.020
A     98 GLU C   . - A     98 GLU O   . mod.= 0.999 id.= 1.231 dev=  0.232 sig.= 0.020
A     99 ALA N   . - A     99 ALA CA  . mod.= 1.894 id.= 1.458 dev= -0.436 sig.= 0.021
A     99 ALA CA  . - A     99 ALA C   . mod.= 0.817 id.= 1.525 dev=  0.708 sig.= 0.021
A     99 ALA C   . - A     99 ALA O   . mod.= 1.529 id.= 1.231 dev= -0.298 sig.= 0.020
A    100 GLY N   . - A    100 GLY CA  . mod.= 1.088 id.= 1.458 dev=  0.370 sig.= 0.021
A    100 GLY CA  . - A    100 GLY C   . mod.= 1.775 id.= 1.516 dev= -0.259 sig.= 0.018
A    101 ILE CA  . - A    101 ILE CB  . mod.= 1.030 id.= 1.540 dev=  0.510 sig.= 0.020
A    101 ILE CB  . - A    101 ILE CG2 . mod.= 1.962 id.= 1.521 dev= -0.441 sig.= 0.020
A    101 ILE CG1 . - A    101 ILE CD1 . mod.= 0.607 id.= 1.513 dev=  0.906 sig.= 0.020
A    101 ILE C   . - A    101 ILE O   . mod.= 0.929 id.= 1.231 dev=  0.302 sig.= 0.020
A    102 ASN CA  . - A    102 ASN CB  . mod.= 1.840 id.= 1.530 dev= -0.310 sig.= 0.020
A    102 ASN CG  . - A    102 ASN ND2 . mod.= 1.852 id.= 1.328 dev= -0.524 sig.= 0.021
A    102 ASN C   . - A    102 ASN O   . mod.= 1.743 id.= 1.231 dev= -0.512 sig.= 0.020
A    102 ASN C   . - A    103 VAL N   . mod.= 0.751 id.= 1.329 dev=  0.578 sig.= 0.014
A    103 VAL N   . - A    103 VAL CA  . mod.= 2.502 id.= 1.458 dev= -1.044 sig.= 0.021
A    103 VAL CA  . - A    103 VAL CB  . mod.= 1.780 id.= 1.540 dev= -0.240 sig.= 0.020
A    103 VAL CA  . - A    103 VAL C   . mod.= 1.308 id.= 1.525 dev=  0.217 sig.= 0.020
A    103 VAL CB  . - A    103 VAL CG1 . mod.= 1.970 id.= 1.521 dev= -0.449 sig.= 0.020
A    103 VAL CB  . - A    103 VAL CG2 . mod.= 0.914 id.= 1.521 dev=  0.607 sig.= 0.020
A    103 VAL C   . - A    103 VAL O   . mod.= 1.583 id.= 1.231 dev= -0.352 sig.= 0.020
A    104 ASP CB  . - A    104 ASP CG  . mod.= 1.180 id.= 1.516 dev=  0.336 sig.= 0.025
A    104 ASP CG  . - A    104 ASP OD1 . mod.= 1.848 id.= 1.249 dev= -0.599 sig.= 0.019
A    104 ASP C   . - A    104 ASP O   . mod.= 1.471 id.= 1.231 dev= -0.240 sig.= 0.020
A    105 TYR N   . - A    105 TYR CA  . mod.= 0.820 id.= 1.458 dev=  0.638 sig.= 0.021
A    105 TYR CA  . - A    105 TYR CB  . mod.= 2.125 id.= 1.530 dev= -0.595 sig.= 0.020
A    105 TYR CA  . - A    105 TYR C   . mod.= 1.150 id.= 1.525 dev=  0.375 sig.= 0.021
A    105 TYR CB  . - A    105 TYR CG  . mod.= 1.860 id.= 1.512 dev= -0.348 sig.= 0.022
A    105 TYR CG  . - A    105 TYR CD1 . mod.= 0.813 id.= 1.389 dev=  0.576 sig.= 0.021
A    105 TYR CE1 . - A    105 TYR CZ  . mod.= 1.982 id.= 1.378 dev= -0.604 sig.= 0.024
A    105 TYR CE2 . - A    105 TYR CD2 . mod.= 1.809 id.= 1.382 dev= -0.427 sig.= 0.020
A    106 VAL CB  . - A    106 VAL CG1 . mod.= 2.134 id.= 1.521 dev= -0.613 sig.= 0.020
A    106 VAL CB  . - A    106 VAL CG2 . mod.= 1.002 id.= 1.521 dev=  0.519 sig.= 0.020
A    106 VAL C   . - A    106 VAL O   . mod.= 1.848 id.= 1.231 dev= -0.617 sig.= 0.020
A    107 LEU N   . - A    107 LEU CA  . mod.= 1.883 id.= 1.458 dev= -0.425 sig.= 0.021
A    107 LEU CA  . - A    107 LEU C   . mod.= 1.845 id.= 1.525 dev= -0.320 sig.= 0.021
A    107 LEU CB  . - A    107 LEU CG  . mod.= 0.755 id.= 1.530 dev=  0.775 sig.= 0.020
A    107 LEU CG  . - A    107 LEU CD2 . mod.= 2.337 id.= 1.521 dev= -0.816 sig.= 0.020
A    107 LEU C   . - A    107 LEU O   . mod.= 1.721 id.= 1.231 dev= -0.490 sig.= 0.020
A    108 GLU CA  . - A    108 GLU CB  . mod.= 1.296 id.= 1.530 dev=  0.234 sig.= 0.020
A    108 GLU CB  . - A    108 GLU CG  . mod.= 2.396 id.= 1.520 dev= -0.876 sig.= 0.020
A    108 GLU CG  . - A    108 GLU CD  . mod.= 1.138 id.= 1.516 dev=  0.378 sig.= 0.020
A    108 GLU CD  . - A    108 GLU OE1 . mod.= 1.552 id.= 1.249 dev= -0.303 sig.= 0.019
A    108 GLU C   . - A    109 PHE N   . mod.= 1.690 id.= 1.329 dev= -0.361 sig.= 0.014
A    109 PHE N   . - A    109 PHE CA  . mod.= 1.880 id.= 1.458 dev= -0.422 sig.= 0.021
A    109 PHE CA  . - A    109 PHE C   . mod.= 2.091 id.= 1.525 dev= -0.566 sig.= 0.020
A    109 PHE CB  . - A    109 PHE CG  . mod.= 1.216 id.= 1.502 dev=  0.286 sig.= 0.020
A    109 PHE CG  . - A    109 PHE CD1 . mod.= 0.850 id.= 1.384 dev=  0.534 sig.= 0.021
A    109 PHE CD1 . - A    109 PHE CE1 . mod.= 2.191 id.= 1.382 dev= -0.809 sig.= 0.020
A    109 PHE CE2 . - A    109 PHE CD2 . mod.= 1.705 id.= 1.382 dev= -0.323 sig.= 0.020
A    110 ASP N   . - A    110 ASP CA  . mod.= 1.668 id.= 1.458 dev= -0.210 sig.= 0.021
A    110 ASP CA  . - A    110 ASP C   . mod.= 1.299 id.= 1.525 dev=  0.226 sig.= 0.021
A    110 ASP CB  . - A    110 ASP CG  . mod.= 2.462 id.= 1.516 dev= -0.946 sig.= 0.025
A    110 ASP C   . - A    110 ASP O   . mod.= 1.991 id.= 1.231 dev= -0.760 sig.= 0.020
A    110 ASP C   . - A    111 VAL N   . mod.= 1.104 id.= 1.329 dev=  0.225 sig.= 0.014
A    111 VAL CA  . - A    111 VAL CB  . mod.= 1.768 id.= 1.540 dev= -0.228 sig.= 0.020
A    111 VAL CA  . - A    111 VAL C   . mod.= 2.159 id.= 1.525 dev= -0.634 sig.= 0.020
A    111 VAL CB  . - A    111 VAL CG1 . mod.= 1.200 id.= 1.521 dev=  0.321 sig.= 0.020
A    111 VAL CB  . - A    111 VAL CG2 . mod.= 1.884 id.= 1.521 dev= -0.363 sig.= 0.020
A    111 VAL C   . - A    112 PRO N   . mod.= 1.529 id.= 1.341 dev= -0.188 sig.= 0.016
A    112 PRO N   . - A    112 PRO CA  . mod.= 1.085 id.= 1.458 dev=  0.373 sig.= 0.021
A    112 PRO N   . - A    112 PRO CD  . mod.= 0.962 id.= 1.473 dev=  0.511 sig.= 0.014
A    112 PRO CB  . - A    112 PRO CG  . mod.= 0.956 id.= 1.492 dev=  0.536 sig.= 0.025
A    112 PRO CG  . - A    112 PRO CD  . mod.= 1.247 id.= 1.503 dev=  0.256 sig.= 0.022
A    112 PRO C   . - A    112 PRO O   . mod.= 1.727 id.= 1.231 dev= -0.496 sig.= 0.020
A    113 ASP N   . - A    113 ASP CA  . mod.= 1.883 id.= 1.458 dev= -0.425 sig.= 0.021
A    113 ASP CA  . - A    113 ASP CB  . mod.= 1.072 id.= 1.530 dev=  0.458 sig.= 0.020
A    113 ASP CA  . - A    113 ASP C   . mod.= 1.081 id.= 1.525 dev=  0.444 sig.= 0.021
A    113 ASP CB  . - A    113 ASP CG  . mod.= 2.122 id.= 1.516 dev= -0.606 sig.= 0.025
A    113 ASP CG  . - A    113 ASP OD1 . mod.= 0.990 id.= 1.249 dev=  0.259 sig.= 0.019
A    113 ASP CG  . - A    113 ASP OD2 . mod.= 1.967 id.= 1.249 dev= -0.718 sig.= 0.019
A    113 ASP C   . - A    113 ASP O   . mod.= 1.664 id.= 1.231 dev= -0.433 sig.= 0.020
A    114 GLU CA  . - A    114 GLU CB  . mod.= 2.062 id.= 1.530 dev= -0.532 sig.= 0.020
A    114 GLU CG  . - A    114 GLU CD  . mod.= 1.861 id.= 1.516 dev= -0.345 sig.= 0.020
A    114 GLU CD  . - A    114 GLU OE2 . mod.= 0.768 id.= 1.249 dev=  0.481 sig.= 0.019
A    114 GLU C   . - A    114 GLU O   . mod.= 2.123 id.= 1.231 dev= -0.892 sig.= 0.020
A    115 LEU N   . - A    115 LEU CA  . mod.= 1.904 id.= 1.458 dev= -0.446 sig.= 0.021
A    115 LEU CA  . - A    115 LEU C   . mod.= 2.340 id.= 1.525 dev= -0.815 sig.= 0.021
A    115 LEU CG  . - A    115 LEU CD2 . mod.= 2.328 id.= 1.521 dev= -0.807 sig.= 0.020
A    115 LEU C   . - A    115 LEU O   . mod.= 1.775 id.= 1.231 dev= -0.544 sig.= 0.020
A    115 LEU C   . - A    116 ILE N   . mod.= 0.701 id.= 1.329 dev=  0.628 sig.= 0.014
A    116 ILE CA  . - A    116 ILE CB  . mod.= 1.314 id.= 1.540 dev=  0.226 sig.= 0.020
A    116 ILE CB  . - A    116 ILE CG1 . mod.= 2.084 id.= 1.530 dev= -0.554 sig.= 0.020
A    116 ILE CB  . - A    116 ILE CG2 . mod.= 2.072 id.= 1.521 dev= -0.551 sig.= 0.020
A    116 ILE CG1 . - A    116 ILE CD1 . mod.= 1.912 id.= 1.513 dev= -0.399 sig.= 0.020
A    116 ILE C   . - A    117 VAL N   . mod.= 1.177 id.= 1.329 dev=  0.152 sig.= 0.014
A    117 VAL CA  . - A    117 VAL CB  . mod.= 1.236 id.= 1.540 dev=  0.304 sig.= 0.020
A    117 VAL CA  . - A    117 VAL C   . mod.= 2.225 id.= 1.525 dev= -0.700 sig.= 0.020
A    117 VAL CB  . - A    117 VAL CG1 . mod.= 0.987 id.= 1.521 dev=  0.534 sig.= 0.020
A    117 VAL CB  . - A    117 VAL CG2 . mod.= 1.981 id.= 1.521 dev= -0.460 sig.= 0.020
A    117 VAL C   . - A    117 VAL O   . mod.= 1.457 id.= 1.231 dev= -0.226 sig.= 0.020
A    118 ASP N   . - A    118 ASP CA  . mod.= 2.060 id.= 1.458 dev= -0.602 sig.= 0.021
A    118 ASP CB  . - A    118 ASP CG  . mod.= 1.774 id.= 1.516 dev= -0.258 sig.= 0.025
A    118 ASP CG  . - A    118 ASP OD1 . mod.= 0.986 id.= 1.249 dev=  0.263 sig.= 0.019
A    118 ASP C   . - A    118 ASP O   . mod.= 1.852 id.= 1.231 dev= -0.621 sig.= 0.020
A    118 ASP C   . - A    119 ARG N   . mod.= 1.529 id.= 1.329 dev= -0.200 sig.= 0.014
A    119 ARG N   . - A    119 ARG CA  . mod.= 1.802 id.= 1.458 dev= -0.344 sig.= 0.021
A    119 ARG CA  . - A    119 ARG C   . mod.= 0.760 id.= 1.525 dev=  0.765 sig.= 0.021
A    119 ARG CG  . - A    119 ARG CD  . mod.= 1.768 id.= 1.520 dev= -0.248 sig.= 0.020
A    119 ARG CD  . - A    119 ARG NE  . mod.= 1.880 id.= 1.460 dev= -0.420 sig.= 0.018
A    119 ARG CZ  . - A    119 ARG NH2 . mod.= 1.693 id.= 1.326 dev= -0.367 sig.= 0.018
A    120 ILE N   . - A    120 ILE CA  . mod.= 0.581 id.= 1.458 dev=  0.877 sig.= 0.021
A    120 ILE CA  . - A    120 ILE CB  . mod.= 1.833 id.= 1.540 dev= -0.293 sig.= 0.020
A    120 ILE CA  . - A    120 ILE C   . mod.= 1.896 id.= 1.525 dev= -0.371 sig.= 0.020
A    120 ILE CB  . - A    120 ILE CG1 . mod.= 1.080 id.= 1.530 dev=  0.450 sig.= 0.020
A    120 ILE CB  . - A    120 ILE CG2 . mod.= 2.102 id.= 1.521 dev= -0.581 sig.= 0.020
A    120 ILE CG1 . - A    120 ILE CD1 . mod.= 1.839 id.= 1.513 dev= -0.326 sig.= 0.020
A    120 ILE C   . - A    120 ILE O   . mod.= 1.499 id.= 1.231 dev= -0.268 sig.= 0.020
A    120 ILE C   . - A    121 VAL N   . mod.= 1.648 id.= 1.329 dev= -0.319 sig.= 0.014
A    121 VAL CA  . - A    121 VAL CB  . mod.= 2.032 id.= 1.540 dev= -0.492 sig.= 0.020
A    121 VAL CB  . - A    121 VAL CG2 . mod.= 1.277 id.= 1.521 dev=  0.244 sig.= 0.020
A    121 VAL C   . - A    121 VAL O   . mod.= 1.910 id.= 1.231 dev= -0.679 sig.= 0.020
A    121 VAL C   . - A    122 GLY N   . mod.= 0.840 id.= 1.329 dev=  0.489 sig.= 0.014
A    122 GLY N   . - A    122 GLY CA  . mod.= 0.989 id.= 1.458 dev=  0.469 sig.= 0.021
A    122 GLY CA  . - A    122 GLY C   . mod.= 2.222 id.= 1.516 dev= -0.706 sig.= 0.018
A    123 ARG CA  . - A    123 ARG CB  . mod.= 1.322 id.= 1.530 dev=  0.208 sig.= 0.020
A    123 ARG CA  . - A    123 ARG C   . mod.= 1.169 id.= 1.525 dev=  0.356 sig.= 0.021
A    123 ARG CD  . - A    123 ARG NE  . mod.= 1.733 id.= 1.460 dev= -0.273 sig.= 0.018
A    123 ARG NE  . - A    123 ARG CZ  . mod.= 1.165 id.= 1.329 dev=  0.164 sig.= 0.014
A    123 ARG CZ  . - A    123 ARG NH1 . mod.= 1.793 id.= 1.326 dev= -0.467 sig.= 0.018
A    123 ARG C   . - A    123 ARG O   . mod.= 0.956 id.= 1.231 dev=  0.275 sig.= 0.020
A    123 ARG C   . - A    124 ARG N   . mod.= 1.666 id.= 1.329 dev= -0.337 sig.= 0.014
A    124 ARG CA  . - A    124 ARG CB  . mod.= 1.932 id.= 1.530 dev= -0.402 sig.= 0.020
A    124 ARG CA  . - A    124 ARG C   . mod.= 1.009 id.= 1.525 dev=  0.516 sig.= 0.021
A    124 ARG CG  . - A    124 ARG CD  . mod.= 1.180 id.= 1.520 dev=  0.340 sig.= 0.020
A    124 ARG CD  . - A    124 ARG NE  . mod.= 2.025 id.= 1.460 dev= -0.565 sig.= 0.018
A    124 ARG NE  . - A    124 ARG CZ  . mod.= 0.742 id.= 1.329 dev=  0.587 sig.= 0.014
A    124 ARG CZ  . - A    124 ARG NH2 . mod.= 2.233 id.= 1.326 dev= -0.907 sig.= 0.018
A    124 ARG C   . - A    124 ARG O   . mod.= 1.460 id.= 1.231 dev= -0.229 sig.= 0.020
A    125 VAL N   . - A    125 VAL CA  . mod.= 1.669 id.= 1.458 dev= -0.211 sig.= 0.021
A    125 VAL CA  . - A    125 VAL CB  . mod.= 1.133 id.= 1.540 dev=  0.407 sig.= 0.020
A    125 VAL CB  . - A    125 VAL CG2 . mod.= 1.094 id.= 1.521 dev=  0.427 sig.= 0.020
A    125 VAL C   . - A    126 HIS N   . mod.= 1.018 id.= 1.329 dev=  0.311 sig.= 0.014
A    126 HIS N   . - A    126 HIS CA  . mod.= 1.784 id.= 1.458 dev= -0.326 sig.= 0.021
A    126 HIS CA  . - A    126 HIS CB  . mod.= 0.997 id.= 1.530 dev=  0.533 sig.= 0.020
A    126 HIS CA  . - A    126 HIS C   . mod.= 1.882 id.= 1.525 dev= -0.357 sig.= 0.021
A    126 HIS CB  . - A    126 HIS CG  . mod.= 2.066 id.= 1.497 dev= -0.569 sig.= 0.014
A    126 HIS CG  . - A    126 HIS CD2 . mod.= 1.760 id.= 1.354 dev= -0.406 sig.= 0.011
A    126 HIS ND1 . - A    126 HIS CE1 . mod.= 1.131 id.= 1.321 dev=  0.190 sig.= 0.010
A    126 HIS CE1 . - A    126 HIS NE2 . mod.= 1.744 id.= 1.321 dev= -0.423 sig.= 0.010
A    126 HIS NE2 . - A    126 HIS CD2 . mod.= 1.488 id.= 1.374 dev= -0.114 sig.= 0.011
A    127 ALA N   . - A    127 ALA CA  . mod.= 0.970 id.= 1.458 dev=  0.488 sig.= 0.021
A    127 ALA CA  . - A    127 ALA CB  . mod.= 1.923 id.= 1.521 dev= -0.402 sig.= 0.020
A    128 PRO N   . - A    128 PRO CD  . mod.= 2.167 id.= 1.473 dev= -0.694 sig.= 0.014
A    128 PRO CA  . - A    128 PRO CB  . mod.= 1.968 id.= 1.530 dev= -0.438 sig.= 0.020
A    128 PRO C   . - A    128 PRO O   . mod.= 1.659 id.= 1.231 dev= -0.428 sig.= 0.020
A    128 PRO C   . - A    129 SER N   . mod.= 1.541 id.= 1.329 dev= -0.212 sig.= 0.014
A    129 SER N   . - A    129 SER CA  . mod.= 1.203 id.= 1.458 dev=  0.255 sig.= 0.021
A    129 SER CA  . - A    129 SER CB  . mod.= 1.096 id.= 1.530 dev=  0.434 sig.= 0.020
A    129 SER CA  . - A    129 SER C   . mod.= 1.931 id.= 1.525 dev= -0.406 sig.= 0.021
A    129 SER C   . - A    129 SER O   . mod.= 1.703 id.= 1.231 dev= -0.472 sig.= 0.020
A    129 SER C   . - A    130 GLY N   . mod.= 0.671 id.= 1.329 dev=  0.658 sig.= 0.014
A    130 GLY C   . - A    130 GLY O   . mod.= 0.902 id.= 1.231 dev=  0.329 sig.= 0.020
A    130 GLY C   . - A    131 ARG N   . mod.= 0.937 id.= 1.329 dev=  0.392 sig.= 0.014
A    131 ARG N   . - A    131 ARG CA  . mod.= 2.064 id.= 1.458 dev= -0.606 sig.= 0.021
A    131 ARG CA  . - A    131 ARG CB  . mod.= 1.053 id.= 1.530 dev=  0.477 sig.= 0.020
A    131 ARG CB  . - A    131 ARG CG  . mod.= 2.040 id.= 1.520 dev= -0.520 sig.= 0.020
A    131 ARG CG  . - A    131 ARG CD  . mod.= 1.786 id.= 1.520 dev= -0.266 sig.= 0.020
A    131 ARG CD  . - A    131 ARG NE  . mod.= 1.920 id.= 1.460 dev= -0.460 sig.= 0.018
A    131 ARG NE  . - A    131 ARG CZ  . mod.= 1.117 id.= 1.329 dev=  0.212 sig.= 0.014
A    132 VAL N   . - A    132 VAL CA  . mod.= 0.776 id.= 1.458 dev=  0.682 sig.= 0.021
A    132 VAL CA  . - A    132 VAL CB  . mod.= 2.197 id.= 1.540 dev= -0.657 sig.= 0.020
A    132 VAL CA  . - A    132 VAL C   . mod.= 2.328 id.= 1.525 dev= -0.803 sig.= 0.020
A    132 VAL CB  . - A    132 VAL CG1 . mod.= 0.968 id.= 1.521 dev=  0.553 sig.= 0.020
A    132 VAL CB  . - A    132 VAL CG2 . mod.= 2.015 id.= 1.521 dev= -0.494 sig.= 0.020
A    132 VAL C   . - A    132 VAL O   . mod.= 1.623 id.= 1.231 dev= -0.392 sig.= 0.020
A    132 VAL C   . - A    133 TYR N   . mod.= 1.709 id.= 1.329 dev= -0.380 sig.= 0.014
A    133 TYR N   . - A    133 TYR CA  . mod.= 1.092 id.= 1.458 dev=  0.366 sig.= 0.021
A    133 TYR CA  . - A    133 TYR CB  . mod.= 2.142 id.= 1.530 dev= -0.612 sig.= 0.020
A    133 TYR CA  . - A    133 TYR C   . mod.= 0.636 id.= 1.525 dev=  0.889 sig.= 0.021
A    133 TYR CG  . - A    133 TYR CD2 . mod.= 1.031 id.= 1.389 dev=  0.358 sig.= 0.021
A    133 TYR CZ  . - A    133 TYR OH  . mod.= 1.607 id.= 1.376 dev= -0.231 sig.= 0.021
A    133 TYR CZ  . - A    133 TYR CE2 . mod.= 1.580 id.= 1.378 dev= -0.202 sig.= 0.020
A    133 TYR C   . - A    134 HIS N   . mod.= 1.619 id.= 1.329 dev= -0.290 sig.= 0.014
A    134 HIS N   . - A    134 HIS CA  . mod.= 1.941 id.= 1.458 dev= -0.483 sig.= 0.021
A    134 HIS CA  . - A    134 HIS C   . mod.= 1.950 id.= 1.525 dev= -0.425 sig.= 0.021
A    134 HIS CB  . - A    134 HIS CG  . mod.= 1.868 id.= 1.497 dev= -0.371 sig.= 0.014
A    134 HIS CG  . - A    134 HIS ND1 . mod.= 2.038 id.= 1.378 dev= -0.660 sig.= 0.011
A    134 HIS ND1 . - A    134 HIS CE1 . mod.= 1.936 id.= 1.321 dev= -0.615 sig.= 0.010
A    134 HIS CE1 . - A    134 HIS NE2 . mod.= 1.461 id.= 1.321 dev= -0.140 sig.= 0.010
A    134 HIS NE2 . - A    134 HIS CD2 . mod.= 1.664 id.= 1.374 dev= -0.290 sig.= 0.011
A    134 HIS C   . - A    134 HIS O   . mod.= 1.631 id.= 1.231 dev= -0.400 sig.= 0.020
A    135 VAL CA  . - A    135 VAL CB  . mod.= 1.099 id.= 1.540 dev=  0.441 sig.= 0.020
A    135 VAL CA  . - A    135 VAL C   . mod.= 2.535 id.= 1.525 dev= -1.010 sig.= 0.020
A    136 LYS N   . - A    136 LYS CA  . mod.= 1.236 id.= 1.458 dev=  0.222 sig.= 0.021
A    136 LYS CA  . - A    136 LYS CB  . mod.= 0.875 id.= 1.530 dev=  0.655 sig.= 0.020
A    136 LYS CA  . - A    136 LYS C   . mod.= 2.315 id.= 1.525 dev= -0.790 sig.= 0.021
A    136 LYS CB  . - A    136 LYS CG  . mod.= 2.433 id.= 1.520 dev= -0.913 sig.= 0.020
A    136 LYS CG  . - A    136 LYS CD  . mod.= 2.222 id.= 1.520 dev= -0.702 sig.= 0.020
A    136 LYS CD  . - A    136 LYS CE  . mod.= 1.239 id.= 1.520 dev=  0.281 sig.= 0.020
A    137 PHE N   . - A    137 PHE CA  . mod.= 2.216 id.= 1.458 dev= -0.758 sig.= 0.021
A    137 PHE CA  . - A    137 PHE C   . mod.= 2.368 id.= 1.525 dev= -0.843 sig.= 0.020
A    137 PHE CD1 . - A    137 PHE CE1 . mod.= 0.916 id.= 1.382 dev=  0.466 sig.= 0.020
A    137 PHE CE1 . - A    137 PHE CZ  . mod.= 1.091 id.= 1.382 dev=  0.291 sig.= 0.020
A    137 PHE CZ  . - A    137 PHE CE2 . mod.= 2.127 id.= 1.382 dev= -0.745 sig.= 0.020
A    137 PHE CE2 . - A    137 PHE CD2 . mod.= 0.936 id.= 1.382 dev=  0.446 sig.= 0.020
A    138 ASN N   . - A    138 ASN CA  . mod.= 0.650 id.= 1.458 dev=  0.808 sig.= 0.021
A    138 ASN CA  . - A    138 ASN C   . mod.= 1.233 id.= 1.525 dev=  0.292 sig.= 0.021
A    138 ASN CB  . - A    138 ASN CG  . mod.= 1.801 id.= 1.516 dev= -0.285 sig.= 0.020
A    138 ASN CG  . - A    138 ASN ND2 . mod.= 1.612 id.= 1.328 dev= -0.284 sig.= 0.021
A    138 ASN C   . - A    138 ASN O   . mod.= 1.711 id.= 1.231 dev= -0.480 sig.= 0.020
A    139 PRO N   . - A    139 PRO CA  . mod.= 2.499 id.= 1.458 dev= -1.041 sig.= 0.021
A    139 PRO CA  . - A    139 PRO C   . mod.= 1.751 id.= 1.525 dev= -0.226 sig.= 0.021
A    139 PRO CB  . - A    139 PRO CG  . mod.= 2.062 id.= 1.492 dev= -0.570 sig.= 0.025
A    140 PRO N   . - A    140 PRO CA  . mod.= 1.891 id.= 1.458 dev= -0.433 sig.= 0.021
A    140 PRO N   . - A    140 PRO CD  . mod.= 1.087 id.= 1.473 dev=  0.386 sig.= 0.014
A    140 PRO CB  . - A    140 PRO CG  . mod.= 1.964 id.= 1.492 dev= -0.472 sig.= 0.025
A    140 PRO CG  . - A    140 PRO CD  . mod.= 1.278 id.= 1.503 dev=  0.225 sig.= 0.022
A    140 PRO C   . - A    140 PRO O   . mod.= 1.487 id.= 1.231 dev= -0.256 sig.= 0.020
A    141 LYS N   . - A    141 LYS CA  . mod.= 0.728 id.= 1.458 dev=  0.730 sig.= 0.021
A    141 LYS CA  . - A    141 LYS CB  . mod.= 1.280 id.= 1.530 dev=  0.250 sig.= 0.020
A    141 LYS CA  . - A    141 LYS C   . mod.= 2.226 id.= 1.525 dev= -0.701 sig.= 0.021
A    141 LYS CB  . - A    141 LYS CG  . mod.= 1.127 id.= 1.520 dev=  0.393 sig.= 0.020
A    141 LYS CG  . - A    141 LYS CD  . mod.= 2.241 id.= 1.520 dev= -0.721 sig.= 0.020
A    141 LYS C   . - A    141 LYS O   . mod.= 0.969 id.= 1.231 dev=  0.262 sig.= 0.020
A    141 LYS C   . - A    142 VAL N   . mod.= 0.971 id.= 1.329 dev=  0.358 sig.= 0.014
A    142 VAL N   . - A    142 VAL CA  . mod.= 1.950 id.= 1.458 dev= -0.492 sig.= 0.021
A    142 VAL CB  . - A    142 VAL CG1 . mod.= 1.287 id.= 1.521 dev=  0.234 sig.= 0.020
A    142 VAL C   . - A    143 GLU N   . mod.= 1.008 id.= 1.329 dev=  0.321 sig.= 0.014
A    143 GLU CA  . - A    143 GLU C   . mod.= 1.801 id.= 1.525 dev= -0.276 sig.= 0.021
A    143 GLU CG  . - A    143 GLU CD  . mod.= 1.896 id.= 1.516 dev= -0.380 sig.= 0.020
A    143 GLU CD  . - A    143 GLU OE1 . mod.= 1.500 id.= 1.249 dev= -0.251 sig.= 0.019
A    143 GLU CD  . - A    143 GLU OE2 . mod.= 0.827 id.= 1.249 dev=  0.422 sig.= 0.019
A    143 GLU C   . - A    143 GLU O   . mod.= 1.658 id.= 1.231 dev= -0.427 sig.= 0.020
A    144 GLY N   . - A    144 GLY CA  . mod.= 0.912 id.= 1.458 dev=  0.546 sig.= 0.021
A    144 GLY CA  . - A    144 GLY C   . mod.= 1.861 id.= 1.516 dev= -0.345 sig.= 0.018
A    144 GLY C   . - A    144 GLY O   . mod.= 1.485 id.= 1.231 dev= -0.254 sig.= 0.020
A    145 LYS N   . - A    145 LYS CA  . mod.= 1.958 id.= 1.458 dev= -0.500 sig.= 0.021
A    145 LYS CA  . - A    145 LYS C   . mod.= 1.221 id.= 1.525 dev=  0.304 sig.= 0.021
A    145 LYS CE  . - A    145 LYS NZ  . mod.= 1.703 id.= 1.489 dev= -0.214 sig.= 0.020
A    146 ASP CA  . - A    146 ASP CB  . mod.= 2.136 id.= 1.530 dev= -0.606 sig.= 0.020
A    146 ASP CB  . - A    146 ASP CG  . mod.= 1.073 id.= 1.516 dev=  0.443 sig.= 0.025
A    146 ASP CG  . - A    146 ASP OD1 . mod.= 0.749 id.= 1.249 dev=  0.500 sig.= 0.019
A    146 ASP CG  . - A    146 ASP OD2 . mod.= 1.607 id.= 1.249 dev= -0.358 sig.= 0.019
A    146 ASP C   . - A    147 ASP N   . mod.= 0.848 id.= 1.329 dev=  0.481 sig.= 0.014
A    147 ASP N   . - A    147 ASP CA  . mod.= 1.706 id.= 1.458 dev= -0.248 sig.= 0.021
A    147 ASP CA  . - A    147 ASP CB  . mod.= 2.318 id.= 1.530 dev= -0.788 sig.= 0.020
A    147 ASP CG  . - A    147 ASP OD1 . mod.= 2.093 id.= 1.249 dev= -0.844 sig.= 0.019
A    147 ASP CG  . - A    147 ASP OD2 . mod.= 0.583 id.= 1.249 dev=  0.666 sig.= 0.019
A    147 ASP C   . - A    148 VAL N   . mod.= 1.608 id.= 1.329 dev= -0.279 sig.= 0.014
A    148 VAL N   . - A    148 VAL CA  . mod.= 1.698 id.= 1.458 dev= -0.240 sig.= 0.021
A    148 VAL CA  . - A    148 VAL C   . mod.= 1.053 id.= 1.525 dev=  0.472 sig.= 0.020
A    148 VAL CB  . - A    148 VAL CG1 . mod.= 0.703 id.= 1.521 dev=  0.818 sig.= 0.020
A    148 VAL C   . - A    149 THR N   . mod.= 1.570 id.= 1.329 dev= -0.241 sig.= 0.014
A    149 THR N   . - A    149 THR CA  . mod.= 1.685 id.= 1.458 dev= -0.227 sig.= 0.021
A    149 THR CA  . - A    149 THR CB  . mod.= 2.013 id.= 1.540 dev= -0.473 sig.= 0.020
A    149 THR CB  . - A    149 THR OG1 . mod.= 1.713 id.= 1.433 dev= -0.280 sig.= 0.016
A    149 THR C   . - A    150 GLY N   . mod.= 1.530 id.= 1.329 dev= -0.201 sig.= 0.014
A    150 GLY N   . - A    150 GLY CA  . mod.= 2.073 id.= 1.458 dev= -0.615 sig.= 0.021
A    150 GLY CA  . - A    150 GLY C   . mod.= 1.736 id.= 1.516 dev= -0.220 sig.= 0.018
A    150 GLY C   . - A    151 GLU N   . mod.= 1.470 id.= 1.329 dev= -0.141 sig.= 0.014
A    151 GLU CA  . - A    151 GLU CB  . mod.= 1.114 id.= 1.530 dev=  0.416 sig.= 0.020
A    151 GLU CB  . - A    151 GLU CG  . mod.= 2.040 id.= 1.520 dev= -0.520 sig.= 0.020
A    151 GLU CG  . - A    151 GLU CD  . mod.= 1.129 id.= 1.516 dev=  0.387 sig.= 0.020
A    151 GLU CD  . - A    151 GLU OE2 . mod.= 0.912 id.= 1.249 dev=  0.337 sig.= 0.019
A    151 GLU C   . - A    151 GLU O   . mod.= 1.673 id.= 1.231 dev= -0.442 sig.= 0.020
A    152 GLU N   . - A    152 GLU CA  . mod.= 2.033 id.= 1.458 dev= -0.575 sig.= 0.021
A    152 GLU CA  . - A    152 GLU C   . mod.= 1.075 id.= 1.525 dev=  0.450 sig.= 0.021
A    152 GLU CD  . - A    152 GLU OE1 . mod.= 1.025 id.= 1.249 dev=  0.224 sig.= 0.019
A    153 LEU CA  . - A    153 LEU CB  . mod.= 1.170 id.= 1.530 dev=  0.360 sig.= 0.020
A    153 LEU CA  . - A    153 LEU C   . mod.= 1.312 id.= 1.525 dev=  0.213 sig.= 0.021
A    153 LEU CB  . - A    153 LEU CG  . mod.= 2.122 id.= 1.530 dev= -0.592 sig.= 0.020
A    153 LEU C   . - A    153 LEU O   . mod.= 0.975 id.= 1.231 dev=  0.256 sig.= 0.020
A    153 LEU C   . - A    154 THR N   . mod.= 0.945 id.= 1.329 dev=  0.384 sig.= 0.014
A    154 THR N   . - A    154 THR CA  . mod.= 1.131 id.= 1.458 dev=  0.327 sig.= 0.021
A    154 THR CA  . - A    154 THR CB  . mod.= 1.310 id.= 1.540 dev=  0.230 sig.= 0.020
A    154 THR CA  . - A    154 THR C   . mod.= 2.322 id.= 1.525 dev= -0.797 sig.= 0.021
A    154 THR CB  . - A    154 THR OG1 . mod.= 1.899 id.= 1.433 dev= -0.466 sig.= 0.016
A    154 THR C   . - A    154 THR O   . mod.= 2.085 id.= 1.231 dev= -0.854 sig.= 0.020
A    155 THR CA  . - A    155 THR CB  . mod.= 2.336 id.= 1.540 dev= -0.796 sig.= 0.020
A    155 THR CB  . - A    155 THR OG1 . mod.= 1.721 id.= 1.433 dev= -0.288 sig.= 0.016
A    155 THR CB  . - A    155 THR CG2 . mod.= 0.893 id.= 1.521 dev=  0.628 sig.= 0.033
A    155 THR C   . - A    155 THR O   . mod.= 2.053 id.= 1.231 dev= -0.822 sig.= 0.020
A    155 THR C   . - A    156 ARG N   . mod.= 0.755 id.= 1.329 dev=  0.574 sig.= 0.014
A    156 ARG N   . - A    156 ARG CA  . mod.= 1.055 id.= 1.458 dev=  0.403 sig.= 0.021
A    156 ARG CA  . - A    156 ARG CB  . mod.= 2.272 id.= 1.530 dev= -0.742 sig.= 0.020
A    156 ARG CA  . - A    156 ARG C   . mod.= 1.901 id.= 1.525 dev= -0.376 sig.= 0.021
A    156 ARG CB  . - A    156 ARG CG  . mod.= 0.971 id.= 1.520 dev=  0.549 sig.= 0.020
A    156 ARG CG  . - A    156 ARG CD  . mod.= 2.022 id.= 1.520 dev= -0.502 sig.= 0.020
A    156 ARG NE  . - A    156 ARG CZ  . mod.= 1.151 id.= 1.329 dev=  0.178 sig.= 0.014
A    156 ARG CZ  . - A    156 ARG NH1 . mod.= 1.730 id.= 1.326 dev= -0.404 sig.= 0.018
A    156 ARG CZ  . - A    156 ARG NH2 . mod.= 0.912 id.= 1.326 dev=  0.414 sig.= 0.018
A    156 ARG C   . - A    156 ARG O   . mod.= 1.549 id.= 1.231 dev= -0.318 sig.= 0.020
A    157 LYS N   . - A    157 LYS CA  . mod.= 2.328 id.= 1.458 dev= -0.870 sig.= 0.021
A    157 LYS CA  . - A    157 LYS CB  . mod.= 1.274 id.= 1.530 dev=  0.256 sig.= 0.020
A    157 LYS CG  . - A    157 LYS CD  . mod.= 1.272 id.= 1.520 dev=  0.248 sig.= 0.020
A    157 LYS CD  . - A    157 LYS CE  . mod.= 1.895 id.= 1.520 dev= -0.375 sig.= 0.020
A    157 LYS C   . - A    157 LYS O   . mod.= 1.493 id.= 1.231 dev= -0.262 sig.= 0.020
A    157 LYS C   . - A    158 ASP N   . mod.= 1.133 id.= 1.329 dev=  0.196 sig.= 0.014
A    158 ASP N   . - A    158 ASP CA  . mod.= 1.669 id.= 1.458 dev= -0.211 sig.= 0.021
A    158 ASP CA  . - A    158 ASP C   . mod.= 1.951 id.= 1.525 dev= -0.426 sig.= 0.021
A    158 ASP CG  . - A    158 ASP OD1 . mod.= 1.004 id.= 1.249 dev=  0.245 sig.= 0.019
A    158 ASP CG  . - A    158 ASP OD2 . mod.= 2.008 id.= 1.249 dev= -0.759 sig.= 0.019
A    159 ASP N   . - A    159 ASP CA  . mod.= 0.988 id.= 1.458 dev=  0.470 sig.= 0.021
A    159 ASP CA  . - A    159 ASP CB  . mod.= 1.842 id.= 1.530 dev= -0.312 sig.= 0.020
A    159 ASP CA  . - A    159 ASP C   . mod.= 2.072 id.= 1.525 dev= -0.547 sig.= 0.021
A    159 ASP CB  . - A    159 ASP CG  . mod.= 1.912 id.= 1.516 dev= -0.396 sig.= 0.025
A    159 ASP CG  . - A    159 ASP OD1 . mod.= 0.899 id.= 1.249 dev=  0.350 sig.= 0.019
A    159 ASP CG  . - A    159 ASP OD2 . mod.= 1.856 id.= 1.249 dev= -0.607 sig.= 0.019
A    159 ASP C   . - A    159 ASP O   . mod.= 0.168 id.= 1.231 dev=  1.063 sig.= 0.020
A    160 GLN N   . - A    160 GLN CA  . mod.= 1.060 id.= 1.458 dev=  0.398 sig.= 0.021
A    160 GLN CD  . - A    160 GLN NE2 . mod.= 2.076 id.= 1.328 dev= -0.748 sig.= 0.021
A    160 GLN C   . - A    160 GLN O   . mod.= 1.640 id.= 1.231 dev= -0.409 sig.= 0.020
A    161 GLU CA  . - A    161 GLU CB  . mod.= 1.030 id.= 1.530 dev=  0.500 sig.= 0.020
A    161 GLU CB  . - A    161 GLU CG  . mod.= 0.939 id.= 1.520 dev=  0.581 sig.= 0.020
A    161 GLU CD  . - A    161 GLU OE1 . mod.= 1.570 id.= 1.249 dev= -0.321 sig.= 0.019
A    161 GLU CD  . - A    161 GLU OE2 . mod.= 0.827 id.= 1.249 dev=  0.422 sig.= 0.019
A    161 GLU C   . - A    161 GLU O   . mod.= 1.469 id.= 1.231 dev= -0.238 sig.= 0.020
A    162 GLU CA  . - A    162 GLU C   . mod.= 2.172 id.= 1.525 dev= -0.647 sig.= 0.021
A    162 GLU CD  . - A    162 GLU OE1 . mod.= 2.037 id.= 1.249 dev= -0.788 sig.= 0.019
A    162 GLU CD  . - A    162 GLU OE2 . mod.= 0.972 id.= 1.249 dev=  0.277 sig.= 0.019
A    162 GLU C   . - A    163 THR N   . mod.= 1.572 id.= 1.329 dev= -0.243 sig.= 0.014
A    163 THR CA  . - A    163 THR CB  . mod.= 1.782 id.= 1.540 dev= -0.242 sig.= 0.020
A    163 THR CB  . - A    163 THR OG1 . mod.= 2.308 id.= 1.433 dev= -0.875 sig.= 0.016
A    163 THR CB  . - A    163 THR CG2 . mod.= 2.042 id.= 1.521 dev= -0.521 sig.= 0.033
A    163 THR C   . - A    164 VAL N   . mod.= 1.648 id.= 1.329 dev= -0.319 sig.= 0.014
A    164 VAL N   . - A    164 VAL CA  . mod.= 1.883 id.= 1.458 dev= -0.425 sig.= 0.021
A    164 VAL CB  . - A    164 VAL CG1 . mod.= 2.028 id.= 1.521 dev= -0.507 sig.= 0.020
A    164 VAL CB  . - A    164 VAL CG2 . mod.= 1.309 id.= 1.521 dev=  0.212 sig.= 0.020
A    164 VAL C   . - A    164 VAL O   . mod.= 1.647 id.= 1.231 dev= -0.416 sig.= 0.020
A    164 VAL C   . - A    165 ARG N   . mod.= 0.754 id.= 1.329 dev=  0.575 sig.= 0.014
A    165 ARG CA  . - A    165 ARG C   . mod.= 1.858 id.= 1.525 dev= -0.333 sig.= 0.021
A    165 ARG CG  . - A    165 ARG CD  . mod.= 1.878 id.= 1.520 dev= -0.358 sig.= 0.020
A    165 ARG CD  . - A    165 ARG NE  . mod.= 0.538 id.= 1.460 dev=  0.922 sig.= 0.018
A    165 ARG CZ  . - A    165 ARG NH1 . mod.= 1.873 id.= 1.326 dev= -0.547 sig.= 0.018
A    165 ARG CZ  . - A    165 ARG NH2 . mod.= 1.612 id.= 1.326 dev= -0.286 sig.= 0.018
A    165 ARG C   . - A    165 ARG O   . mod.= 0.797 id.= 1.231 dev=  0.434 sig.= 0.020
A    166 LYS N   . - A    166 LYS CA  . mod.= 2.133 id.= 1.458 dev= -0.675 sig.= 0.021
A    166 LYS CA  . - A    166 LYS C   . mod.= 1.296 id.= 1.525 dev=  0.229 sig.= 0.021
A    166 LYS CG  . - A    166 LYS CD  . mod.= 0.713 id.= 1.520 dev=  0.807 sig.= 0.020
A    166 LYS CD  . - A    166 LYS CE  . mod.= 2.021 id.= 1.520 dev= -0.501 sig.= 0.020
A    166 LYS CE  . - A    166 LYS NZ  . mod.= 0.975 id.= 1.489 dev=  0.514 sig.= 0.020
A    166 LYS C   . - A    166 LYS O   . mod.= 1.665 id.= 1.231 dev= -0.434 sig.= 0.020
A    166 LYS C   . - A    167 ARG N   . mod.= 0.970 id.= 1.329 dev=  0.359 sig.= 0.014
A    167 ARG N   . - A    167 ARG CA  . mod.= 1.746 id.= 1.458 dev= -0.288 sig.= 0.021
A    167 ARG CA  . - A    167 ARG CB  . mod.= 1.852 id.= 1.530 dev= -0.322 sig.= 0.020
A    167 ARG CG  . - A    167 ARG CD  . mod.= 2.127 id.= 1.520 dev= -0.607 sig.= 0.020
A    167 ARG CZ  . - A    167 ARG NH2 . mod.= 1.073 id.= 1.326 dev=  0.253 sig.= 0.018
A    167 ARG C   . - A    167 ARG O   . mod.= 1.834 id.= 1.231 dev= -0.603 sig.= 0.020
A    167 ARG C   . - A    168 LEU N   . mod.= 1.578 id.= 1.329 dev= -0.249 sig.= 0.014
A    168 LEU CA  . - A    168 LEU CB  . mod.= 1.087 id.= 1.530 dev=  0.443 sig.= 0.020
A    168 LEU CA  . - A    168 LEU C   . mod.= 1.745 id.= 1.525 dev= -0.220 sig.= 0.021
A    168 LEU CB  . - A    168 LEU CG  . mod.= 1.926 id.= 1.530 dev= -0.396 sig.= 0.020
A    168 LEU CG  . - A    168 LEU CD1 . mod.= 1.932 id.= 1.521 dev= -0.411 sig.= 0.020
A    168 LEU CG  . - A    168 LEU CD2 . mod.= 2.439 id.= 1.521 dev= -0.918 sig.= 0.020
A    168 LEU C   . - A    168 LEU O   . mod.= 1.018 id.= 1.231 dev=  0.213 sig.= 0.020
A    168 LEU C   . - A    169 VAL N   . mod.= 1.044 id.= 1.329 dev=  0.285 sig.= 0.014
A    169 VAL N   . - A    169 VAL CA  . mod.= 1.153 id.= 1.458 dev=  0.305 sig.= 0.021
A    169 VAL CA  . - A    169 VAL CB  . mod.= 2.096 id.= 1.540 dev= -0.556 sig.= 0.020
A    169 VAL CA  . - A    169 VAL C   . mod.= 1.206 id.= 1.525 dev=  0.319 sig.= 0.020
A    169 VAL CB  . - A    169 VAL CG2 . mod.= 1.280 id.= 1.521 dev=  0.241 sig.= 0.020
A    169 VAL C   . - A    170 GLU N   . mod.= 1.005 id.= 1.329 dev=  0.324 sig.= 0.014
A    170 GLU CA  . - A    170 GLU CB  . mod.= 1.969 id.= 1.530 dev= -0.439 sig.= 0.020
A    170 GLU CA  . - A    170 GLU C   . mod.= 1.289 id.= 1.525 dev=  0.236 sig.= 0.021
A    170 GLU CG  . - A    170 GLU CD  . mod.= 0.969 id.= 1.516 dev=  0.547 sig.= 0.020
A    170 GLU CD  . - A    170 GLU OE1 . mod.= 2.241 id.= 1.249 dev= -0.992 sig.= 0.019
A    170 GLU C   . - A    170 GLU O   . mod.= 1.883 id.= 1.231 dev= -0.652 sig.= 0.020
A    171 TYR N   . - A    171 TYR CA  . mod.= 1.039 id.= 1.458 dev=  0.419 sig.= 0.021
A    171 TYR CA  . - A    171 TYR C   . mod.= 1.844 id.= 1.525 dev= -0.319 sig.= 0.021
A    171 TYR CE1 . - A    171 TYR CZ  . mod.= 1.675 id.= 1.378 dev= -0.297 sig.= 0.024
A    171 TYR CZ  . - A    171 TYR CE2 . mod.= 1.813 id.= 1.378 dev= -0.435 sig.= 0.020
A    171 TYR CE2 . - A    171 TYR CD2 . mod.= 1.825 id.= 1.382 dev= -0.443 sig.= 0.020
A    171 TYR C   . - A    171 TYR O   . mod.= 1.669 id.= 1.231 dev= -0.438 sig.= 0.020
A    172 HIS N   . - A    172 HIS CA  . mod.= 1.130 id.= 1.458 dev=  0.328 sig.= 0.021
A    172 HIS CG  . - A    172 HIS ND1 . mod.= 0.753 id.= 1.378 dev=  0.625 sig.= 0.011
A    172 HIS CG  . - A    172 HIS CD2 . mod.= 1.810 id.= 1.354 dev= -0.456 sig.= 0.011
A    172 HIS ND1 . - A    172 HIS CE1 . mod.= 2.007 id.= 1.321 dev= -0.686 sig.= 0.010
A    172 HIS CE1 . - A    172 HIS NE2 . mod.= 0.658 id.= 1.321 dev=  0.663 sig.= 0.010
A    172 HIS NE2 . - A    172 HIS CD2 . mod.= 2.219 id.= 1.374 dev= -0.845 sig.= 0.011
A    172 HIS C   . - A    172 HIS O   . mod.= 2.095 id.= 1.231 dev= -0.864 sig.= 0.020
A    172 HIS C   . - A    173 GLN N   . mod.= 0.395 id.= 1.329 dev=  0.934 sig.= 0.014
A    173 GLN CB  . - A    173 GLN CG  . mod.= 1.107 id.= 1.520 dev=  0.413 sig.= 0.020
A    173 GLN CD  . - A    173 GLN OE1 . mod.= 2.189 id.= 1.231 dev= -0.958 sig.= 0.019
A    173 GLN CD  . - A    173 GLN NE2 . mod.= 1.036 id.= 1.328 dev=  0.292 sig.= 0.021
A    173 GLN C   . - A    174 MET N   . mod.= 1.603 id.= 1.329 dev= -0.274 sig.= 0.014
A    174 MET N   . - A    174 MET CA  . mod.= 1.009 id.= 1.458 dev=  0.449 sig.= 0.021
A    174 MET CA  . - A    174 MET C   . mod.= 1.913 id.= 1.525 dev= -0.388 sig.= 0.020
A    174 MET CB  . - A    174 MET CG  . mod.= 1.030 id.= 1.520 dev=  0.490 sig.= 0.020
A    174 MET C   . - A    174 MET O   . mod.= 1.469 id.= 1.231 dev= -0.238 sig.= 0.020
A    174 MET C   . - A    175 THR N   . mod.= 1.652 id.= 1.329 dev= -0.323 sig.= 0.014
A    175 THR N   . - A    175 THR CA  . mod.= 1.691 id.= 1.458 dev= -0.233 sig.= 0.021
A    175 THR CA  . - A    175 THR CB  . mod.= 2.365 id.= 1.540 dev= -0.825 sig.= 0.020
A    175 THR CB  . - A    175 THR OG1 . mod.= 0.900 id.= 1.433 dev=  0.533 sig.= 0.016
A    175 THR C   . - A    176 ALA N   . mod.= 0.717 id.= 1.329 dev=  0.612 sig.= 0.014
A    176 ALA CA  . - A    176 ALA CB  . mod.= 1.809 id.= 1.521 dev= -0.288 sig.= 0.020
A    176 ALA CA  . - A    176 ALA C   . mod.= 2.088 id.= 1.525 dev= -0.563 sig.= 0.021
A    176 ALA C   . - A    176 ALA O   . mod.= 1.464 id.= 1.231 dev= -0.233 sig.= 0.020
A    177 PRO N   . - A    177 PRO CD  . mod.= 2.328 id.= 1.473 dev= -0.855 sig.= 0.014
A    177 PRO CA  . - A    177 PRO CB  . mod.= 1.188 id.= 1.530 dev=  0.342 sig.= 0.020
A    177 PRO CA  . - A    177 PRO C   . mod.= 1.773 id.= 1.525 dev= -0.248 sig.= 0.021
A    177 PRO C   . - A    177 PRO O   . mod.= 0.995 id.= 1.231 dev=  0.236 sig.= 0.020
A    177 PRO C   . - A    178 LEU N   . mod.= 1.157 id.= 1.329 dev=  0.172 sig.= 0.014
A    178 LEU N   . - A    178 LEU CA  . mod.= 1.128 id.= 1.458 dev=  0.330 sig.= 0.021
A    178 LEU CA  . - A    178 LEU CB  . mod.= 1.272 id.= 1.530 dev=  0.258 sig.= 0.020
A    178 LEU CB  . - A    178 LEU CG  . mod.= 1.003 id.= 1.530 dev=  0.527 sig.= 0.020
A    178 LEU CG  . - A    178 LEU CD1 . mod.= 2.300 id.= 1.521 dev= -0.779 sig.= 0.020
A    178 LEU CG  . - A    178 LEU CD2 . mod.= 1.934 id.= 1.521 dev= -0.413 sig.= 0.020
A    178 LEU C   . - A    178 LEU O   . mod.= 2.060 id.= 1.231 dev= -0.829 sig.= 0.020
A    179 ILE CA  . - A    179 ILE CB  . mod.= 2.043 id.= 1.540 dev= -0.503 sig.= 0.020
A    179 ILE CA  . - A    179 ILE C   . mod.= 2.085 id.= 1.525 dev= -0.560 sig.= 0.020
A    179 ILE CB  . - A    179 ILE CG1 . mod.= 2.120 id.= 1.530 dev= -0.590 sig.= 0.020
A    179 ILE C   . - A    179 ILE O   . mod.= 0.627 id.= 1.231 dev=  0.604 sig.= 0.020
A    180 GLY N   . - A    180 GLY CA  . mod.= 0.998 id.= 1.458 dev=  0.460 sig.= 0.021
A    181 TYR N   . - A    181 TYR CA  . mod.= 1.740 id.= 1.458 dev= -0.282 sig.= 0.021
A    181 TYR CA  . - A    181 TYR C   . mod.= 1.801 id.= 1.525 dev= -0.276 sig.= 0.021
A    181 TYR CB  . - A    181 TYR CG  . mod.= 2.076 id.= 1.512 dev= -0.564 sig.= 0.022
A    181 TYR CG  . - A    181 TYR CD2 . mod.= 0.866 id.= 1.389 dev=  0.523 sig.= 0.021
A    181 TYR CZ  . - A    181 TYR OH  . mod.= 2.380 id.= 1.376 dev= -1.004 sig.= 0.021
A    181 TYR CZ  . - A    181 TYR CE2 . mod.= 0.734 id.= 1.378 dev=  0.644 sig.= 0.020
A    181 TYR CE2 . - A    181 TYR CD2 . mod.= 1.609 id.= 1.382 dev= -0.227 sig.= 0.020
A    181 TYR C   . - A    182 TYR N   . mod.= 1.120 id.= 1.329 dev=  0.209 sig.= 0.014
A    182 TYR N   . - A    182 TYR CA  . mod.= 1.223 id.= 1.458 dev=  0.235 sig.= 0.021
A    182 TYR CA  . - A    182 TYR C   . mod.= 2.303 id.= 1.525 dev= -0.778 sig.= 0.021
A    182 TYR CG  . - A    182 TYR CD1 . mod.= 0.969 id.= 1.389 dev=  0.420 sig.= 0.021
A    182 TYR CG  . - A    182 TYR CD2 . mod.= 1.634 id.= 1.389 dev= -0.245 sig.= 0.021
A    182 TYR CD1 . - A    182 TYR CE1 . mod.= 1.050 id.= 1.382 dev=  0.332 sig.= 0.020
A    182 TYR CE1 . - A    182 TYR CZ  . mod.= 1.748 id.= 1.378 dev= -0.370 sig.= 0.024
A    182 TYR CZ  . - A    182 TYR OH  . mod.= 1.074 id.= 1.376 dev=  0.302 sig.= 0.021
A    182 TYR CZ  . - A    182 TYR CE2 . mod.= 2.088 id.= 1.378 dev= -0.710 sig.= 0.020
A    182 TYR CE2 . - A    182 TYR CD2 . mod.= 0.771 id.= 1.382 dev=  0.611 sig.= 0.020
A    182 TYR C   . - A    183 SER N   . mod.= 0.869 id.= 1.329 dev=  0.460 sig.= 0.014
A    183 SER N   . - A    183 SER CA  . mod.= 1.760 id.= 1.458 dev= -0.302 sig.= 0.021
A    183 SER CA  . - A    183 SER C   . mod.= 2.525 id.= 1.525 dev= -1.000 sig.= 0.021
A    183 SER C   . - A    183 SER O   . mod.= 1.473 id.= 1.231 dev= -0.242 sig.= 0.020
A    183 SER C   . - A    184 LYS N   . mod.= 1.144 id.= 1.329 dev=  0.185 sig.= 0.014
A    184 LYS N   . - A    184 LYS CA  . mod.= 1.137 id.= 1.458 dev=  0.321 sig.= 0.021
A    184 LYS CA  . - A    184 LYS CB  . mod.= 1.150 id.= 1.530 dev=  0.380 sig.= 0.020
A    184 LYS CB  . - A    184 LYS CG  . mod.= 1.201 id.= 1.520 dev=  0.319 sig.= 0.020
A    184 LYS CD  . - A    184 LYS CE  . mod.= 2.065 id.= 1.520 dev= -0.545 sig.= 0.020
A    184 LYS CE  . - A    184 LYS NZ  . mod.= 1.864 id.= 1.489 dev= -0.375 sig.= 0.020
A    184 LYS C   . - A    184 LYS O   . mod.= 1.959 id.= 1.231 dev= -0.728 sig.= 0.020
A    184 LYS C   . - A    185 GLU N   . mod.= 1.029 id.= 1.329 dev=  0.300 sig.= 0.014
A    185 GLU N   . - A    185 GLU CA  . mod.= 2.457 id.= 1.458 dev= -0.999 sig.= 0.021
A    185 GLU CA  . - A    185 GLU CB  . mod.= 1.751 id.= 1.530 dev= -0.221 sig.= 0.020
A    185 GLU CA  . - A    185 GLU C   . mod.= 0.872 id.= 1.525 dev=  0.653 sig.= 0.021
A    185 GLU CG  . - A    185 GLU CD  . mod.= 2.227 id.= 1.516 dev= -0.711 sig.= 0.020
A    185 GLU CD  . - A    185 GLU OE1 . mod.= 1.050 id.= 1.249 dev=  0.199 sig.= 0.019
A    185 GLU CD  . - A    185 GLU OE2 . mod.= 0.589 id.= 1.249 dev=  0.660 sig.= 0.019
A    186 ALA N   . - A    186 ALA CA  . mod.= 1.193 id.= 1.458 dev=  0.265 sig.= 0.021
A    186 ALA C   . - A    186 ALA O   . mod.= 2.030 id.= 1.231 dev= -0.799 sig.= 0.020
A    186 ALA C   . - A    187 GLU N   . mod.= 0.665 id.= 1.329 dev=  0.664 sig.= 0.014
A    187 GLU CA  . - A    187 GLU CB  . mod.= 2.191 id.= 1.530 dev= -0.661 sig.= 0.020
A    187 GLU CA  . - A    187 GLU C   . mod.= 0.887 id.= 1.525 dev=  0.638 sig.= 0.021
A    187 GLU CB  . - A    187 GLU CG  . mod.= 1.954 id.= 1.520 dev= -0.434 sig.= 0.020
A    187 GLU CD  . - A    187 GLU OE1 . mod.= 1.497 id.= 1.249 dev= -0.248 sig.= 0.019
A    187 GLU CD  . - A    187 GLU OE2 . mod.= 2.052 id.= 1.249 dev= -0.803 sig.= 0.019
A    187 GLU C   . - A    187 GLU O   . mod.= 1.671 id.= 1.231 dev= -0.440 sig.= 0.020
A    188 ALA CA  . - A    188 ALA CB  . mod.= 1.834 id.= 1.521 dev= -0.313 sig.= 0.020
A    188 ALA CA  . - A    188 ALA C   . mod.= 2.317 id.= 1.525 dev= -0.792 sig.= 0.021
A    188 ALA C   . - A    188 ALA O   . mod.= 1.535 id.= 1.231 dev= -0.304 sig.= 0.020
A    189 GLY N   . - A    189 GLY CA  . mod.= 1.954 id.= 1.458 dev= -0.496 sig.= 0.021
A    189 GLY C   . - A    189 GLY O   . mod.= 0.820 id.= 1.231 dev=  0.411 sig.= 0.020
A    189 GLY C   . - A    190 ASN N   . mod.= 1.554 id.= 1.329 dev= -0.225 sig.= 0.014
A    190 ASN N   . - A    190 ASN CA  . mod.= 1.761 id.= 1.458 dev= -0.303 sig.= 0.021
A    190 ASN CA  . - A    190 ASN C   . mod.= 1.284 id.= 1.525 dev=  0.241 sig.= 0.021
A    190 ASN CB  . - A    190 ASN CG  . mod.= 1.905 id.= 1.516 dev= -0.389 sig.= 0.020
A    190 ASN CG  . - A    190 ASN ND2 . mod.= 1.841 id.= 1.328 dev= -0.513 sig.= 0.021
A    191 THR CA  . - A    191 THR CB  . mod.= 2.027 id.= 1.540 dev= -0.487 sig.= 0.020
A    191 THR CA  . - A    191 THR C   . mod.= 1.931 id.= 1.525 dev= -0.406 sig.= 0.021
A    192 LYS N   . - A    192 LYS CA  . mod.= 1.109 id.= 1.458 dev=  0.349 sig.= 0.021
A    192 LYS CA  . - A    192 LYS C   . mod.= 1.036 id.= 1.525 dev=  0.489 sig.= 0.021
A    192 LYS CB  . - A    192 LYS CG  . mod.= 2.195 id.= 1.520 dev= -0.675 sig.= 0.020
A    192 LYS CG  . - A    192 LYS CD  . mod.= 2.041 id.= 1.520 dev= -0.521 sig.= 0.020
A    192 LYS CD  . - A    192 LYS CE  . mod.= 2.042 id.= 1.520 dev= -0.522 sig.= 0.020
A    192 LYS CE  . - A    192 LYS NZ  . mod.= 1.053 id.= 1.489 dev=  0.436 sig.= 0.020
A    192 LYS C   . - A    192 LYS O   . mod.= 1.848 id.= 1.231 dev= -0.617 sig.= 0.020
A    193 TYR CA  . - A    193 TYR CB  . mod.= 1.858 id.= 1.530 dev= -0.328 sig.= 0.020
A    193 TYR CA  . - A    193 TYR C   . mod.= 1.070 id.= 1.525 dev=  0.455 sig.= 0.021
A    193 TYR CB  . - A    193 TYR CG  . mod.= 2.041 id.= 1.512 dev= -0.529 sig.= 0.022
A    193 TYR CG  . - A    193 TYR CD1 . mod.= 1.054 id.= 1.389 dev=  0.335 sig.= 0.021
A    193 TYR CG  . - A    193 TYR CD2 . mod.= 1.163 id.= 1.389 dev=  0.226 sig.= 0.021
A    193 TYR CZ  . - A    193 TYR OH  . mod.= 0.794 id.= 1.376 dev=  0.582 sig.= 0.021
A    193 TYR CZ  . - A    193 TYR CE2 . mod.= 0.772 id.= 1.378 dev=  0.606 sig.= 0.020
A    193 TYR CE2 . - A    193 TYR CD2 . mod.= 1.976 id.= 1.382 dev= -0.594 sig.= 0.020
A    193 TYR C   . - A    194 ALA N   . mod.= 1.531 id.= 1.329 dev= -0.202 sig.= 0.014
A    194 ALA N   . - A    194 ALA CA  . mod.= 2.225 id.= 1.458 dev= -0.767 sig.= 0.021
A    194 ALA CA  . - A    194 ALA C   . mod.= 1.101 id.= 1.525 dev=  0.424 sig.= 0.021
A    195 LYS CA  . - A    195 LYS CB  . mod.= 2.196 id.= 1.530 dev= -0.666 sig.= 0.020
A    195 LYS CA  . - A    195 LYS C   . mod.= 0.843 id.= 1.525 dev=  0.682 sig.= 0.021
A    195 LYS CB  . - A    195 LYS CG  . mod.= 1.921 id.= 1.520 dev= -0.401 sig.= 0.020
A    195 LYS CG  . - A    195 LYS CD  . mod.= 0.994 id.= 1.520 dev=  0.526 sig.= 0.020
A    195 LYS CD  . - A    195 LYS CE  . mod.= 1.759 id.= 1.520 dev= -0.239 sig.= 0.020
A    195 LYS CE  . - A    195 LYS NZ  . mod.= 0.790 id.= 1.489 dev=  0.699 sig.= 0.020
A    195 LYS C   . - A    195 LYS O   . mod.= 2.084 id.= 1.231 dev= -0.853 sig.= 0.020
A    196 VAL N   . - A    196 VAL CA  . mod.= 1.858 id.= 1.458 dev= -0.400 sig.= 0.021
A    196 VAL CA  . - A    196 VAL C   . mod.= 2.103 id.= 1.525 dev= -0.578 sig.= 0.020
A    196 VAL CB  . - A    196 VAL CG1 . mod.= 2.025 id.= 1.521 dev= -0.504 sig.= 0.020
A    196 VAL C   . - A    196 VAL O   . mod.= 0.481 id.= 1.231 dev=  0.750 sig.= 0.020
A    196 VAL C   . - A    197 ASP N   . mod.= 1.570 id.= 1.329 dev= -0.241 sig.= 0.014
A    197 ASP N   . - A    197 ASP CA  . mod.= 0.784 id.= 1.458 dev=  0.674 sig.= 0.021
A    197 ASP CA  . - A    197 ASP CB  . mod.= 1.859 id.= 1.530 dev= -0.329 sig.= 0.020
A    197 ASP CG  . - A    197 ASP OD1 . mod.= 1.575 id.= 1.249 dev= -0.326 sig.= 0.019
A    197 ASP CG  . - A    197 ASP OD2 . mod.= 1.861 id.= 1.249 dev= -0.612 sig.= 0.019
A    197 ASP C   . - A    197 ASP O   . mod.= 1.680 id.= 1.231 dev= -0.449 sig.= 0.020
A    197 ASP C   . - A    198 GLY N   . mod.= 0.957 id.= 1.329 dev=  0.372 sig.= 0.014
A    198 GLY N   . - A    198 GLY CA  . mod.= 1.812 id.= 1.458 dev= -0.354 sig.= 0.021
A    199 THR N   . - A    199 THR CA  . mod.= 1.713 id.= 1.458 dev= -0.255 sig.= 0.021
A    199 THR CA  . - A    199 THR C   . mod.= 2.082 id.= 1.525 dev= -0.557 sig.= 0.021
A    199 THR C   . - A    199 THR O   . mod.= 0.785 id.= 1.231 dev=  0.446 sig.= 0.020
A    199 THR C   . - A    200 LYS N   . mod.= 0.877 id.= 1.329 dev=  0.452 sig.= 0.014
A    200 LYS N   . - A    200 LYS CA  . mod.= 2.145 id.= 1.458 dev= -0.687 sig.= 0.021
A    200 LYS CA  . - A    200 LYS C   . mod.= 1.199 id.= 1.525 dev=  0.326 sig.= 0.021
A    200 LYS CE  . - A    200 LYS NZ  . mod.= 1.723 id.= 1.489 dev= -0.234 sig.= 0.020
A    200 LYS C   . - A    200 LYS O   . mod.= 1.891 id.= 1.231 dev= -0.660 sig.= 0.020
A    201 PRO N   . - A    201 PRO CD  . mod.= 2.191 id.= 1.473 dev= -0.718 sig.= 0.014
A    201 PRO CB  . - A    201 PRO CG  . mod.= 0.653 id.= 1.492 dev=  0.839 sig.= 0.025
A    201 PRO CG  . - A    201 PRO CD  . mod.= 1.974 id.= 1.503 dev= -0.471 sig.= 0.022
A    201 PRO C   . - A    202 VAL N   . mod.= 0.976 id.= 1.329 dev=  0.353 sig.= 0.014
A    202 VAL N   . - A    202 VAL CA  . mod.= 1.679 id.= 1.458 dev= -0.221 sig.= 0.021
A    202 VAL CB  . - A    202 VAL CG2 . mod.= 1.157 id.= 1.521 dev=  0.364 sig.= 0.020
A    202 VAL C   . - A    202 VAL O   . mod.= 0.912 id.= 1.231 dev=  0.319 sig.= 0.020
A    202 VAL C   . - A    203 ALA N   . mod.= 1.716 id.= 1.329 dev= -0.387 sig.= 0.014
A    203 ALA CA  . - A    203 ALA CB  . mod.= 1.034 id.= 1.521 dev=  0.487 sig.= 0.020
A    203 ALA CA  . - A    203 ALA C   . mod.= 1.878 id.= 1.525 dev= -0.353 sig.= 0.021
A    204 GLU N   . - A    204 GLU CA  . mod.= 1.932 id.= 1.458 dev= -0.474 sig.= 0.021
A    204 GLU CA  . - A    204 GLU C   . mod.= 0.859 id.= 1.525 dev=  0.666 sig.= 0.021
A    204 GLU CB  . - A    204 GLU CG  . mod.= 1.873 id.= 1.520 dev= -0.353 sig.= 0.020
A    204 GLU CD  . - A    204 GLU OE2 . mod.= 1.653 id.= 1.249 dev= -0.404 sig.= 0.019
A    204 GLU C   . - A    204 GLU O   . mod.= 1.611 id.= 1.231 dev= -0.380 sig.= 0.020
A    204 GLU C   . - A    205 VAL N   . mod.= 1.615 id.= 1.329 dev= -0.286 sig.= 0.014
A    205 VAL CA  . - A    205 VAL CB  . mod.= 1.143 id.= 1.540 dev=  0.397 sig.= 0.020
A    205 VAL CB  . - A    205 VAL CG1 . mod.= 1.860 id.= 1.521 dev= -0.339 sig.= 0.020
A    205 VAL C   . - A    206 ARG N   . mod.= 1.503 id.= 1.329 dev= -0.174 sig.= 0.014
A    206 ARG CA  . - A    206 ARG CB  . mod.= 1.219 id.= 1.530 dev=  0.311 sig.= 0.020
A    206 ARG CG  . - A    206 ARG CD  . mod.= 1.952 id.= 1.520 dev= -0.432 sig.= 0.020
A    206 ARG CD  . - A    206 ARG NE  . mod.= 2.253 id.= 1.460 dev= -0.793 sig.= 0.018
A    206 ARG NE  . - A    206 ARG CZ  . mod.= 1.138 id.= 1.329 dev=  0.191 sig.= 0.014
A    206 ARG CZ  . - A    206 ARG NH1 . mod.= 2.143 id.= 1.326 dev= -0.817 sig.= 0.018
A    206 ARG C   . - A    206 ARG O   . mod.= 1.479 id.= 1.231 dev= -0.248 sig.= 0.020
A    206 ARG C   . - A    207 ALA N   . mod.= 1.022 id.= 1.329 dev=  0.307 sig.= 0.014
A    207 ALA N   . - A    207 ALA CA  . mod.= 1.763 id.= 1.458 dev= -0.305 sig.= 0.021
A    207 ALA CA  . - A    207 ALA CB  . mod.= 1.835 id.= 1.521 dev= -0.314 sig.= 0.020
A    207 ALA C   . - A    207 ALA O   . mod.= 1.824 id.= 1.231 dev= -0.593 sig.= 0.020
A    207 ALA C   . - A    208 ASP N   . mod.= 1.079 id.= 1.329 dev=  0.250 sig.= 0.014
A    208 ASP CA  . - A    208 ASP CB  . mod.= 2.093 id.= 1.530 dev= -0.563 sig.= 0.020
A    208 ASP CA  . - A    208 ASP C   . mod.= 2.047 id.= 1.525 dev= -0.522 sig.= 0.021
A    208 ASP CB  . - A    208 ASP CG  . mod.= 2.194 id.= 1.516 dev= -0.678 sig.= 0.025
A    208 ASP CG  . - A    208 ASP OD1 . mod.= 1.871 id.= 1.249 dev= -0.622 sig.= 0.019
A    208 ASP C   . - A    208 ASP O   . mod.= 1.570 id.= 1.231 dev= -0.339 sig.= 0.020
A    209 LEU CB  . - A    209 LEU CG  . mod.= 1.200 id.= 1.530 dev=  0.330 sig.= 0.020
A    209 LEU CG  . - A    209 LEU CD1 . mod.= 2.103 id.= 1.521 dev= -0.582 sig.= 0.020
A    209 LEU C   . - A    209 LEU O   . mod.= 0.446 id.= 1.231 dev=  0.785 sig.= 0.020
A    209 LEU C   . - A    210 GLU N   . mod.= 1.610 id.= 1.329 dev= -0.281 sig.= 0.014
A    210 GLU CA  . - A    210 GLU CB  . mod.= 1.840 id.= 1.530 dev= -0.310 sig.= 0.020
A    210 GLU CA  . - A    210 GLU C   . mod.= 2.119 id.= 1.525 dev= -0.594 sig.= 0.021
A    210 GLU CD  . - A    210 GLU OE2 . mod.= 1.943 id.= 1.249 dev= -0.694 sig.= 0.019
A    210 GLU C   . - A    210 GLU O   . mod.= 0.972 id.= 1.231 dev=  0.259 sig.= 0.020
A    210 GLU C   . - A    211 LYS N   . mod.= 1.067 id.= 1.329 dev=  0.262 sig.= 0.014
A    211 LYS N   . - A    211 LYS CA  . mod.= 1.899 id.= 1.458 dev= -0.441 sig.= 0.021
A    211 LYS CA  . - A    211 LYS C   . mod.= 1.809 id.= 1.525 dev= -0.284 sig.= 0.021
A    211 LYS CB  . - A    211 LYS CG  . mod.= 2.205 id.= 1.520 dev= -0.685 sig.= 0.020
A    211 LYS CD  . - A    211 LYS CE  . mod.= 1.720 id.= 1.520 dev= -0.200 sig.= 0.020
A    211 LYS CE  . - A    211 LYS NZ  . mod.= 1.075 id.= 1.489 dev=  0.414 sig.= 0.020
A    211 LYS C   . - A    211 LYS O   . mod.= 1.519 id.= 1.231 dev= -0.288 sig.= 0.020
A    211 LYS C   . - A    212 ILE N   . mod.= 0.828 id.= 1.329 dev=  0.501 sig.= 0.014
A    212 ILE N   . - A    212 ILE CA  . mod.= 0.763 id.= 1.458 dev=  0.695 sig.= 0.021
A    212 ILE CA  . - A    212 ILE CB  . mod.= 2.135 id.= 1.540 dev= -0.595 sig.= 0.020
A    212 ILE CA  . - A    212 ILE C   . mod.= 2.324 id.= 1.525 dev= -0.799 sig.= 0.020
A    212 ILE CB  . - A    212 ILE CG1 . mod.= 1.115 id.= 1.530 dev=  0.415 sig.= 0.020
A    212 ILE C   . - A    212 ILE O   . mod.= 0.715 id.= 1.231 dev=  0.516 sig.= 0.020
A    212 ILE C   . - A    213 LEU N   . mod.= 1.713 id.= 1.329 dev= -0.384 sig.= 0.014
A    213 LEU CA  . - A    213 LEU CB  . mod.= 1.925 id.= 1.530 dev= -0.395 sig.= 0.020
A    213 LEU CA  . - A    213 LEU C   . mod.= 1.099 id.= 1.525 dev=  0.426 sig.= 0.021
A    213 LEU CB  . - A    213 LEU CG  . mod.= 2.040 id.= 1.530 dev= -0.510 sig.= 0.020
A    213 LEU CG  . - A    213 LEU CD2 . mod.= 2.229 id.= 1.521 dev= -0.708 sig.= 0.020
A    213 LEU C   . - A    213 LEU O   . mod.= 1.754 id.= 1.231 dev= -0.523 sig.= 0.020
A    214 GLY N   . - A    214 GLY CA  . mod.= 0.945 id.= 1.458 dev=  0.513 sig.= 0.021
A    214 GLY CA  . - A    214 GLY C   . mod.= 2.281 id.= 1.516 dev= -0.765 sig.= 0.018
A    214 GLY C   . - A    214 GLY O   . mod.= 0.972 id.= 1.231 dev=  0.259 sig.= 0.020
A    214 GLY C   . - A    214 GLY OXT . mod.= 2.201 id.= 1.231 dev= -0.970 sig.= 0.020

    ****                         Torsion angle outliers                         ****

Torsion angle deviations from the ideal >10.000Sigma will be monitored

A     21 MET CA    - A     22 GLU CA    mod.= -97.34 id.= 180.00 per.= 1 dev= -82.66 sig.=   5.00
A     26 ILE CA    - A     27 PRO CA    mod.=-112.75 id.= 180.00 per.= 1 dev= -67.25 sig.=   5.00
A     62 GLU CA    - A     63 LEU CA    mod.= -58.85 id.=   0.00 per.= 1 dev=  58.85 sig.=   5.00
A     72 ILE CA    - A     73 ALA CA    mod.= -89.09 id.=   0.00 per.= 1 dev=  89.09 sig.=   5.00
A     73 ALA CA    - A     74 GLN CA    mod.=-112.89 id.= 180.00 per.= 1 dev= -67.11 sig.=   5.00
A     75 GLU CA    - A     76 ASP CA    mod.=-126.56 id.= 180.00 per.= 1 dev= -53.44 sig.=   5.00
A     88 ARG CA    - A     89 THR CA    mod.=-118.54 id.= 180.00 per.= 1 dev= -61.46 sig.=   5.00
A    116 ILE CA    - A    117 VAL CA    mod.= 112.45 id.= 180.00 per.= 1 dev=  67.55 sig.=   5.00
A    123 ARG CA    - A    124 ARG CA    mod.= 105.25 id.= 180.00 per.= 1 dev=  74.75 sig.=   5.00
A    129 SER CA    - A    130 GLY CA    mod.= -76.98 id.=   0.00 per.= 1 dev=  76.98 sig.=   5.00
A    136 LYS CA    - A    137 PHE CA    mod.=-110.03 id.= 180.00 per.= 1 dev= -69.97 sig.=   5.00
A    142 VAL CA    - A    143 GLU CA    mod.= -99.53 id.= 180.00 per.= 1 dev= -80.47 sig.=   5.00
A    148 VAL CA    - A    149 THR CA    mod.=-117.43 id.= 180.00 per.= 1 dev= -62.57 sig.=   5.00
A    167 ARG CA    - A    168 LEU CA    mod.=  59.61 id.=   0.00 per.= 1 dev= -59.61 sig.=   5.00
A    170 GLU CA    - A    171 TYR CA    mod.= 121.84 id.= 180.00 per.= 1 dev=  58.16 sig.=   5.00
A    173 GLN CA    - A    174 MET CA    mod.=-113.66 id.= 180.00 per.= 1 dev= -66.34 sig.=   5.00
A    178 LEU CA    - A    179 ILE CA    mod.=-121.65 id.= 180.00 per.= 1 dev= -58.35 sig.=   5.00
A    207 ALA CA    - A    208 ASP CA    mod.= 108.78 id.= 180.00 per.= 1 dev=  71.22 sig.=   5.00

    ****                         Chiral volume outliers                         ****

Chiral volume deviations from the ideal >10.000Sigma will be monitored

A      3 ILE CB    mod.=   6.98 id.=   2.64 dev= -4.336 sig.=  0.200
A      5 LEU CA    mod.=  -4.75 id.=  -2.50 dev=  2.249 sig.=  0.200
A      5 LEU CG    mod.=  -0.55 id.=  -2.59 dev= -2.042 sig.=  0.200
A      9 PRO CA    mod.=   1.45 id.=  -2.71 dev= -4.167 sig.=  0.200
A     11 ALA CA    mod.=  -4.68 id.=  -2.48 dev=  2.203 sig.=  0.200
A     20 ILE CB    mod.=  -3.02 id.=   2.64 dev=  5.666 sig.=  0.200
A     23 LYS CA    mod.=  -0.14 id.=  -2.50 dev= -2.367 sig.=  0.200
A     26 ILE CA    mod.=  -8.29 id.=  -2.52 dev=  5.770 sig.=  0.200
A     29 ILE CA    mod.=  -5.55 id.=  -2.52 dev=  3.030 sig.=  0.200
A     29 ILE CB    mod.=   5.23 id.=   2.64 dev= -2.584 sig.=  0.200
A     31 THR CA    mod.=  -0.05 id.=  -2.52 dev= -2.474 sig.=  0.200
A     35 LEU CA    mod.=  -5.61 id.=  -2.50 dev=  3.107 sig.=  0.200
A     35 LEU CG    mod.=  -7.28 id.=  -2.59 dev=  4.689 sig.=  0.200
A     38 ALA CA    mod.=  -0.23 id.=  -2.48 dev= -2.244 sig.=  0.200
A     39 VAL CA    mod.=  -0.31 id.=  -2.52 dev= -2.210 sig.=  0.200
A     41 SER CA    mod.=   0.18 id.=  -2.50 dev= -2.681 sig.=  0.200
A     43 SER CA    mod.=  -0.04 id.=  -2.50 dev= -2.465 sig.=  0.200
A     47 LYS CA    mod.=   0.37 id.=  -2.50 dev= -2.874 sig.=  0.200
A     53 MET CA    mod.=  -4.78 id.=  -2.50 dev=  2.280 sig.=  0.200
A     58 LEU CA    mod.=  -4.67 id.=  -2.50 dev=  2.171 sig.=  0.200
A     60 THR CA    mod.=  -4.96 id.=  -2.52 dev=  2.444 sig.=  0.200
A     61 ASP CA    mod.=   0.29 id.=  -2.50 dev= -2.788 sig.=  0.200
A     64 VAL CB    mod.=  -6.51 id.=  -2.63 dev=  3.879 sig.=  0.200
A     69 LYS CA    mod.=  -0.42 id.=  -2.50 dev= -2.082 sig.=  0.200
A     74 GLN CA    mod.=  -5.91 id.=  -2.50 dev=  3.410 sig.=  0.200
A     77 CYS CA    mod.=  -4.51 id.=  -2.50 dev=  2.011 sig.=  0.200
A     82 LEU CA    mod.=  -6.08 id.=  -2.50 dev=  3.575 sig.=  0.200
A     83 LEU CA    mod.=  -5.81 id.=  -2.50 dev=  3.306 sig.=  0.200
A     89 THR CA    mod.=   0.50 id.=  -2.52 dev= -3.017 sig.=  0.200
A     89 THR CB    mod.=  -0.98 id.=   2.55 dev=  3.528 sig.=  0.200
A     90 ILE CA    mod.=  -5.91 id.=  -2.52 dev=  3.387 sig.=  0.200
A     90 ILE CB    mod.=   5.26 id.=   2.64 dev= -2.615 sig.=  0.200
A     97 LYS CA    mod.=  -5.48 id.=  -2.50 dev=  2.982 sig.=  0.200
A    103 VAL CA    mod.=  -5.47 id.=  -2.52 dev=  2.952 sig.=  0.200
A    105 TYR CA    mod.=  -0.49 id.=  -2.50 dev= -2.015 sig.=  0.200
A    112 PRO CA    mod.=  -0.02 id.=  -2.71 dev= -2.693 sig.=  0.200
A    115 LEU CA    mod.=  -6.71 id.=  -2.50 dev=  4.205 sig.=  0.200
A    119 ARG CA    mod.=  -0.01 id.=  -2.50 dev= -2.496 sig.=  0.200
A    120 ILE CA    mod.=  -0.13 id.=  -2.52 dev= -2.384 sig.=  0.200
A    127 ALA CA    mod.=  -0.39 id.=  -2.48 dev= -2.084 sig.=  0.200
A    134 HIS CA    mod.=  -5.49 id.=  -2.50 dev=  2.985 sig.=  0.200
A    137 PHE CA    mod.=  -6.78 id.=  -2.50 dev=  4.281 sig.=  0.200
A    139 PRO CA    mod.=  -4.71 id.=  -2.71 dev=  2.001 sig.=  0.200
A    149 THR CA    mod.=  -4.96 id.=  -2.52 dev=  2.437 sig.=  0.200
A    154 THR CA    mod.=   0.60 id.=  -2.52 dev= -3.119 sig.=  0.200
A    163 THR CB    mod.=   7.74 id.=   2.55 dev= -5.184 sig.=  0.200
A    168 LEU CA    mod.=   1.54 id.=  -2.50 dev= -4.040 sig.=  0.200
A    168 LEU CG    mod.=  -8.13 id.=  -2.59 dev=  5.541 sig.=  0.200
A    173 GLN CA    mod.=   0.47 id.=  -2.50 dev= -2.972 sig.=  0.200
A    179 ILE CA    mod.=  -4.78 id.=  -2.52 dev=  2.262 sig.=  0.200
A    179 ILE CB    mod.=   4.76 id.=   2.64 dev= -2.120 sig.=  0.200
A    183 SER CA    mod.=  -5.90 id.=  -2.50 dev=  3.394 sig.=  0.200
A    184 LYS CA    mod.=  -0.37 id.=  -2.50 dev= -2.129 sig.=  0.200
A    188 ALA CA    mod.=  -4.75 id.=  -2.48 dev=  2.276 sig.=  0.200
A    191 THR CA    mod.=  -4.59 id.=  -2.52 dev=  2.073 sig.=  0.200
A    191 THR CB    mod.=   0.28 id.=   2.55 dev=  2.271 sig.=  0.200
A    197 ASP CA    mod.=  -0.19 id.=  -2.50 dev= -2.313 sig.=  0.200
A    199 THR CB    mod.=   0.24 id.=   2.55 dev=  2.315 sig.=  0.200
A    202 VAL CA    mod.=   2.31 id.=  -2.52 dev= -4.833 sig.=  0.200
A    202 VAL CB    mod.=   0.41 id.=   2.63 dev=  2.216 sig.=  0.200
A    205 VAL CB    mod.=  -0.62 id.=  -2.63 dev= -2.009 sig.=  0.200
A    209 LEU CA    mod.=   0.79 id.=  -2.50 dev= -3.296 sig.=  0.200
A    210 GLU CA    mod.=  -4.76 id.=  -2.50 dev=  2.256 sig.=  0.200
A    213 LEU CG    mod.=  -6.19 id.=  -2.59 dev=  3.596 sig.=  0.200

    ****                Large deviation of atoms from planarity                 ****

Deviations from the planarity >10.000Sigma will be monitored
Atom: A      2 ARG CD    deviation=   0.22 sigma.=   0.02
Atom: A      2 ARG NE    deviation=  -0.36 sigma.=   0.02
Atom: A      2 ARG CZ    deviation=  -0.60 sigma.=   0.02
Atom: A      2 ARG HH11  deviation=   0.89 sigma.=   0.02
Atom: A      2 ARG HH12  deviation=  -0.39 sigma.=   0.02
Atom: A      2 ARG HH21  deviation=   0.23 sigma.=   0.02
Atom: A      3 ILE C     deviation=  -0.22 sigma.=   0.02
Atom: A     12 GLY C     deviation=   0.51 sigma.=   0.02
Atom: A     12 GLY O     deviation=  -0.28 sigma.=   0.02
Atom: A     13 LYS N     deviation=  -0.21 sigma.=   0.02
Atom: A     13 LYS CA    deviation=  -0.23 sigma.=   0.02
Atom: A     13 LYS C     deviation=   0.32 sigma.=   0.02
Atom: A     18 GLN CD    deviation=  -0.36 sigma.=   0.02
Atom: A     19 PHE CG    deviation=   0.80 sigma.=   0.02
Atom: A     19 PHE HD1   deviation=  -0.30 sigma.=   0.02
Atom: A     19 PHE HE1   deviation=  -0.28 sigma.=   0.02
Atom: A     19 PHE HZ    deviation=   0.26 sigma.=   0.02
Atom: A     19 PHE HE2   deviation=  -0.28 sigma.=   0.02
Atom: A     19 PHE C     deviation=  -0.23 sigma.=   0.02
Atom: A     21 MET C     deviation=  -0.38 sigma.=   0.02
Atom: A     22 GLU CD    deviation=   0.30 sigma.=   0.02
Atom: A     22 GLU C     deviation=   0.41 sigma.=   0.02
Atom: A     24 TYR CB    deviation=   0.35 sigma.=   0.02
Atom: A     24 TYR CD1   deviation=  -0.36 sigma.=   0.02
Atom: A     24 TYR CE1   deviation=   0.35 sigma.=   0.02
Atom: A     24 TYR OH    deviation=  -0.21 sigma.=   0.02
Atom: A     24 TYR HD1   deviation=  -0.93 sigma.=   0.02
Atom: A     24 TYR HE1   deviation=   0.74 sigma.=   0.02
Atom: A     24 TYR HE2   deviation=  -0.37 sigma.=   0.02
Atom: A     24 TYR HD2   deviation=   0.48 sigma.=   0.02
Atom: A     27 PRO C     deviation=   0.33 sigma.=   0.02
Atom: A     32 GLY C     deviation=  -0.26 sigma.=   0.02
Atom: A     33 ASP C     deviation=  -0.25 sigma.=   0.02
Atom: A     34 MET C     deviation=  -0.34 sigma.=   0.02
Atom: A     35 LEU C     deviation=   0.37 sigma.=   0.02
Atom: A     36 ARG CZ    deviation=   0.28 sigma.=   0.02
Atom: A     36 ARG HH11  deviation=  -0.27 sigma.=   0.02
Atom: A     36 ARG HH21  deviation=  -0.30 sigma.=   0.02
Atom: A     37 ALA C     deviation=  -0.32 sigma.=   0.02
Atom: A     39 VAL C     deviation=   0.27 sigma.=   0.02
Atom: A     43 SER C     deviation=   0.21 sigma.=   0.02
Atom: A     44 GLU CD    deviation=  -0.42 sigma.=   0.02
Atom: A     44 GLU OE2   deviation=   0.25 sigma.=   0.02
Atom: A     52 ILE C     deviation=  -0.24 sigma.=   0.02
Atom: A     54 ASP CG    deviation=  -0.24 sigma.=   0.02
Atom: A     58 LEU C     deviation=   0.30 sigma.=   0.02
Atom: A     62 GLU CD    deviation=  -0.21 sigma.=   0.02
Atom: A     71 ARG CZ    deviation=  -0.24 sigma.=   0.02
Atom: A     71 ARG HH21  deviation=   0.34 sigma.=   0.02
Atom: A     75 GLU CD    deviation=  -0.26 sigma.=   0.02
Atom: A     75 GLU C     deviation=   0.24 sigma.=   0.02
Atom: A     77 CYS C     deviation=  -0.44 sigma.=   0.02
Atom: A     78 ARG CZ    deviation=   0.45 sigma.=   0.02
Atom: A     78 ARG HH11  deviation=  -0.79 sigma.=   0.02
Atom: A     78 ARG HH12  deviation=   0.37 sigma.=   0.02
Atom: A     78 ARG HH21  deviation=  -0.22 sigma.=   0.02
Atom: A     81 PHE CG    deviation=   0.33 sigma.=   0.02
Atom: A     81 PHE CD1   deviation=  -0.27 sigma.=   0.02
Atom: A     81 PHE CD2   deviation=   0.31 sigma.=   0.02
Atom: A     81 PHE HD1   deviation=  -0.64 sigma.=   0.02
Atom: A     81 PHE HE1   deviation=   0.48 sigma.=   0.02
Atom: A     81 PHE HE2   deviation=  -0.49 sigma.=   0.02
Atom: A     81 PHE HD2   deviation=   0.45 sigma.=   0.02
Atom: A     84 ASP CG    deviation=   0.24 sigma.=   0.02
Atom: A     86 PHE CG    deviation=  -0.28 sigma.=   0.02
Atom: A     86 PHE CD1   deviation=  -0.20 sigma.=   0.02
Atom: A     86 PHE CZ    deviation=   0.46 sigma.=   0.02
Atom: A     86 PHE CE2   deviation=  -0.26 sigma.=   0.02
Atom: A     86 PHE HD1   deviation=  -0.26 sigma.=   0.02
Atom: A     86 PHE HE1   deviation=  -0.67 sigma.=   0.02
Atom: A     86 PHE HZ    deviation=   0.96 sigma.=   0.02
Atom: A     86 PHE HE2   deviation=  -0.71 sigma.=   0.02
Atom: A     86 PHE HD2   deviation=   0.66 sigma.=   0.02
Atom: A     88 ARG CZ    deviation=   0.41 sigma.=   0.02
Atom: A     88 ARG HH11  deviation=  -0.25 sigma.=   0.02
Atom: A     88 ARG HH21  deviation=  -0.61 sigma.=   0.02
Atom: A     88 ARG HH22  deviation=   0.33 sigma.=   0.02
Atom: A     89 THR C     deviation=   0.41 sigma.=   0.02
Atom: A     90 ILE C     deviation=   0.49 sigma.=   0.02
Atom: A     90 ILE O     deviation=  -0.36 sigma.=   0.02
Atom: A     91 PRO C     deviation=  -0.36 sigma.=   0.02
Atom: A     92 GLN CD    deviation=  -0.23 sigma.=   0.02
Atom: A     92 GLN C     deviation=   0.42 sigma.=   0.02
Atom: A     93 ALA C     deviation=   0.46 sigma.=   0.02
Atom: A     94 ASP CG    deviation=  -0.22 sigma.=   0.02
Atom: A     95 ALA C     deviation=  -0.43 sigma.=   0.02
Atom: A     96 MET N     deviation=   0.22 sigma.=   0.02
Atom: A    102 ASN C     deviation=  -0.29 sigma.=   0.02
Atom: A    103 VAL C     deviation=  -0.24 sigma.=   0.02
Atom: A    105 TYR CZ    deviation=  -0.37 sigma.=   0.02
Atom: A    105 TYR CE2   deviation=   0.29 sigma.=   0.02
Atom: A    105 TYR OH    deviation=  -0.38 sigma.=   0.02
Atom: A    105 TYR HD1   deviation=   0.44 sigma.=   0.02
Atom: A    105 TYR HE2   deviation=   0.64 sigma.=   0.02
Atom: A    105 TYR HD2   deviation=  -0.38 sigma.=   0.02
Atom: A    107 LEU C     deviation=   0.37 sigma.=   0.02
Atom: A    108 GLU C     deviation=   0.32 sigma.=   0.02
Atom: A    109 PHE CB    deviation=  -0.27 sigma.=   0.02
Atom: A    109 PHE CG    deviation=   0.36 sigma.=   0.02
Atom: A    109 PHE CD1   deviation=   0.30 sigma.=   0.02
Atom: A    109 PHE CE2   deviation=   0.38 sigma.=   0.02
Atom: A    109 PHE HD1   deviation=   0.33 sigma.=   0.02
Atom: A    109 PHE HZ    deviation=  -0.68 sigma.=   0.02
Atom: A    109 PHE HE2   deviation=   0.67 sigma.=   0.02
Atom: A    109 PHE HD2   deviation=  -1.01 sigma.=   0.02
Atom: A    110 ASP CA    deviation=   0.20 sigma.=   0.02
Atom: A    110 ASP C     deviation=  -0.53 sigma.=   0.02
Atom: A    111 VAL N     deviation=   0.24 sigma.=   0.02
Atom: A    113 ASP CG    deviation=  -0.26 sigma.=   0.02
Atom: A    115 LEU C     deviation=  -0.23 sigma.=   0.02
Atom: A    118 ASP CG    deviation=   0.24 sigma.=   0.02
Atom: A    118 ASP CA    deviation=  -0.28 sigma.=   0.02
Atom: A    118 ASP C     deviation=   0.66 sigma.=   0.02
Atom: A    119 ARG N     deviation=  -0.23 sigma.=   0.02
Atom: A    119 ARG CD    deviation=  -0.34 sigma.=   0.02
Atom: A    119 ARG HH11  deviation=   0.46 sigma.=   0.02
Atom: A    123 ARG CZ    deviation=  -0.46 sigma.=   0.02
Atom: A    123 ARG HH11  deviation=   0.51 sigma.=   0.02
Atom: A    123 ARG HH21  deviation=   0.51 sigma.=   0.02
Atom: A    123 ARG HH22  deviation=  -0.21 sigma.=   0.02
Atom: A    123 ARG C     deviation=   0.28 sigma.=   0.02
Atom: A    124 ARG NE    deviation=  -0.21 sigma.=   0.02
Atom: A    124 ARG CZ    deviation=  -0.25 sigma.=   0.02
Atom: A    124 ARG HH11  deviation=   0.35 sigma.=   0.02
Atom: A    124 ARG HH12  deviation=  -0.27 sigma.=   0.02
Atom: A    124 ARG HH21  deviation=   0.22 sigma.=   0.02
Atom: A    126 HIS CG    deviation=   0.22 sigma.=   0.02
Atom: A    126 HIS HE1   deviation=  -0.26 sigma.=   0.02
Atom: A    127 ALA C     deviation=   0.38 sigma.=   0.02
Atom: A    127 ALA O     deviation=  -0.27 sigma.=   0.02
Atom: A    128 PRO N     deviation=  -0.53 sigma.=   0.05
Atom: A    128 PRO C     deviation=   0.25 sigma.=   0.02
Atom: A    131 ARG CD    deviation=  -0.36 sigma.=   0.02
Atom: A    131 ARG NE    deviation=   0.30 sigma.=   0.02
Atom: A    131 ARG HH11  deviation=   0.42 sigma.=   0.02
Atom: A    131 ARG HH12  deviation=  -0.20 sigma.=   0.02
Atom: A    131 ARG HH21  deviation=   0.48 sigma.=   0.02
Atom: A    131 ARG HH22  deviation=  -0.51 sigma.=   0.02
Atom: A    131 ARG C     deviation=  -0.24 sigma.=   0.02
Atom: A    132 VAL C     deviation=  -0.25 sigma.=   0.02
Atom: A    133 TYR CG    deviation=  -0.22 sigma.=   0.02
Atom: A    133 TYR CZ    deviation=   0.27 sigma.=   0.02
Atom: A    133 TYR HE1   deviation=  -0.32 sigma.=   0.02
Atom: A    133 TYR HE2   deviation=  -0.23 sigma.=   0.02
Atom: A    133 TYR HD2   deviation=   0.50 sigma.=   0.02
Atom: A    134 HIS CB    deviation=  -0.34 sigma.=   0.02
Atom: A    134 HIS HD1   deviation=   0.31 sigma.=   0.02
Atom: A    134 HIS HE1   deviation=  -0.46 sigma.=   0.02
Atom: A    134 HIS HE2   deviation=   0.21 sigma.=   0.02
Atom: A    136 LYS C     deviation=  -0.26 sigma.=   0.02
Atom: A    137 PHE HE1   deviation=  -0.26 sigma.=   0.02
Atom: A    142 VAL C     deviation=  -0.22 sigma.=   0.02
Atom: A    147 ASP C     deviation=  -0.25 sigma.=   0.02
Atom: A    150 GLY C     deviation=   0.50 sigma.=   0.02
Atom: A    150 GLY O     deviation=  -0.25 sigma.=   0.02
Atom: A    151 GLU CD    deviation=  -0.46 sigma.=   0.02
Atom: A    151 GLU OE2   deviation=   0.22 sigma.=   0.02
Atom: A    153 LEU C     deviation=   0.23 sigma.=   0.02
Atom: A    154 THR C     deviation=  -0.40 sigma.=   0.02
Atom: A    155 THR N     deviation=   0.25 sigma.=   0.02
Atom: A    156 ARG CD    deviation=   0.27 sigma.=   0.02
Atom: A    156 ARG NE    deviation=  -0.38 sigma.=   0.02
Atom: A    156 ARG CZ    deviation=  -0.31 sigma.=   0.02
Atom: A    156 ARG HH21  deviation=   0.51 sigma.=   0.02
Atom: A    156 ARG HH22  deviation=  -0.23 sigma.=   0.02
Atom: A    156 ARG C     deviation=  -0.30 sigma.=   0.02
Atom: A    157 LYS C     deviation=  -0.26 sigma.=   0.02
Atom: A    159 ASP CG    deviation=  -0.25 sigma.=   0.02
Atom: A    160 GLN CD    deviation=   0.23 sigma.=   0.02
Atom: A    160 GLN C     deviation=   0.30 sigma.=   0.02
Atom: A    162 GLU CD    deviation=  -0.48 sigma.=   0.02
Atom: A    162 GLU OE2   deviation=   0.36 sigma.=   0.02
Atom: A    162 GLU C     deviation=   0.53 sigma.=   0.02
Atom: A    162 GLU O     deviation=  -0.30 sigma.=   0.02
Atom: A    163 THR C     deviation=  -0.36 sigma.=   0.02
Atom: A    164 VAL C     deviation=   0.21 sigma.=   0.02
Atom: A    165 ARG HH11  deviation=   0.22 sigma.=   0.02
Atom: A    165 ARG HH21  deviation=   0.35 sigma.=   0.02
Atom: A    165 ARG HH22  deviation=  -0.26 sigma.=   0.02
Atom: A    165 ARG C     deviation=  -0.24 sigma.=   0.02
Atom: A    167 ARG CD    deviation=  -0.61 sigma.=   0.02
Atom: A    167 ARG NE    deviation=   0.41 sigma.=   0.02
Atom: A    167 ARG HH11  deviation=   0.39 sigma.=   0.02
Atom: A    167 ARG HH21  deviation=   0.26 sigma.=   0.02
Atom: A    167 ARG HH22  deviation=  -0.52 sigma.=   0.02
Atom: A    170 GLU CD    deviation=  -0.34 sigma.=   0.02
Atom: A    171 TYR CB    deviation=   0.28 sigma.=   0.02
Atom: A    171 TYR CE2   deviation=   0.49 sigma.=   0.02
Atom: A    171 TYR CD2   deviation=  -0.42 sigma.=   0.02
Atom: A    171 TYR OH    deviation=  -0.67 sigma.=   0.02
Atom: A    171 TYR HD1   deviation=   0.21 sigma.=   0.02
Atom: A    171 TYR HE2   deviation=   1.01 sigma.=   0.02
Atom: A    171 TYR HD2   deviation=  -1.23 sigma.=   0.02
Atom: A    171 TYR C     deviation=   0.29 sigma.=   0.02
Atom: A    172 HIS HE1   deviation=   0.44 sigma.=   0.02
Atom: A    172 HIS HE2   deviation=  -0.33 sigma.=   0.02
Atom: A    173 GLN CD    deviation=   0.26 sigma.=   0.02
Atom: A    173 GLN C     deviation=  -0.32 sigma.=   0.02
Atom: A    174 MET C     deviation=  -0.30 sigma.=   0.02
Atom: A    176 ALA C     deviation=  -0.49 sigma.=   0.02
Atom: A    176 ALA O     deviation=   0.22 sigma.=   0.02
Atom: A    177 PRO N     deviation=   0.22 sigma.=   0.02
Atom: A    177 PRO C     deviation=   0.24 sigma.=   0.02
Atom: A    181 TYR CD1   deviation=  -0.25 sigma.=   0.02
Atom: A    181 TYR CE1   deviation=   0.33 sigma.=   0.02
Atom: A    181 TYR CZ    deviation=   0.22 sigma.=   0.02
Atom: A    181 TYR OH    deviation=  -0.34 sigma.=   0.02
Atom: A    181 TYR HD1   deviation=  -0.68 sigma.=   0.02
Atom: A    181 TYR HE1   deviation=   0.67 sigma.=   0.02
Atom: A    181 TYR HE2   deviation=  -0.35 sigma.=   0.02
Atom: A    181 TYR HD2   deviation=   0.40 sigma.=   0.02
Atom: A    181 TYR C     deviation=   0.25 sigma.=   0.02
Atom: A    182 TYR HD1   deviation=   0.64 sigma.=   0.02
Atom: A    182 TYR HE1   deviation=  -0.43 sigma.=   0.02
Atom: A    182 TYR HE2   deviation=   0.57 sigma.=   0.02
Atom: A    182 TYR HD2   deviation=  -0.97 sigma.=   0.02
Atom: A    184 LYS C     deviation=  -0.26 sigma.=   0.02
Atom: A    187 GLU CD    deviation=   0.39 sigma.=   0.02
Atom: A    190 ASN CG    deviation=   0.39 sigma.=   0.02
Atom: A    192 LYS C     deviation=   0.25 sigma.=   0.02
Atom: A    193 TYR CG    deviation=  -0.21 sigma.=   0.02
Atom: A    193 TYR HE2   deviation=  -0.22 sigma.=   0.02
Atom: A    200 LYS C     deviation=  -0.27 sigma.=   0.02
Atom: A    201 PRO C     deviation=  -0.23 sigma.=   0.02
Atom: A    206 ARG CD    deviation=  -0.33 sigma.=   0.02
Atom: A    206 ARG NE    deviation=   0.56 sigma.=   0.02
Atom: A    206 ARG CZ    deviation=   0.59 sigma.=   0.02
Atom: A    206 ARG HH21  deviation=  -0.58 sigma.=   0.02
Atom: A    208 ASP CG    deviation=  -0.59 sigma.=   0.02
Atom: A    208 ASP OD2   deviation=   0.44 sigma.=   0.02
Atom: A    208 ASP C     deviation=  -0.33 sigma.=   0.02
Atom: A    210 GLU C     deviation=   0.34 sigma.=   0.02
Atom: A    214 GLY C     deviation=   0.28 sigma.=   0.02
Atom: A    214 GLY O     deviation=  -0.22 sigma.=   0.02

    ****                              VDW outliers                              ****

VDW deviations from the ideal >10.000Sigma or dist <  1.000 will be monitored

A     24 TYR HB2 . - A     24 TYR HD2 . mod.= 0.963 id.= 2.400 dev= -1.44 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1
A     24 TYR HB2 . - A     24 TYR HD2 . mod.= 0.963 id.= 2.400 dev= -1.44 sig.= 0.20 sym.=  1  0  0  0 ncs  -1 type =  1
A     57 LYS HB2 . - A     57 LYS H   . mod.= 0.487 id.= 2.400 dev= -1.91 sig.= 0.20 sym.=  1  0  0  0 ncs  -1 type =  1
A     57 LYS HB2 . - A     57 LYS H   . mod.= 0.487 id.= 2.400 dev= -1.91 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1
A     58 LEU HA  . - A     58 LEU HD23. mod.= 0.861 id.= 2.400 dev= -1.54 sig.= 0.20 sym.=  1  0  0  0 ncs  -1 type =  1
A     58 LEU HA  . - A     58 LEU HD23. mod.= 0.861 id.= 2.400 dev= -1.54 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1
A     61 ASP O   . - A     65 ILE H   . mod.= 0.914 id.= 1.620 dev= -0.71 sig.= 0.20 sym.=  1  0  0  0 ncs  -1 type =  3
A     61 ASP O   . - A     65 ILE H   . mod.= 0.914 id.= 1.620 dev= -0.71 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  3
A     69 LYS HA  . - A     69 LYS HB3 . mod.= 0.623 id.= 2.100 dev= -1.48 sig.= 0.20 sym.=  1  0  0  0 ncs  -1 type =  2
A     69 LYS HA  . - A     69 LYS HB3 . mod.= 0.623 id.= 2.100 dev= -1.48 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  2
A     74 GLN O   . - A     77 CYS H   . mod.= 0.916 id.= 1.620 dev= -0.70 sig.= 0.20 sym.=  1  0  0  0 ncs  -1 type =  3
A     74 GLN O   . - A     77 CYS H   . mod.= 0.916 id.= 1.620 dev= -0.70 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  3
A    119 ARG O   . - A    120 ILE H   . mod.= 0.885 id.= 1.620 dev= -0.74 sig.= 0.20 sym.=  1  0  0  0 ncs  -1 type =  3
A    119 ARG O   . - A    120 ILE H   . mod.= 0.885 id.= 1.620 dev= -0.74 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  3
A    133 TYR CD1 . - A    133 TYR HD2 . mod.= 0.884 id.= 2.600 dev= -1.72 sig.= 0.20 sym.=  1  0  0  0 ncs  -1 type =  2
A    133 TYR CD1 . - A    133 TYR HD2 . mod.= 0.884 id.= 2.600 dev= -1.72 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  2
A    151 GLU HG3 . - A    151 GLU OE2 . mod.= 0.938 id.= 2.470 dev= -1.53 sig.= 0.20 sym.=  1  0  0  0 ncs  -1 type =  2
A    151 GLU HG3 . - A    151 GLU OE2 . mod.= 0.938 id.= 2.470 dev= -1.53 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  2
A    152 GLU O   . - A    153 LEU H   . mod.= 0.716 id.= 1.620 dev= -0.90 sig.= 0.20 sym.=  1  0  0  0 ncs  -1 type =  3
A    152 GLU O   . - A    153 LEU H   . mod.= 0.716 id.= 1.620 dev= -0.90 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  3
A    203 ALA HB3 . - A    203 ALA C   . mod.= 0.983 id.= 2.650 dev= -1.67 sig.= 0.20 sym.=  1  0  0  0 ncs  -1 type =  2
A    203 ALA HB3 . - A    203 ALA C   . mod.= 0.983 id.= 2.650 dev= -1.67 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  2

 Limits of asymmetric unit      : 1.00 1.00 1.00
 Grid spacing to be used        :    56   54   56
 Maximuum H,K,L                 :     7    6    7
 Minimum acceptable grid spacing:    37   34   37
 File opened           20
 Weight matrix    4.39436053E-06
 Actual weight    10.0000000      is applied to the X-ray term
Norm of X_ray positional gradient                7.68
Norm of Geom. positional gradient                946.
Norm of X_ray B-factor gradient                  3.91
Norm of Geom. B-factor gradient                  0.00
Product of X_ray and Geom posit. gradients      0.212E+06
 Cosine of angle between them                       0.003
Product of X_ray and Geom B-fact gradients       0.00
 Cosine of angle between them                       0.000


Residuals: XRAY=    -0.1483E+06 GEOM=     0.6720E+06 TOTAL=     0.5237E+06
 function value    523676.875    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1628     0.403     0.020
Bond distances: others                         1664     0.000     0.020
Bond angles  : refined atoms                   2107    23.362     2.001
Bond angles  : others                          3789    10.563     3.000
Torsion angles, period  1. refined              161    32.420     5.000
Torsion angles, period  2. refined               75    46.730    24.533
Torsion angles, period  3. refined              313    29.600    15.000
Torsion angles, period  4. refined               13    25.135    15.000
Chiral centres: refined atoms                   254     1.852     0.200
Planar groups: refined atoms                   1523     0.129     0.021
Planar groups: others                           292     0.271     0.020
VDW repulsions: refined_atoms                  1616     0.560     0.200
VDW repulsions.others                          4304     0.504     0.200
VDW; torsion: refined_atoms                    1290     0.404     0.200
VDW; torsion.others                            2908     0.439     0.200
HBOND: refined_atoms                            212     0.418     0.200
HBOND.others                                     38     0.410     0.200
M. chain bond B values: refined atoms           803     0.000     4.000
M. chain bond B values: others                  802     0.000     4.000
M. chain angle B values: refined atoms          911     0.000     6.000
M. chain angle B values: others                 912     0.000     6.000
S. chain bond B values: refined atoms           825     0.000     4.000
S. chain bond B values: others                  825     0.000     4.000
S. chain angle B values: refined atoms         1196     0.000     6.000
S. chain angle B values: others                1196     0.000     6.000
Long range B values: refined atoms             7449     0.000    38.120
Long range B values: others                    7450     0.000    38.121
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale = 2906.892, B  =  41.463
Overall anisotropic scale factors
   B11 =  1.25 B22 = 14.25 B33 =-15.50 B12 =-11.53 B13 = -3.51 B23 = -7.32
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1. M(Rfactor) v. resln :N:1,6,7:
:Cycle    1. M(Fobs) and M(Fc) v. resln :N:1,4,5:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used $$
$$
 0.001       9 100.00  2384.0  1610.9  0.32  0.32
 0.001       6 100.00   765.5   518.0  0.32  0.32
 0.001      21 100.00   411.0   329.6  0.20  0.20
 0.002       6 100.00   411.9   327.4  0.21  0.21
 0.002      18 100.00   393.8   304.7  0.23  0.23
 0.003      17 100.00   355.0   278.7  0.22  0.22
 0.003      16 100.00   264.7   212.6  0.23  0.23
 0.004      24 100.00   171.1   155.1  0.14  0.14
 0.004      14 100.00   206.7   186.5  0.13  0.13
 0.005      22 100.00   187.7   181.4  0.07  0.07
 0.005      21 100.00   156.0   150.6  0.09  0.09
 0.006      32 100.00   149.4   153.1  0.12  0.12
 0.006      16 100.00   147.3   152.8  0.11  0.11
 0.007      22 100.00   146.6   163.9  0.13  0.13
 0.007      32 100.00   104.2   139.4  0.35  0.35
 0.008      28 100.00   118.9   146.5  0.24  0.24
 0.008      41 100.00   110.6   149.1  0.37  0.37
 0.009      14 100.00    79.3   104.9  0.32  0.32
 0.009      20 100.00    83.1   121.4  0.48  0.48
 0.010      42 100.00    72.9   103.1  0.44  0.44
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle    1. FSC and  Fom(<cos(DelPhi)>-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCwork CorrFofcWork$$
 $$
  0.0005      9   1.000      0   0.000      9   1.000  1.359  0.9997  0.9997
  0.0010      6   0.998      0   0.000      6   0.998  1.285  0.9797  0.9256
  0.0015     21   0.995      0   0.000     21   0.995  1.215  0.9928  0.9843
  0.0020      6   0.995      0   0.000      6   0.995  1.173  0.9913  0.9907
  0.0025     18   0.995      0   0.000     18   0.995  1.121  0.9941  0.9933
  0.0029     17   0.994      0   0.000     17   0.994  1.093  0.9921  0.9886
  0.0034     16   0.994      0   0.000     16   0.994  1.053  0.9868  0.9405
  0.0039     24   0.992      0   0.000     24   0.992  1.020  0.9818  0.9696
  0.0044     14   0.993      0   0.000     14   0.993  0.989  0.9863  0.9645
  0.0049     22   0.992      0   0.000     22   0.992  0.962  0.9907  0.9895
  0.0054     21   0.992      0   0.000     21   0.992  0.934  0.9861  0.9700
  0.0059     32   0.992      0   0.000     32   0.992  0.909  0.9845  0.9753
  0.0064     16   0.993      0   0.000     16   0.993  0.877  0.9775  0.9601
  0.0068     22   0.993      0   0.000     22   0.993  0.860  0.9855  0.9689
  0.0073     32   0.992      0   0.000     32   0.992  0.834  0.9724  0.9396
  0.0078     28   0.993      0   0.000     28   0.993  0.808  0.9810  0.9455
  0.0083     41   0.993      0   0.000     41   0.993  0.785  0.9803  0.9376
  0.0088     14   0.993      0   0.000     14   0.993  0.763  0.9761  0.9469
  0.0093     20   0.994      0   0.000     20   0.994  0.745  0.9748  0.9095
  0.0098     42   0.995      0   0.000     42   0.995  0.723  0.9767  0.9058
 $$
Resolution limits                    =     60.500    10.000
Number of used reflections           =        421
Percentage observed                  =   100.0000
Percentage of free reflections       =     0.0000
Overall R factor                     =     0.2438
Average Fourier shell correlation    =     0.9831
Overall weighted R factor            =     0.2438
Overall weighted R2 factor           =     0.3009
Average correlation coefficient      =     0.9553
Overall correlation coefficient      =     0.9886
Overall figure of merit              =     0.9933
ML based su of positional parameters =    15.1590
ML based su of thermal parameters    =  2634.3538
-----------------------------------------------------------------------------
 Trying gamma equal    0.00000000    
 Trying gamma equal    5.00000007E-02
 Gamma decreased to    3.99999991E-02


 fvalues   -14761.8711       672025.188       116749.062       524406.500    


     CGMAT cycle number =      2

 File opened           20
 Weight matrix    2.83055169E-06
 Actual weight    10.0000000      is applied to the X-ray term


 function value    117010.531    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1628     0.234     0.020
Bond distances: others                         1664     0.050     0.020
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale = 2890.361, B  =   4.358
Overall anisotropic scale factors
   B11 = -2.41 B22 = 12.79 B33 =-10.38 B12 =-13.52 B13 = -4.83 B23 = -5.39
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2417
Average Fourier shell correlation    =     0.9846
Average correlation coefficient      =     0.9593
Overall figure of merit              =     0.9935
-----------------------------------------------------------------------------
 Trying gamma equal    3.99999991E-02
 Gamma decreased to    3.09090894E-02


 fvalues   -14848.1660       265513.625       5091.71875       117031.969    


     CGMAT cycle number =      3

 File opened           20
 Weight matrix    1.68966096E-06
 Actual weight    10.0000000      is applied to the X-ray term


 function value    5533.07812    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1628     0.164     0.020
Bond distances: others                         1664     0.027     0.020
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale = 2858.952, B  =   8.771
Overall anisotropic scale factors
   B11 = -0.76 B22 = 12.53 B33 =-11.77 B12 =-14.99 B13 = -5.00 B23 = -8.01
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2416
Average Fourier shell correlation    =     0.9868
Average correlation coefficient      =     0.9650
Overall figure of merit              =     0.9938
-----------------------------------------------------------------------------
 Trying gamma equal    3.09090894E-02
 Gamma decreased to    2.26446278E-02


 fvalues   -14872.4355       154362.516      -40943.0859       5638.15625    


     CGMAT cycle number =      4

 File opened           20
 Weight matrix    5.90872551E-05
 Actual weight    10.0000000      is applied to the X-ray term


 function value   -44913.0391    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1628     0.126     0.020
Bond distances: others                         1664     0.017     0.020
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale = 4433.327, B  = 331.462
Overall anisotropic scale factors
   B11 =  2.80 B22 =  3.31 B33 = -6.11 B12 = -6.88 B13 =  0.11 B23 = -1.18
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.0688
Average Fourier shell correlation    =     0.9911
Average correlation coefficient      =     0.9782
Overall figure of merit              =     0.9951
-----------------------------------------------------------------------------
 Trying gamma equal    2.26446278E-02
 Gamma decreased to    1.51314801E-02


 fvalues   -4177.28564       108685.367       8927.38281       66912.5156    


     CGMAT cycle number =      5

 File opened           20
 Weight matrix    5.21547954E-05
 Actual weight    10.0000000      is applied to the X-ray term


 function value   -69602.4688    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1628     0.102     0.020
Bond distances: others                         1664     0.012     0.020
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale = 4381.490, B  = 281.697
Overall anisotropic scale factors
   B11 =  3.76 B22 =  2.32 B33 = -6.08 B12 = -7.66 B13 =  0.55 B23 = -0.94
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.0672
Average Fourier shell correlation    =     0.9914
Average correlation coefficient      =     0.9791
Overall figure of merit              =     0.9952
-----------------------------------------------------------------------------
 Trying gamma equal    1.51314801E-02
 Gamma decreased to    8.30134563E-03


 fvalues   -7890.21436       84096.0625      -33447.5078       5193.92188    


     CGMAT cycle number =      6

 File opened           20
 Weight matrix    4.59749972E-05
 Actual weight    10.0000000      is applied to the X-ray term


 function value   -85041.6250    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1628     0.087     0.020
Bond distances: others                         1664     0.010     0.020
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale = 4411.669, B  = 251.753
Overall anisotropic scale factors
   B11 =  3.24 B22 =  2.41 B33 = -5.65 B12 = -6.04 B13 =  0.56 B23 = -1.62
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.0653
Average Fourier shell correlation    =     0.9917
Average correlation coefficient      =     0.9801
Overall figure of merit              =     0.9953
-----------------------------------------------------------------------------
 Trying gamma equal    8.30134563E-03
 Gamma decreased to    2.09213281E-03


 fvalues   -9573.11523       68842.3438      -48671.3672      -26888.8125    


     CGMAT cycle number =      7

 File opened           20
 Weight matrix    4.37145718E-05
 Actual weight    10.0000000      is applied to the X-ray term


 function value   -95288.4922    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1628     0.076     0.020
Bond distances: others                         1664     0.012     0.020
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale = 4391.998, B  = 226.712
Overall anisotropic scale factors
   B11 =  4.56 B22 =  2.16 B33 = -6.72 B12 = -5.68 B13 = -0.17 B23 = -1.31
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.0637
Average Fourier shell correlation    =     0.9920
Average correlation coefficient      =     0.9808
Overall figure of merit              =     0.9954
-----------------------------------------------------------------------------
 Trying gamma equal    2.09213281E-03
 Gamma decreased to    9.99999975E-05


 fvalues   -10782.4619       58719.5703      -66367.2812      -49105.0469    


     CGMAT cycle number =      8

 File opened           20
 Weight matrix    4.13811431E-05
 Actual weight    10.0000000      is applied to the X-ray term


 function value   -102580.047    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1628     0.067     0.020
Bond distances: others                         1664     0.016     0.020
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale = 4378.834, B  = 203.262
Overall anisotropic scale factors
   B11 =  5.72 B22 =  1.67 B33 = -7.39 B12 = -5.01 B13 = -0.68 B23 = -1.21
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.0621
Average Fourier shell correlation    =     0.9924
Average correlation coefficient      =     0.9817
Overall figure of merit              =     0.9955
-----------------------------------------------------------------------------
 Trying gamma equal    9.99999975E-05
 Trying gamma equal    2.57579032E-02
 Gamma decreased to    2.06263214E-02


 fvalues   -11680.7021       51589.3594      -79495.5938      -65217.6641    


     CGMAT cycle number =      9

 File opened           20
 Weight matrix    3.66642162E-05
 Actual weight    10.0000000      is applied to the X-ray term


 function value   -108368.203    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1628     0.061     0.020
Bond distances: others                         1664     0.009     0.020
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale = 4381.659, B  = 182.989
Overall anisotropic scale factors
   B11 =  6.23 B22 =  1.00 B33 = -7.23 B12 = -5.28 B13 = -0.78 B23 = -1.19
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.0614
Average Fourier shell correlation    =     0.9926
Average correlation coefficient      =     0.9821
Overall figure of merit              =     0.9955
-----------------------------------------------------------------------------
 Trying gamma equal    2.06263214E-02
 Gamma decreased to    1.59612484E-02


 fvalues   -12449.8916       45884.7305      -90208.1719      -78614.1875    


     CGMAT cycle number =     10

    ****                         Bond distance outliers                         ****

Bond distance deviations from the ideal >10.000Sigma will be monitored

A    122 GLY N   . - A    122 GLY CA  . mod.= 1.246 id.= 1.458 dev=  0.212 sig.= 0.021
A    193 TYR CZ  . - A    193 TYR OH  . mod.= 1.154 id.= 1.376 dev=  0.222 sig.= 0.021

    ****                         Torsion angle outliers                         ****

Torsion angle deviations from the ideal >10.000Sigma will be monitored

A     13 LYS CA    - A     14 GLY CA    mod.= 109.04 id.= 180.00 per.= 1 dev=  70.96 sig.=   5.00
A     62 GLU CA    - A     63 LEU CA    mod.=-125.13 id.=   0.00 per.= 1 dev= 125.13 sig.=   5.00
A     72 ILE CA    - A     73 ALA CA    mod.=-140.85 id.=   0.00 per.= 1 dev= 140.85 sig.=   5.00
A    129 SER CA    - A    130 GLY CA    mod.= -77.75 id.=   0.00 per.= 1 dev=  77.75 sig.=   5.00
A    167 ARG CA    - A    168 LEU CA    mod.=  92.90 id.=   0.00 per.= 1 dev= -92.90 sig.=   5.00
A    195 LYS CA    - A    196 VAL CA    mod.=-121.58 id.=   0.00 per.= 1 dev= 121.58 sig.=   5.00

    ****                         Chiral volume outliers                         ****

Chiral volume deviations from the ideal >10.000Sigma will be monitored

A     20 ILE CB    mod.=   0.28 id.=   2.64 dev=  2.369 sig.=  0.200
A     38 ALA CA    mod.=  -0.25 id.=  -2.48 dev= -2.227 sig.=  0.200
A     41 SER CA    mod.=  -0.46 id.=  -2.50 dev= -2.047 sig.=  0.200
A     89 THR CB    mod.=  -0.16 id.=   2.55 dev=  2.714 sig.=  0.200
A    168 LEU CA    mod.=   2.02 id.=  -2.50 dev= -4.527 sig.=  0.200
A    173 GLN CA    mod.=   0.18 id.=  -2.50 dev= -2.684 sig.=  0.200
A    209 LEU CA    mod.=  -0.27 id.=  -2.50 dev= -2.228 sig.=  0.200

    ****                Large deviation of atoms from planarity                 ****

Deviations from the planarity >10.000Sigma will be monitored
Atom: A     13 LYS C     deviation=   0.22 sigma.=   0.02

 Limits of asymmetric unit      : 1.00 1.00 1.00
 Grid spacing to be used        :    56   54   56
 Maximuum H,K,L                 :     7    6    7
 Minimum acceptable grid spacing:    37   34   37
 File opened           20
 Weight matrix    3.24826760E-05
 Actual weight    10.0000000      is applied to the X-ray term
Norm of X_ray positional gradient                6.59
Norm of Geom. positional gradient                90.4
Norm of X_ray B-factor gradient                  3.13
Norm of Geom. B-factor gradient                 0.424
Product of X_ray and Geom posit. gradients     -0.678E+05
 Cosine of angle between them                      -0.011
Product of X_ray and Geom B-fact gradients     -0.228E+04
 Cosine of angle between them                      -0.519


Residuals: XRAY=    -0.1543E+06 GEOM=     0.4170E+05 TOTAL=    -0.1126E+06
 function value   -112640.047    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1628     0.056     0.020
Bond distances: others                         1664     0.005     0.020
Bond angles  : refined atoms                   2107     6.999     2.001
Bond angles  : others                          3789     3.872     3.000
Torsion angles, period  1. refined              161    26.005     5.000
Torsion angles, period  2. refined               75    39.469    24.533
Torsion angles, period  3. refined              313    24.729    15.000
Torsion angles, period  4. refined               13    21.843    15.000
Chiral centres: refined atoms                   254     0.591     0.200
Planar groups: refined atoms                   1523     0.037     0.021
Planar groups: others                           292     0.006     0.020
VDW repulsions: refined_atoms                  1450     0.547     0.200
VDW repulsions.others                          3980     0.285     0.200
VDW; torsion: refined_atoms                    1222     0.295     0.200
VDW; torsion.others                            2192     0.189     0.200
HBOND: refined_atoms                            204     0.372     0.200
HBOND.others                                     28     0.175     0.200
M. chain bond B values: refined atoms           803     1.881    19.419
M. chain bond B values: others                  802     1.880    19.416
M. chain angle B values: refined atoms          911     3.554    29.122
M. chain angle B values: others                 912     3.553    29.126
S. chain bond B values: refined atoms           825     1.599    19.571
S. chain bond B values: others                  825     1.598    19.571
S. chain angle B values: refined atoms         1196     3.099    29.306
S. chain angle B values: others                1196     3.097    29.306
Long range B values: refined atoms             7708    11.430   185.280
Long range B values: others                    7709    11.429   185.283
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale = 4381.058, B  = 163.272
Overall anisotropic scale factors
   B11 =  6.64 B22 =  0.72 B33 = -7.37 B12 = -5.12 B13 = -0.59 B23 = -1.38
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10. M(Rfactor) v. resln :N:1,6,7:
:Cycle   10. M(Fobs) and M(Fc) v. resln :N:1,4,5:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used $$
$$
 0.001       9 100.00  1581.8  1582.1  0.02  0.02
 0.001       6 100.00   508.0   493.9  0.07  0.07
 0.001      21 100.00   272.7   290.5  0.10  0.10
 0.002       6 100.00   273.3   281.1  0.08  0.08
 0.002      18 100.00   261.3   258.4  0.03  0.03
 0.003      17 100.00   235.5   230.7  0.05  0.05
 0.003      16 100.00   175.6   171.5  0.06  0.06
 0.004      24 100.00   113.5   113.3  0.07  0.07
 0.004      14 100.00   137.1   130.8  0.07  0.07
 0.005      22 100.00   124.6   121.5  0.06  0.06
 0.005      21 100.00   103.5   101.1  0.06  0.06
 0.006      32 100.00    99.1    98.5  0.09  0.09
 0.006      16 100.00    97.7    94.0  0.07  0.07
 0.007      22 100.00    97.3    95.6  0.05  0.05
 0.007      32 100.00    69.1    74.4  0.12  0.12
 0.008      28 100.00    78.9    79.6  0.07  0.07
 0.008      41 100.00    73.4    74.8  0.10  0.10
 0.009      14 100.00    52.6    54.9  0.10  0.10
 0.009      20 100.00    55.1    55.0  0.09  0.09
 0.010      42 100.00    48.4    48.0  0.11  0.11
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle   10. FSC and  Fom(<cos(DelPhi)>-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCwork CorrFofcWork$$
 $$
  0.0005      9   1.000      0   0.000      9   1.000  0.993  0.9999  0.9998
  0.0010      6   0.999      0   0.000      6   0.999  0.992  0.9904  0.9635
  0.0015     21   0.998      0   0.000     21   0.998  0.991  0.9969  0.9893
  0.0020      6   0.998      0   0.000      6   0.998  0.991  0.9947  0.9861
  0.0025     18   0.998      0   0.000     18   0.998  0.991  0.9978  0.9966
  0.0029     17   0.997      0   0.000     17   0.997  0.990  0.9959  0.9919
  0.0034     16   0.997      0   0.000     16   0.997  0.990  0.9950  0.9809
  0.0039     24   0.995      0   0.000     24   0.995  0.990  0.9926  0.9886
  0.0044     14   0.996      0   0.000     14   0.996  0.990  0.9946  0.9868
  0.0049     22   0.996      0   0.000     22   0.996  0.989  0.9950  0.9924
  0.0054     21   0.995      0   0.000     21   0.995  0.989  0.9931  0.9825
  0.0059     32   0.995      0   0.000     32   0.995  0.989  0.9927  0.9863
  0.0064     16   0.995      0   0.000     16   0.995  0.989  0.9923  0.9856
  0.0068     22   0.995      0   0.000     22   0.995  0.988  0.9951  0.9934
  0.0073     32   0.994      0   0.000     32   0.994  0.988  0.9889  0.9766
  0.0078     28   0.995      0   0.000     28   0.995  0.988  0.9930  0.9828
  0.0083     41   0.995      0   0.000     41   0.995  0.988  0.9909  0.9702
  0.0088     14   0.994      0   0.000     14   0.994  0.988  0.9888  0.9772
  0.0093     20   0.995      0   0.000     20   0.995  0.987  0.9920  0.9824
  0.0098     42   0.995      0   0.000     42   0.995  0.987  0.9884  0.9672
 $$
Resolution limits                    =     60.500    10.000
Number of used reflections           =        421
Percentage observed                  =   100.0000
Percentage of free reflections       =     0.0000
Overall R factor                     =     0.0607
Average Fourier shell correlation    =     0.9928
Overall weighted R factor            =     0.0607
Overall weighted R2 factor           =     0.0459
Average correlation coefficient      =     0.9826
Overall correlation coefficient      =     0.9986
Overall figure of merit              =     0.9956
ML based su of positional parameters =     5.5165
ML based su of thermal parameters    =   985.8438
-----------------------------------------------------------------------------
 Trying gamma equal    1.59612484E-02
 Gamma decreased to    1.17202727E-02


 fvalues   -13100.6855       41697.4414      -98949.7031      -89309.4219    

    ****                         Torsion angle outliers                         ****

Torsion angle deviations from the ideal >10.000Sigma will be monitored

A     13 LYS CA    - A     14 GLY CA    mod.= 111.44 id.= 180.00 per.= 1 dev=  68.56 sig.=   5.00
A     62 GLU CA    - A     63 LEU CA    mod.=-125.87 id.=   0.00 per.= 1 dev= 125.87 sig.=   5.00
A     72 ILE CA    - A     73 ALA CA    mod.=-141.04 id.=   0.00 per.= 1 dev= 141.04 sig.=   5.00
A    129 SER CA    - A    130 GLY CA    mod.= -76.40 id.=   0.00 per.= 1 dev=  76.40 sig.=   5.00
A    167 ARG CA    - A    168 LEU CA    mod.=  96.03 id.=   0.00 per.= 1 dev= -96.03 sig.=   5.00
A    195 LYS CA    - A    196 VAL CA    mod.=-121.68 id.=   0.00 per.= 1 dev= 121.68 sig.=   5.00

    ****                         Chiral volume outliers                         ****

Chiral volume deviations from the ideal >10.000Sigma will be monitored

A     20 ILE CB    mod.=   0.40 id.=   2.64 dev=  2.240 sig.=  0.200
A     38 ALA CA    mod.=  -0.44 id.=  -2.48 dev= -2.042 sig.=  0.200
A     41 SER CA    mod.=  -0.50 id.=  -2.50 dev= -2.003 sig.=  0.200
A     89 THR CB    mod.=  -0.10 id.=   2.55 dev=  2.647 sig.=  0.200
A    168 LEU CA    mod.=   1.98 id.=  -2.50 dev= -4.482 sig.=  0.200
A    173 GLN CA    mod.=   0.14 id.=  -2.50 dev= -2.646 sig.=  0.200
A    209 LEU CA    mod.=  -0.34 id.=  -2.50 dev= -2.168 sig.=  0.200

    ****                Large deviation of atoms from planarity                 ****

Deviations from the planarity >10.000Sigma will be monitored
Atom: A     13 LYS C     deviation=  -0.21 sigma.=   0.02


 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/1AKE_cha_molrep_refine_shaken_refine_rframe.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1628     0.052     0.020
Bond distances: others                         1664     0.006     0.020
Bond angles  : refined atoms                   2107     6.627     2.001
Bond angles  : others                          3789     3.842     3.000
Torsion angles, period  1. refined              161    25.861     5.000
Torsion angles, period  2. refined               75    39.356    24.533
Torsion angles, period  3. refined              313    24.544    15.000
Torsion angles, period  4. refined               13    22.115    15.000
Chiral centres: refined atoms                   254     0.570     0.200
Planar groups: refined atoms                   1523     0.034     0.021
Planar groups: others                           292     0.005     0.020
VDW repulsions: refined_atoms                  1446     0.546     0.200
VDW repulsions.others                          3994     0.279     0.200
VDW; torsion: refined_atoms                    1224     0.289     0.200
VDW; torsion.others                            2170     0.183     0.200
HBOND: refined_atoms                            206     0.367     0.200
HBOND.others                                     24     0.189     0.200
M. chain bond B values: refined atoms           803     1.953    21.411
M. chain bond B values: others                  802     1.952    21.408
M. chain angle B values: refined atoms          911     3.628    32.115
M. chain angle B values: others                 912     3.626    32.118
S. chain bond B values: refined atoms           825     2.132    21.544
S. chain bond B values: others                  825     2.132    21.544
S. chain angle B values: refined atoms         1196     3.783    32.271
S. chain angle B values: others                1196     3.781    32.270
Long range B values: refined atoms             7666    11.823   204.056
Long range B values: others                    7667    11.822   204.060
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale = 4376.791, B  = 142.760
Overall anisotropic scale factors
   B11 =  7.09 B22 =  0.15 B33 = -7.24 B12 = -5.00 B13 = -0.16 B23 = -1.33
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11. M(Rfactor) v. resln :N:1,6,7:
:Cycle   11. M(Fobs) and M(Fc) v. resln :N:1,4,5:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used $$
$$
 0.001       9 100.00  1583.4  1583.2  0.02  0.02
 0.001       6 100.00   508.4   494.1  0.07  0.07
 0.001      21 100.00   273.0   290.3  0.09  0.09
 0.002       6 100.00   273.5   281.1  0.08  0.08
 0.002      18 100.00   261.5   258.7  0.03  0.03
 0.003      17 100.00   235.7   230.7  0.05  0.05
 0.003      16 100.00   175.8   172.0  0.05  0.05
 0.004      24 100.00   113.7   113.5  0.06  0.06
 0.004      14 100.00   137.3   130.8  0.07  0.07
 0.005      22 100.00   124.7   121.4  0.06  0.06
 0.005      21 100.00   103.6   101.2  0.06  0.06
 0.006      32 100.00    99.2    98.6  0.08  0.08
 0.006      16 100.00    97.8    94.3  0.06  0.06
 0.007      22 100.00    97.4    95.8  0.05  0.05
 0.007      32 100.00    69.2    74.2  0.12  0.12
 0.008      28 100.00    79.0    79.6  0.07  0.07
 0.008      41 100.00    73.5    74.8  0.09  0.09
 0.009      14 100.00    52.7    55.1  0.10  0.10
 0.009      20 100.00    55.2    54.9  0.09  0.09
 0.010      42 100.00    48.4    48.0  0.11  0.11
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle   11. FSC and  Fom(<cos(DelPhi)>-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCwork CorrFofcWork$$
 $$
  0.0005      9   1.000      0   0.000      9   1.000  0.993  0.9999  0.9998
  0.0010      6   0.999      0   0.000      6   0.999  0.993  0.9907  0.9649
  0.0015     21   0.998      0   0.000     21   0.998  0.992  0.9970  0.9895
  0.0020      6   0.998      0   0.000      6   0.998  0.992  0.9946  0.9859
  0.0025     18   0.998      0   0.000     18   0.998  0.991  0.9978  0.9967
  0.0029     17   0.997      0   0.000     17   0.997  0.991  0.9961  0.9922
  0.0034     16   0.997      0   0.000     16   0.997  0.991  0.9952  0.9820
  0.0039     24   0.995      0   0.000     24   0.995  0.991  0.9929  0.9890
  0.0044     14   0.996      0   0.000     14   0.996  0.990  0.9948  0.9873
  0.0049     22   0.996      0   0.000     22   0.996  0.990  0.9952  0.9928
  0.0054     21   0.995      0   0.000     21   0.995  0.990  0.9933  0.9834
  0.0059     32   0.995      0   0.000     32   0.995  0.990  0.9930  0.9869
  0.0064     16   0.995      0   0.000     16   0.995  0.989  0.9926  0.9861
  0.0068     22   0.996      0   0.000     22   0.996  0.989  0.9952  0.9936
  0.0073     32   0.994      0   0.000     32   0.994  0.989  0.9895  0.9781
  0.0078     28   0.995      0   0.000     28   0.995  0.989  0.9932  0.9835
  0.0083     41   0.995      0   0.000     41   0.995  0.989  0.9914  0.9717
  0.0088     14   0.994      0   0.000     14   0.994  0.989  0.9892  0.9779
  0.0093     20   0.995      0   0.000     20   0.995  0.988  0.9923  0.9832
  0.0098     42   0.995      0   0.000     42   0.995  0.988  0.9890  0.9687
 $$
Resolution limits                    =     60.500    10.000
Number of used reflections           =        421
Percentage observed                  =   100.0000
Percentage of free reflections       =     0.0000
Overall R factor                     =     0.0597
Average Fourier shell correlation    =     0.9931
Overall weighted R factor            =     0.0597
Overall weighted R2 factor           =     0.0451
Average correlation coefficient      =     0.9833
Overall correlation coefficient      =     0.9986
Overall figure of merit              =     0.9957
ML based su of positional parameters =     5.5165
ML based su of thermal parameters    =   985.8438
-----------------------------------------------------------------------------
  Time in seconds: CPU =        20.34
             Elapsed =           0.00

    ****           Things for loggraph, R factor and others vs cycle            ****


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS:<Rfactor> vs cycle :N:1,2,3:
:FOM vs cycle :N:1,4:
:-LL vs cycle :N:1,5:
:-LLfree vs cycle :N:1,6:
:Geometry vs cycle:N:1,7,8,9,10,11:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2438   0.0      0.993      -14835.       0.0   0.4032 21.120  23.362 12.771   1.852
       1   0.2417   0.0      0.994      -14850.       0.0   0.2337 11.888  16.621  8.808   1.219
       2   0.2416   0.0      0.994      -14883.       0.0   0.1635  8.208  13.553  7.075   0.996
       3   0.0688   0.0      0.995      -15360.       0.0   0.1256  6.265  11.697  6.038   0.872
       4   0.0672   0.0      0.995      -15370.       0.0   0.1022  5.088  10.387  5.309   0.789
       5   0.0653   0.0      0.995      -15388.       0.0   0.0867  4.312   9.390  4.759   0.730
       6   0.0637   0.0      0.995      -15401.       0.0   0.0757  3.764   8.598  4.327   0.683
       7   0.0621   0.0      0.995      -15417.       0.0   0.0674  3.354   7.945  3.972   0.644
       8   0.0614   0.0      0.996      -15425.       0.0   0.0611  3.041   7.434  3.695   0.615
       9   0.0607   0.0      0.996      -15434.       0.0   0.0562  2.797   6.999  3.461   0.591
      10   0.0597   0.0      0.996      -15446.       0.0   0.0521  2.597   6.627  3.261   0.570
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2438   0.0597
     Rms BondLength    0.4032   0.0521
      Rms BondAngle   23.3619   6.6275
     Rms ChirVolume    1.8519   0.5703
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
 Refmac_5.8.0131:  End of Refmac_5.8.0131  
Times: User:      26.2s System:    0.2s Elapsed:     0:26  
</pre>
</html>
<!--SUMMARY_END--></FONT></B>


CCP-EM job finished: Wednesday, 12. August 2015 10:33AM ______________________
_______________________________________________________________________________

_________ CCP-EM Job launch/home/tom/Code/devtools/install/bin/refmac5 ________



CCP-EM pipeline job 7 of 10 ___________________________________________________

__ Command ____________________________________________________________________
/home/tom/Code/devtools/install/bin/refmac5 xyzin /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/1AKE_cha_molrep_refine_shaken_refine_rframe.pdb xyzout /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/1AKE_cha_molrep_refine_shaken_refine.pdb atomsf /home/tom/Code/devtools/checkout/refmac5.8/data/atomsf_electron.lib << eof
/home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/job_data/stdin_shake.txt
eof
_______________________________________________________________________________
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<html> <!-- CCP4 HTML LOGFILE -->
<hr>
<!--SUMMARY_END--></FONT></B>
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<pre>
 
 ###############################################################
 ###############################################################
 ###############################################################
 ### CCP4 6.5.011: Refmac_5.8.0131 version 5.8.0131 : 06/08/15##
 ###############################################################
 User: unknown  Run date: 12/ 8/2015 Run time: 10:33:16 


 Please reference: Collaborative Computational Project, Number 4. 2011.
 "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242.
 as well as any specific reference in the program write-up.

<!--SUMMARY_END--></FONT></B>
 $TEXT:Reference1: $$ Main reference $$ 
   "REFMAC5 for the refinement of macromolecular crystal structures:"
   G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011) 
   Acta Crystallogr. D67, 355-367

 $$
 $SUMMARY :Reference1:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference2: $$ Secondary reference $$ 
   "Refinement of Macromolecular Structures by the  Maximum-Likelihood Method:"
   G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
   Acta Crystallogr. D53, 240-255
   EU  Validation contract: BIO2CT-92-0524

 $$
 $SUMMARY :Reference2:  $$ Refmac: $$
 :TEXT:Reference2: $$

 Data line--- noise 0.5
 Data line--- solvent no
 Data line--- end
  Data line--- noise 0.5
===> Warning: Unrecognized keyword: NOIS
  Data line--- solvent no
  Data line--- END
===> Warning: Reflections file has not been defined
===> Warning: Switching to the idealisation mode

    ****                     Input and Default parameters#                      ****


Input coordinate file.  Logical name - XYZIN actual file name  - /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/1AKE_cha_molrep_refine_shaken_refine_rframe.pdb
Output coordinate file. Logical name - XYZOUT actual file name - /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/1AKE_cha_molrep_refine_shaken_refine.pdb

  Refinement type                        : Idealisation

    ****                           Makecif parameters                           ****

Dictionary files for restraints : /usr/local/sci_local/mx/ccp4-6.5/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /usr/local/sci_local/mx/ccp4-6.5/lib/data/monomers/ener_lib.cif
    Apart from amino acids and DNA/RNA all monomers will be checked to see if atom names and connectivity is correct
    Hydrogens will be restored in their riding positions
    Links between monomers will be checked. Only those links present in the coordinate file will be used
    Standard sugar links will be analysed and used
    For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
    Symmetry related links will be analysed and used
    Cis peptides will be found and used automatically


  Method of minimisation                 : Sparse Matrix

  Damping factors:     1.0000  1.0000


    ****                    Geometry restraints and weights                     ****


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

 Planar groups (all and main chain)
          WEIGHT= 1.00 1.00

 Chiral centers
          Weight= 1.00

 NON-BONDED CONTACTS
          Overall weight                          =  1.00
          Sigma for simple VDW                    =  0.20
          Sigma for VDW trhough torsion angle     =  0.20
          Sigma for HBOND                         =  0.20
          Sigma for metal-ion                     =  0.20
          Sigma for DUMMY and other atom          =  0.30
          Distance for donor-accepetor = vdw1+vdw2+(-0.30)
          Distance for acceptor - H    = vdw1+     ( 0.10)
          VDW distance through torsion = vdw1+vdw2+(-0.30)
          Distance for DUMMY-others    = vdw1+vdw2+(-0.70)

 TORSION ANGLES
          Weight= 1.00

 RESTRAINTS AGAINST EXCESSIVE SHIFTS
     Positional parameters                   0.00A
     Thermal parameters                      0.00A
     Occupancy parameters                    0.00

 RADIUS OF CONFIDENCE
     Positional parameters 0.00A
     Thermal parameters    0.00A**2
     Occupancy parameters  0.00

Monitoring style is "MEDIUM". Complete information will be printed out in the
first and last cycle. In all other cycles minimum information will be printed out
Sigma cutoffs for printing out outliers
If deviation of restraint parameter > alpha*sigma then information will be printed out
Distance outliers      10.000
Angle outliers         10.000
Torsion outliers       10.000
Chiral volume outliers 10.000
Plane outliers         10.000
Non-bonding outliers   10.000
---------------------------------------------------------------

 Input file :/home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/re
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.44
 _lib_update       30/05/14
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 11608
                with complete description    : 11608
  NUMBER OF MODIFICATIONS                    :    61
  NUMBER OF LINKS                            :    71
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )

FORMATTED      OLD     file opened on unit  45
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
Logical name: ATOMSF, Filename: /home/tom/Code/devtools/checkout/refmac5.8/data/atomsf_electron.lib
<!--SUMMARY_END--></FONT></B>

  Number of atoms    :    1656
  Number of residues :     214
  Number of chains   :       1
  I am reading library. Please wait.
                mon_lib.cif
  WARNING : TRANS peptide bond (not be changed CIS) angle =    125.84
            ch:AA   res:  62  GLU              -->  63  LEU
  WARNING : TRANS peptide bond (not be changed CIS) angle =    141.03
            ch:AA   res:  72  ILE              -->  73  ALA
  WARNING : TRANS peptide bond (not be changed CIS) angle =     96.00
            ch:AA   res: 167  ARG              --> 168  LEU
  WARNING : TRANS peptide bond (not be changed CIS) angle =    121.62
            ch:AA   res: 195  LYS              --> 196  VAL
  --------------------------------
  --- title of input coord file ---

  PDB_code:XXXX
  PDB_name:----
  PDB_date:12-AUG-15
  --------------------------------
  Number of chains                  :       1
  Total number of monomers          :     214
  Number of atoms                   :    3344
  Number of missing atoms           :       0
  Number of rebuilt atoms           :    1688
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0


 loop_
     _atom_type_symbol
     _atom_type_scat_Cromer_Mann_a1
     _atom_type_scat_Cromer_Mann_b1
     _atom_type_scat_Cromer_Mann_a2
     _atom_type_scat_Cromer_Mann_b2
     _atom_type_scat_Cromer_Mann_a3
     _atom_type_scat_Cromer_Mann_b3
     _atom_type_scat_Cromer_Mann_a4
     _atom_type_scat_Cromer_Mann_b4
     _atom_type_scat_Cromer_Mann_c


  N      0.1022   0.2451   0.3219   1.7481   0.7982   6.1925   0.8197  17.3894   0.0000
  C      0.0893   0.2465   0.2563   1.7100   0.7570   6.4094   1.0487  18.6113   0.0000
  H      0.0349   0.5347   0.1201   3.5867   0.1970  12.3471   0.0573  18.9525   0.0000
  S      0.2497   0.2681   0.5628   1.6711   1.3899   7.0267   2.1865  19.5377   0.0000
  O      0.0974   0.2067   0.2921   1.3815   0.6910   4.6943   0.6990  12.7105   0.0000


 Number of distances         :           0
 Number of angles            :           0
 Number of torsions          :           0
 Number of planes            :           0
 Number of chirals           :           0
 Number of intervals         :           0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
                        Standard  External       All
                Bonds:      3303         0      3303
               Angles:      5940         0      5940
              Chirals:       254         0       254
               Planes:       431         0       431
             Torsions:      1210         0      1210
            Intervals:         0         0         0
--------------------------------------------------------------------------------


  Number of harmonic restraints       =            0
  Number of atoms in special position =            0
 -----------------------------------------------------



     CGMAT cycle number =      1

    ****                         Bond distance outliers                         ****

Bond distance deviations from the ideal >10.000Sigma will be monitored

A     30 SER C   . - A     31 THR N   . mod.= 1.703 id.= 1.329 dev= -0.374 sig.= 0.014
A     94 ASP C   . - A     95 ALA N   . mod.= 1.726 id.= 1.329 dev= -0.397 sig.= 0.014
A     99 ALA C   . - A    100 GLY N   . mod.= 1.595 id.= 1.329 dev= -0.266 sig.= 0.014
A    101 ILE C   . - A    102 ASN N   . mod.= 1.708 id.= 1.329 dev= -0.379 sig.= 0.014
A    105 TYR C   . - A    106 VAL N   . mod.= 1.629 id.= 1.329 dev= -0.300 sig.= 0.014
A    113 ASP C   . - A    114 GLU N   . mod.= 1.646 id.= 1.329 dev= -0.317 sig.= 0.014
A    124 ARG C   . - A    125 VAL N   . mod.= 1.688 id.= 1.329 dev= -0.359 sig.= 0.014
A    140 PRO C   . - A    141 LYS N   . mod.= 1.547 id.= 1.329 dev= -0.218 sig.= 0.014
A    152 GLU C   . - A    153 LEU N   . mod.= 1.639 id.= 1.329 dev= -0.310 sig.= 0.014
A    190 ASN C   . - A    191 THR N   . mod.= 1.715 id.= 1.329 dev= -0.386 sig.= 0.014

    ****                         Torsion angle outliers                         ****

Torsion angle deviations from the ideal >10.000Sigma will be monitored

A     13 LYS CA    - A     14 GLY CA    mod.= 111.37 id.= 180.00 per.= 1 dev=  68.63 sig.=   5.00
A     62 GLU CA    - A     63 LEU CA    mod.=-125.84 id.=   0.00 per.= 1 dev= 125.84 sig.=   5.00
A     72 ILE CA    - A     73 ALA CA    mod.=-141.03 id.=   0.00 per.= 1 dev= 141.03 sig.=   5.00
A    129 SER CA    - A    130 GLY CA    mod.= -76.36 id.=   0.00 per.= 1 dev=  76.36 sig.=   5.00
A    152 GLU CA    - A    153 LEU CA    mod.=-108.86 id.= 180.00 per.= 1 dev= -71.14 sig.=   5.00
A    167 ARG CA    - A    168 LEU CA    mod.=  96.00 id.=   0.00 per.= 1 dev= -96.00 sig.=   5.00
A    195 LYS CA    - A    196 VAL CA    mod.=-121.62 id.=   0.00 per.= 1 dev= 121.62 sig.=   5.00

    ****                         Chiral volume outliers                         ****

Chiral volume deviations from the ideal >10.000Sigma will be monitored

A     20 ILE CB    mod.=   0.40 id.=   2.64 dev=  2.241 sig.=  0.200
A     38 ALA CA    mod.=  -0.44 id.=  -2.48 dev= -2.039 sig.=  0.200
A     41 SER CA    mod.=  -0.50 id.=  -2.50 dev= -2.003 sig.=  0.200
A     89 THR CB    mod.=  -0.09 id.=   2.55 dev=  2.646 sig.=  0.200
A    168 LEU CA    mod.=   1.98 id.=  -2.50 dev= -4.482 sig.=  0.200
A    173 GLN CA    mod.=   0.14 id.=  -2.50 dev= -2.644 sig.=  0.200
A    209 LEU CA    mod.=  -0.34 id.=  -2.50 dev= -2.166 sig.=  0.200

    ****                Large deviation of atoms from planarity                 ****

Deviations from the planarity >10.000Sigma will be monitored
Atom: A     13 LYS C     deviation=  -0.21 sigma.=   0.02
Atom: A     86 PHE HE2   deviation=  -0.21 sigma.=   0.02
Atom: A     99 ALA C     deviation=   0.35 sigma.=   0.02
Atom: A    105 TYR C     deviation=  -0.25 sigma.=   0.02
Atom: A    119 ARG C     deviation=   0.23 sigma.=   0.02
Atom: A    133 TYR HE2   deviation=  -0.31 sigma.=   0.02
Atom: A    133 TYR HD2   deviation=   0.36 sigma.=   0.02
Atom: A    137 PHE HE1   deviation=  -0.28 sigma.=   0.02
Atom: A    152 GLU C     deviation=  -0.33 sigma.=   0.02
Atom: A    190 ASN C     deviation=   0.25 sigma.=   0.02

    ****                              VDW outliers                              ****

VDW deviations from the ideal >10.000Sigma or dist <  1.000 will be monitored

A     42 GLY C   . - A     43 SER H   . mod.= 0.993 id.= 2.950 dev= -1.96 sig.= 0.20 sym.=  1  0  0  0 ncs  -1 type =  1
A     42 GLY C   . - A     43 SER H   . mod.= 0.993 id.= 2.950 dev= -1.96 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1
A     56 GLY H   . - A     57 LYS H   . mod.= 0.744 id.= 2.400 dev= -1.66 sig.= 0.20 sym.=  1  0  0  0 ncs  -1 type =  1
A     56 GLY H   . - A     57 LYS H   . mod.= 0.744 id.= 2.400 dev= -1.66 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1
A    185 GLU C   . - A    186 ALA H   . mod.= 0.872 id.= 2.950 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs  -1 type =  1
A    185 GLU C   . - A    186 ALA H   . mod.= 0.872 id.= 2.950 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1
A    213 LEU C   . - A    214 GLY H   . mod.= 0.951 id.= 2.950 dev= -2.00 sig.= 0.20 sym.=  1  0  0  0 ncs  -1 type =  1
A    213 LEU C   . - A    214 GLY H   . mod.= 0.951 id.= 2.950 dev= -2.00 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 function value    50828.6289    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1639     0.058     0.020
Bond distances: others                         1664     0.000     0.020
Bond angles  : refined atoms                   2140     7.134     1.998
Bond angles  : others                          3800     5.089     3.000
Torsion angles, period  1. refined              172    26.259     5.000
Torsion angles, period  2. refined               75    39.357    24.533
Torsion angles, period  3. refined              313    24.545    15.000
Torsion angles, period  4. refined               13    22.106    15.000
Chiral centres: refined atoms                   254     0.570     0.200
Planar groups: refined atoms                   1600     0.039     0.021
Planar groups: others                           303     0.060     0.020
VDW repulsions: refined_atoms                  1330     0.505     0.200
VDW repulsions.others                          3858     0.382     0.200
VDW; torsion: refined_atoms                    1252     0.289     0.200
VDW; torsion.others                            2076     0.201     0.200
HBOND: refined_atoms                            184     0.309     0.200
HBOND.others                                     16     0.238     0.200
-------------------------------------------------------------------------------
 Trying gamma equal    0.00000000    
 Trying gamma equal    5.00000007E-02
 Gamma decreased to    3.99999991E-02


 fvalues    0.00000000       50828.6289       14187.1582       50828.6289    


     CGMAT cycle number =      2

 function value    14187.1582    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1639     0.023     0.020
Bond distances: others                         1664     0.020     0.020
-------------------------------------------------------------------------------
 Trying gamma equal    3.99999991E-02
 Gamma decreased to    3.09090894E-02


 fvalues    0.00000000       14187.1582       8367.32324       14187.1582    


     CGMAT cycle number =      3

 function value    8367.32324    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1639     0.013     0.020
Bond distances: others                         1664     0.008     0.020
-------------------------------------------------------------------------------
 Trying gamma equal    3.09090894E-02
 Gamma decreased to    2.26446278E-02


 fvalues    0.00000000       8367.32324       6512.79736       8367.32324    


     CGMAT cycle number =      4

 function value    6512.79736    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1639     0.010     0.020
Bond distances: others                         1664     0.006     0.020
-------------------------------------------------------------------------------
 Trying gamma equal    2.26446278E-02
 Gamma decreased to    1.51314801E-02


 fvalues    0.00000000       6512.79736       5399.99658       6512.79736    


     CGMAT cycle number =      5

    ****                         Torsion angle outliers                         ****

Torsion angle deviations from the ideal >10.000Sigma will be monitored

A     62 GLU CA    - A     63 LEU CA    mod.= -81.36 id.=   0.00 per.= 1 dev=  81.36 sig.=   5.00
A     72 ILE CA    - A     73 ALA CA    mod.=-125.90 id.=   0.00 per.= 1 dev= 125.90 sig.=   5.00
A    167 ARG CA    - A    168 LEU CA    mod.=  53.39 id.=   0.00 per.= 1 dev= -53.39 sig.=   5.00
A    195 LYS CA    - A    196 VAL CA    mod.= -81.43 id.=   0.00 per.= 1 dev=  81.43 sig.=   5.00

    ****                         Chiral volume outliers                         ****

Chiral volume deviations from the ideal >10.000Sigma will be monitored

A    168 LEU CA    mod.=   0.76 id.=  -2.50 dev= -3.267 sig.=  0.200

 function value    5399.99658    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1639     0.009     0.020
Bond distances: others                         1664     0.005     0.020
Bond angles  : refined atoms                   2140     1.816     1.998
Bond angles  : others                          3800     1.334     3.000
Torsion angles, period  1. refined              172    16.217     5.000
Torsion angles, period  2. refined               75    38.297    24.533
Torsion angles, period  3. refined              313    20.923    15.000
Torsion angles, period  4. refined               13    18.743    15.000
Chiral centres: refined atoms                   254     0.252     0.200
Planar groups: refined atoms                   1600     0.006     0.021
Planar groups: others                           303     0.003     0.020
VDW repulsions: refined_atoms                   884     0.239     0.200
VDW repulsions.others                          3378     0.163     0.200
VDW; torsion: refined_atoms                    1352     0.159     0.200
VDW; torsion.others                            1764     0.082     0.200
HBOND: refined_atoms                            122     0.154     0.200
HBOND.others                                      2     0.011     0.200
-------------------------------------------------------------------------------
 Trying gamma equal    1.51314801E-02
 Gamma decreased to    8.30134563E-03


 fvalues    0.00000000       5399.99658       4656.86816       5399.99658    
  Time in seconds: CPU =         2.07
             Elapsed =           0.00

    ****           Things for loggraph, R factor and others vs cycle            ****


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS:<Rfactor> vs cycle :N:1,2,3:
:FOM vs cycle :N:1,4:
:-LL vs cycle :N:1,5:
:-LLfree vs cycle :N:1,6:
:Geometry vs cycle:N:1,7,8,9,10,11:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.0      0.0      0.0             0.       0.0   0.0582  3.194   7.134  3.622   0.570
       1   0.0      0.0      0.0             0.       0.0   0.0233  1.184   3.221  1.492   0.350
       2   0.0      0.0      0.0             0.       0.0   0.0135  0.674   2.341  1.047   0.312
       3   0.0      0.0      0.0             0.       0.0   0.0103  0.516   1.999  0.898   0.279
       4   0.0      0.0      0.0             0.       0.0   0.0086  0.434   1.816  0.822   0.252
 $$
 $TEXT:Result: $$ Final results $$
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
 Refmac_5.8.0131:  End of Refmac_5.8.0131  
Times: User:       8.0s System:    0.1s Elapsed:     0:08  
</pre>
</html>
<!--SUMMARY_END--></FONT></B>


CCP-EM job finished: Wednesday, 12. August 2015 10:33AM ______________________
_______________________________________________________________________________

_________ CCP-EM Job launch/home/tom/Code/devtools/install/bin/refmac5 ________



CCP-EM pipeline job 8 of 10 ___________________________________________________

__ Command ____________________________________________________________________
/home/tom/Code/devtools/install/bin/refmac5 xyzin /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/1AKE_cha_molrep_refine_shaken_refine.pdb xyzout /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/1AKE_cha_molrep_refine_shaken_refine_rframe.pdb mapin /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc mapref /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc atomsf /home/tom/Code/devtools/checkout/refmac5.8/data/atomsf_electron.lib << eof
/home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/job_data/stdin_map2mtz.txt
eof
_______________________________________________________________________________
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<html> <!-- CCP4 HTML LOGFILE -->
<hr>
<!--SUMMARY_END--></FONT></B>
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<pre>
 
 ###############################################################
 ###############################################################
 ###############################################################
 ### CCP4 6.5.011: Refmac_5.8.0131 version 5.8.0131 : 06/08/15##
 ###############################################################
 User: unknown  Run date: 12/ 8/2015 Run time: 10:33:24 


 Please reference: Collaborative Computational Project, Number 4. 2011.
 "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242.
 as well as any specific reference in the program write-up.

<!--SUMMARY_END--></FONT></B>
 $TEXT:Reference1: $$ Main reference $$ 
   "REFMAC5 for the refinement of macromolecular crystal structures:"
   G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011) 
   Acta Crystallogr. D67, 355-367

 $$
 $SUMMARY :Reference1:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference2: $$ Secondary reference $$ 
   "Refinement of Macromolecular Structures by the  Maximum-Likelihood Method:"
   G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
   Acta Crystallogr. D53, 240-255
   EU  Validation contract: BIO2CT-92-0524

 $$
 $SUMMARY :Reference2:  $$ Refmac: $$
 :TEXT:Reference2: $$

 Data line--- mode sfcalc
 Data line--- source EM
 Data line--- sfcalc mrad 4.0
 Data line--- sfcalc shift
 Data line--- end
  Data line--- mode sfcalc
  Data line--- source EM
  Data line--- sfcalc mrad 4.0
  Data line--- sfcalc shift
  Data line--- END
===> Warning: Reflections file has not been defined
===> Warning: Switching to the idealisation mode

    ****                     Input and Default parameters#                      ****


Input coordinate file.  Logical name - XYZIN actual file name  - /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/1AKE_cha_molrep_refine_shaken_refine.pdb
Output coordinate file. Logical name - XYZOUT actual file name - /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/1AKE_cha_molrep_refine_shaken_refine_rframe.pdb

  Refinement type                        : Idealisation
  Refinement type                        : NONE
  SF calculation from MAP: /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc
  SF calculation from CRD: /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/1AKE_cha_molrep_refine_shaken_refine.pdb


    ****                           Makecif parameters                           ****

Dictionary files for restraints : /usr/local/sci_local/mx/ccp4-6.5/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /usr/local/sci_local/mx/ccp4-6.5/lib/data/monomers/ener_lib.cif
    Apart from amino acids and DNA/RNA all monomers will be checked to see if atom names and connectivity is correct
    Hydrogens will be restored in their riding positions
    Links between monomers will be checked. Only those links present in the coordinate file will be used
    Standard sugar links will be analysed and used
    For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
    Symmetry related links will be analysed and used
    Cis peptides will be found and used automatically




Monitoring style is "MEDIUM". Complete information will be printed out in the
first and last cycle. In all other cycles minimum information will be printed out
Sigma cutoffs for printing out outliers
If deviation of restraint parameter > alpha*sigma then information will be printed out
Distance outliers      10.000
Angle outliers         10.000
Torsion outliers       10.000
Chiral volume outliers 10.000
Plane outliers         10.000
Non-bonding outliers   10.000
---------------------------------------------------------------

 Input file :/home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/re
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.44
 _lib_update       30/05/14
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 11608
                with complete description    : 11608
  NUMBER OF MODIFICATIONS                    :    61
  NUMBER OF LINKS                            :    71
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )

FORMATTED      OLD     file opened on unit  45
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
Logical name: ATOMSF, Filename: /home/tom/Code/devtools/checkout/refmac5.8/data/atomsf_electron.lib
<!--SUMMARY_END--></FONT></B>

  Number of atoms    :    1656
  Number of residues :     214
  Number of chains   :       1
  I am reading library. Please wait.
                mon_lib.cif
  WARNING : TRANS peptide bond (not be changed CIS) angle =    119.74
            ch:AA   res:  72  ILE              -->  73  ALA
  --------------------------------
  --- title of input coord file ---

  PDB_code:XXXX
  PDB_name:----
  PDB_date:12-AUG-15
  --------------------------------
  Number of chains                  :       1
  Total number of monomers          :     214
  Number of atoms                   :    3344
  Number of missing atoms           :       0
  Number of rebuilt atoms           :    1688
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0


 loop_
     _atom_type_symbol
     _atom_type_scat_Cromer_Mann_a1
     _atom_type_scat_Cromer_Mann_b1
     _atom_type_scat_Cromer_Mann_a2
     _atom_type_scat_Cromer_Mann_b2
     _atom_type_scat_Cromer_Mann_a3
     _atom_type_scat_Cromer_Mann_b3
     _atom_type_scat_Cromer_Mann_a4
     _atom_type_scat_Cromer_Mann_b4
     _atom_type_scat_Cromer_Mann_a5
     _atom_type_scat_Cromer_Mann_b5


  N      0.1022   0.2451   0.3219   1.7481   0.7982   6.1925   0.8197  17.3894   0.1715  48.1431
  C      0.0893   0.2465   0.2563   1.7100   0.7570   6.4094   1.0487  18.6113   0.3575  50.2523
  H      0.0116   0.5347   0.0400   3.5867   0.0657  12.3471   0.0191  18.9525   0.0398  38.6269
  S      0.2497   0.2681   0.5628   1.6711   1.3899   7.0267   2.1865  19.5377   0.7715  50.3888
  O      0.0974   0.2067   0.2921   1.3815   0.6910   4.6943   0.6990  12.7105   0.2039  32.4726


 Number of distances         :           0
 Number of angles            :           0
 Number of torsions          :           0
 Number of planes            :           0
 Number of chirals           :           0
 Number of intervals         :           0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
                        Standard  External       All
                Bonds:      3303         0      3303
               Angles:      5940         0      5940
              Chirals:       254         0       254
               Planes:       431         0       431
             Torsions:      1210         0      1210
            Intervals:         0         0         0
--------------------------------------------------------------------------------


  Number of harmonic restraints       =            0
  Number of atoms in special position =            0
 -----------------------------------------------------

 Map file here /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc

 Logical Name: /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc   Filename: /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc 

File name for input map file on unit  10 : /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc
file size 56320 ; logical name /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc



           Number of columns, rows, sections ...............   24   24   24
           Map mode ........................................    2
           Start and stop points on columns, rows, sections     0   23    0   23    0   23
           Grid sampling on x, y, z ........................   24   24   24
           Cell dimensions .................................   66.0000    66.0000    66.0000    90.0000    90.0000    90.0000
           Fast, medium, slow axes .........................    X    Y    Z
           Minimum density .................................     0.00000
           Maximum density .................................    43.92188
           Mean density ....................................     3.79930
           Rms deviation from mean density .................     9.01953
           Space-group .....................................    1
           Number of titles ................................    1


     Labels:                            
  MODIM M CCP4    Chimera 1.3.2570 Mon Sep  7 14:1                    ?    ?


 nsym 1           1
 res max nominal    5.50000000      res max used    5.51102161    
 Map manupilation mode = M
 reference map

  Reference structure factors will be calculated from the map: /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc

 Logical Name: /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc   Filename: /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc 

File name for input map file on unit  10 : /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc
file size 56320 ; logical name /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc



           Number of columns, rows, sections ...............   24   24   24
           Map mode ........................................    2
           Start and stop points on columns, rows, sections     0   23    0   23    0   23
           Grid sampling on x, y, z ........................   24   24   24
           Cell dimensions .................................   66.0000    66.0000    66.0000    90.0000    90.0000    90.0000
           Fast, medium, slow axes .........................    X    Y    Z
           Minimum density .................................     0.00000
           Maximum density .................................    43.92188
           Mean density ....................................     3.79930
           Rms deviation from mean density .................     9.01953
           Space-group .....................................    1
           Number of titles ................................    1


     Labels:                            
  MODIM M CCP4    Chimera 1.3.2570 Mon Sep  7 14:1                    ?    ?


 nsym            1
 Start reading            0           0           0          23          23          23
 After map_reader_0           24          24          24           1           1
 After redalli
 Starting reso    9.07272771E-02   5.51102161    
 RelVol    20.7968750    
 Number of resolution bins            9

  The number of bins for reference SF :           9

 Logical Name: /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc   Filename: /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc 

File name for input map file on unit  10 : /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc
file size 56320 ; logical name /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc



           Number of columns, rows, sections ...............   24   24   24
           Map mode ........................................    2
           Start and stop points on columns, rows, sections     0   23    0   23    0   23
           Grid sampling on x, y, z ........................   24   24   24
           Cell dimensions .................................   66.0000    66.0000    66.0000    90.0000    90.0000    90.0000
           Fast, medium, slow axes .........................    X    Y    Z
           Minimum density .................................     0.00000
           Maximum density .................................    43.92188
           Mean density ....................................     3.79930
           Rms deviation from mean density .................     9.01953
           Space-group .....................................    1
           Number of titles ................................    1


     Labels:                            
  MODIM M CCP4    Chimera 1.3.2570 Mon Sep  7 14:1                    ?    ?


 Starting (nominal) resolution    9.07272771E-02   5.51102161    
 Number of all maps for SF calculation :           1
 Map file number 1 /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc
 File number            1 /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc
 nsym            1
 Start reading            0           0           0          23          23          23
 logname : MAPIN1 file name: 
 Number of maps            1

 Structure factors will be sharpened using reference map/curveR 

   Map maximum =    823.776184    
   Map minimum =   -83.4723816    
   Map mean    =   -5.52176316E-05
   Map rmsd    =    187.567963    

 Print stats of the original data to the file: orig_data_rescut.txt
 Number of resolution bins            9

    ****      Mean(|F|) and other statistics: Without accounting for mask       ****

 $TABLE: Mean(|F|) and other statistics
 $GRAPH: Mean(|F|), Mean(|F|^2), Mean(|F|^4) vs resolutions: 1,6,7,8
 $$
 2sin(th)/l 2sin(th)/l dmin dmax NREF Mn(|F|) Mn(|F|^2) Mn(|F|^4) Mn(A) Mn(B) Mn(A^2) Mn(B^2) cor(A,B)
 $$
   2.29558413E-04   3.82614089E-03   66.0014420       16.1666298             128   95328.2500       2.40946852E+10   6.51926839E+21  -3696.90869       307.820740       2.09389629E+10   3.15573555E+09 -0.512377143    
   3.82614089E-03   7.42271356E-03   16.1666298       11.6069651             247   23897.9883       750422208.       1.41633329E+18  -261.609009       112.736351       330608384.       419813984.       7.18705133E-02
   7.42271356E-03   1.10192858E-02   11.6069651       9.52627850             307   12450.3135       206873024.       1.03798047E+17  -73.2363052       10.8966894       97557008.0       109315952.      -5.62837981E-02
   1.10192858E-02   1.46158580E-02   9.52627850       8.27156830             369   6129.10352       49164156.0       5.34098511E+15   6.69177151       43.2775269       24954084.0       24210060.0      -4.54078652E-02
   1.46158580E-02   1.82124302E-02   8.27156830       7.40996313             421   3312.30225       14152484.0       3.99343543E+14   75.5258026       13.9446774       6491955.50       7660535.50      -2.25085244E-02
   1.82124302E-02   2.18090024E-02   7.40996313       6.77145624             471   2022.59546       5340126.00       5.99383574E+13  -41.9749718      -23.0784550       2560635.00       2779489.75      0.110711731    
   2.18090024E-02   2.54055746E-02   6.77145624       6.27386951             529   1284.58362       2186623.25       1.09444417E+13  -12.4967918      -8.95258045       1030568.06       1156055.25      0.151062414    
   2.54055746E-02   2.90021468E-02   6.27386951       5.87198448             543   879.239746       1073904.25       2.86502106E+12   8.87541771       11.1791744       520015.625       553887.938      0.165690720    
   2.90021468E-02   3.26087289E-02   5.87198448       5.53774643             546   633.729736       586554.312       1.20355317E+12   19.7794971      -5.89431477       268104.031       318450.719       1.60751659E-02
 $$
 sharpening things:            0           1   0.00000000       0.00000000    

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: starting_map.mtz   Filename: starting_map.mtz 

 New limits for the box
           1           1           1
          21          19          21


 Box limits :
           1           1           1
          21          19          21
 New grid   :          22          20          22
 New cell   :   60.5000000       55.0000000       60.5000000       90.0000000       90.0000000       90.0000000    
 Shifts     :  -0.00000000      -0.00000000      -0.00000000    

 Testing in apply mask    1.52181013E-42          24          24          24   1.00000000    
        2523           1
 sharpening things:            0           1   0.00000000       0.00000000    

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: masked_fs.mtz   Filename: masked_fs.mtz 

  Time in seconds: CPU =         0.04
             Elapsed =           0.00

    ****           Things for loggraph, R factor and others vs cycle            ****


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS:<Rfactor> vs cycle :N:1,2,3:
:FOM vs cycle :N:1,4:
:-LL vs cycle :N:1,5:
:-LLfree vs cycle :N:1,6:
:Geometry vs cycle:N:1,7,8,9,10,11:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
 $$
 $TEXT:Result: $$ Final results $$
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
 Refmac_5.8.0131:  End of Refmac_5.8.0131  
Times: User:       5.9s System:    0.1s Elapsed:     0:06  
</pre>
</html>
<!--SUMMARY_END--></FONT></B>


CCP-EM job finished: Wednesday, 12. August 2015 10:33AM ______________________
_______________________________________________________________________________

_________ CCP-EM Job launch/home/tom/Code/devtools/install/bin/refmac5 ________



CCP-EM pipeline job 9 of 10 ___________________________________________________

__ Command ____________________________________________________________________
/home/tom/Code/devtools/install/bin/refmac5 xyzin /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/1AKE_cha_molrep_refine_shaken_refine_rframe.pdb hklin masked_fs.mtz xyzout /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/job_data/fsc_out.pdb hklout /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/job_data/fsc_out.mtz atomsf /home/tom/Code/devtools/checkout/refmac5.8/data/atomsf_electron.lib << eof
/home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/job_data/stdin_model_fsc.txt
eof
_______________________________________________________________________________
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<html> <!-- CCP4 HTML LOGFILE -->
<hr>
<!--SUMMARY_END--></FONT></B>
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<pre>
 
 ###############################################################
 ###############################################################
 ###############################################################
 ### CCP4 6.5.011: Refmac_5.8.0131 version 5.8.0131 : 06/08/15##
 ###############################################################
 User: unknown  Run date: 12/ 8/2015 Run time: 10:33:30 


 Please reference: Collaborative Computational Project, Number 4. 2011.
 "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242.
 as well as any specific reference in the program write-up.

<!--SUMMARY_END--></FONT></B>
 $TEXT:Reference1: $$ Main reference $$ 
   "REFMAC5 for the refinement of macromolecular crystal structures:"
   G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011) 
   Acta Crystallogr. D67, 355-367

 $$
 $SUMMARY :Reference1:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference2: $$ Secondary reference $$ 
   "Refinement of Macromolecular Structures by the  Maximum-Likelihood Method:"
   G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
   Acta Crystallogr. D53, 240-255
   EU  Validation contract: BIO2CT-92-0524

 $$
 $SUMMARY :Reference2:  $$ Refmac: $$
 :TEXT:Reference2: $$

 Data line--- labin FP=Fout0 PHIB=Pout0
 Data line--- weight auto 10
 Data line--- RESO 10.0
 Data line--- solvent no
 Data line--- source EM
 Data line--- ncycle 1
 Data line--- end
  Data line--- labin FP=Fout0 PHIB=Pout0
  Data line--- weight auto 10
  Data line--- RESO 10.0
  Data line--- solvent no
  Data line--- source EM
  Data line--- ncycle 1
  Data line--- END

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN   Filename: masked_fs.mtz 

===> Warning: Figure of merit of phases has not been assigned
===> Warning: They will be assumed to be equal to 1.0

    ****                     Input and Default parameters#                      ****


Input coordinate file.  Logical name - XYZIN actual file name  - /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/1AKE_cha_molrep_refine_shaken_refine_rframe.pdb
Output coordinate file. Logical name - XYZOUT actual file name - /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/job_data/fsc_out.pdb
Input reflection file.  Logical name - HKLIN actual file name  - masked_fs.mtz
Output reflection file. Logical name - HKLOUT actual file name - /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/job_data/fsc_out.mtz

Cell from mtz :    60.500    55.000    60.500    90.000    90.000    90.000
Space group from mtz: number -    1; name - P 1

  Refinement type                        : Restrained

    ****                           Makecif parameters                           ****

Dictionary files for restraints : /usr/local/sci_local/mx/ccp4-6.5/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /usr/local/sci_local/mx/ccp4-6.5/lib/data/monomers/ener_lib.cif
    Apart from amino acids and DNA/RNA all monomers will be checked to see if atom names and connectivity is correct
    Hydrogens will be restored in their riding positions
    Links between monomers will be checked. Only those links present in the coordinate file will be used
    Standard sugar links will be analysed and used
    For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
    Symmetry related links will be analysed and used
    Cis peptides will be found and used automatically


  Residual                               : Phase modified Maximum Likelihood for Fs
 Phase Blurred by  Scale*Exp(-B s**2)    :    1.00    0.00

    ****                    Least-square scaling parameters                     ****

Overall scale
Overall B value
Overall anisotropic B with tr(B) = 0.0


    ****                 Map sharpening parameters and methods                  ****

No map sharpening will be performed

  Method of minimisation                 : Sparse Matrix
  Experimental sigmas used for weighting
  Number of Bins and width:    20       0.0005
  Refinement of individual isotropic Bfactors
  Refinement resln        :    60.5000  9.9998
  Estimated number of reflections :        823
  Auto weighting. An attempt
  Refinement cycles       :     1
  Scaling type                           :
          Bulk solvent using using Babinet principle

  Estimation of D/Sigma in resolution bins
  using  working set of reflns with experimental sigmas
  Input phases not used in SigmaA estimation

  Scaling and SigmaA resln:    60.5000  9.9998

  Damping factors:     1.0000  1.0000


    ****                    Geometry restraints and weights                     ****


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

 Planar groups (all and main chain)
          WEIGHT= 1.00 1.00

 Chiral centers
          Weight= 1.00

 NON-BONDED CONTACTS
          Overall weight                          =  1.00
          Sigma for simple VDW                    =  0.20
          Sigma for VDW trhough torsion angle     =  0.20
          Sigma for HBOND                         =  0.20
          Sigma for metal-ion                     =  0.20
          Sigma for DUMMY and other atom          =  0.30
          Distance for donor-accepetor = vdw1+vdw2+(-0.30)
          Distance for acceptor - H    = vdw1+     ( 0.10)
          VDW distance through torsion = vdw1+vdw2+(-0.30)
          Distance for DUMMY-others    = vdw1+vdw2+(-0.70)

 TORSION ANGLES
          Weight= 1.00

 THERMAL FACTORS
          Weight= 1.00
     Main chain bond (1-2 neighbour)          1.5A**2
     Main chain angle (1-3 neighbour)         2.0A**2
     Side chain bond                          3.0A**2
     Side chain angle                         4.5A**2

 RESTRAINTS AGAINST EXCESSIVE SHIFTS
     Positional parameters                   0.00A
     Thermal parameters                      0.00A
     Occupancy parameters                    0.00

 RADIUS OF CONFIDENCE
     Positional parameters 0.00A
     Thermal parameters    0.00A**2
     Occupancy parameters  0.00

Monitoring style is "MEDIUM". Complete information will be printed out in the
first and last cycle. In all other cycles minimum information will be printed out
Sigma cutoffs for printing out outliers
If deviation of restraint parameter > alpha*sigma then information will be printed out
Distance outliers      10.000
Angle outliers         10.000
Torsion outliers       10.000
Chiral volume outliers 10.000
Plane outliers         10.000
Non-bonding outliers   10.000
B value  outliers      10.000
---------------------------------------------------------------

 Input file :/home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/re
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.44
 _lib_update       30/05/14
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 11608
                with complete description    : 11608
  NUMBER OF MODIFICATIONS                    :    61
  NUMBER OF LINKS                            :    71
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )

FORMATTED      OLD     file opened on unit  45
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
Logical name: ATOMSF, Filename: /home/tom/Code/devtools/checkout/refmac5.8/data/atomsf_electron.lib
<!--SUMMARY_END--></FONT></B>

  Number of atoms    :    1656
  Number of residues :     214
  Number of chains   :       1
  I am reading library. Please wait.
                mon_lib.cif
  WARNING : TRANS peptide bond (not be changed CIS) angle =    119.74
            ch:AA   res:  72  ILE              -->  73  ALA
  --------------------------------
  --- title of input coord file ---

  PDB_code:XXXX
  PDB_name:----
  PDB_date:12-AUG-15
  --------------------------------
  Number of chains                  :       1
  Total number of monomers          :     214
  Number of atoms                   :    3344
  Number of missing atoms           :       0
  Number of rebuilt atoms           :    1688
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0


 loop_
     _atom_type_symbol
     _atom_type_scat_Cromer_Mann_a1
     _atom_type_scat_Cromer_Mann_b1
     _atom_type_scat_Cromer_Mann_a2
     _atom_type_scat_Cromer_Mann_b2
     _atom_type_scat_Cromer_Mann_a3
     _atom_type_scat_Cromer_Mann_b3
     _atom_type_scat_Cromer_Mann_a4
     _atom_type_scat_Cromer_Mann_b4
     _atom_type_scat_Cromer_Mann_a5
     _atom_type_scat_Cromer_Mann_b5


  N      0.1022   0.2451   0.3219   1.7481   0.7982   6.1925   0.8197  17.3894   0.1715  48.1431
  C      0.0893   0.2465   0.2563   1.7100   0.7570   6.4094   1.0487  18.6113   0.3575  50.2523
  H      0.0116   0.5347   0.0400   3.5867   0.0657  12.3471   0.0191  18.9525   0.0398  38.6269
  S      0.2497   0.2681   0.5628   1.6711   1.3899   7.0267   2.1865  19.5377   0.7715  50.3888
  O      0.0974   0.2067   0.2921   1.3815   0.6910   4.6943   0.6990  12.7105   0.2039  32.4726


 Number of distances         :           0
 Number of angles            :           0
 Number of torsions          :           0
 Number of planes            :           0
 Number of chirals           :           0
 Number of intervals         :           0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
                        Standard  External       All
                Bonds:      3303         0      3303
               Angles:      5940         0      5940
              Chirals:       254         0       254
               Planes:       431         0       431
             Torsions:      1210         0      1210
            Intervals:         0         0         0
--------------------------------------------------------------------------------


  Number of harmonic restraints       =            0
  Number of atoms in special position =            0
 -----------------------------------------------------


    ****                           Info from mtz file                           ****

FreeR flag                         -999
Number of "free" reflections          0
Number of   all  reflections        421
 Warning ==>The number of free reflections with flag         -999  is zero
 Warning ==> Switching off use of free R
--------------------------------------------------------------------------------
 Number of reflections in file       2523
 Number of reflections read            421


######  TLS Group Definitions ######



     CGMAT cycle number =      1

    ****                         Torsion angle outliers                         ****

Torsion angle deviations from the ideal >10.000Sigma will be monitored

A     62 GLU CA    - A     63 LEU CA    mod.= -68.14 id.=   0.00 per.= 1 dev=  68.14 sig.=   5.00
A     72 ILE CA    - A     73 ALA CA    mod.=-119.74 id.=   0.00 per.= 1 dev= 119.74 sig.=   5.00
A    195 LYS CA    - A    196 VAL CA    mod.= -69.88 id.=   0.00 per.= 1 dev=  69.88 sig.=   5.00

    ****                         Chiral volume outliers                         ****

Chiral volume deviations from the ideal >10.000Sigma will be monitored

A    168 LEU CA    mod.=   0.50 id.=  -2.50 dev= -3.001 sig.=  0.200

 Limits of asymmetric unit      : 1.00 1.00 1.00
 Grid spacing to be used        :    56   54   56
 Maximuum H,K,L                 :     7    6    7
 Minimum acceptable grid spacing:    37   34   37
 File opened           20
 Weight matrix    9.11904772E-06
 Actual weight    10.0000000      is applied to the X-ray term
Norm of X_ray positional gradient                1.08
Norm of Geom. positional gradient                36.5
Norm of X_ray B-factor gradient                 0.477
Norm of Geom. B-factor gradient                 0.552E+05
Product of X_ray and Geom posit. gradients     -0.275E+04
 Cosine of angle between them                      -0.007
Product of X_ray and Geom B-fact gradients      0.279E+05
 Cosine of angle between them                       0.000


Residuals: XRAY=    -0.1414E+06 GEOM=     0.5138E+06 TOTAL=     0.3725E+06
 function value    372467.500    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1639     0.009     0.020
Bond distances: others                         1664     0.000     0.020
Bond angles  : refined atoms                   2140     1.692     1.998
Bond angles  : others                          3800     3.603     3.000
Torsion angles, period  1. refined              172    14.683     5.000
Torsion angles, period  2. refined               75    37.311    24.533
Torsion angles, period  3. refined              313    20.171    15.000
Torsion angles, period  4. refined               13    17.885    15.000
Chiral centres: refined atoms                   254     0.234     0.200
Planar groups: refined atoms                   1600     0.005     0.021
Planar groups: others                           303     0.003     0.020
VDW repulsions: refined_atoms                   830     0.214     0.200
VDW repulsions.others                          3210     0.226     0.200
VDW; torsion: refined_atoms                    1366     0.154     0.200
VDW; torsion.others                            1608     0.102     0.200
HBOND: refined_atoms                            118     0.136     0.200
HBOND.others                                      4     0.088     0.200
M. chain bond B values: refined atoms           814     2.190    21.423
M. chain bond B values: others                  813     2.189    21.420
M. chain angle B values: refined atoms          944     3.952    32.159
M. chain angle B values: others                 945     3.950    32.162
S. chain bond B values: refined atoms           825     2.132    21.544
S. chain bond B values: others                  825     2.132    21.544
S. chain angle B values: refined atoms         1196     3.783    32.271
S. chain angle B values: others                1196     3.781    32.271
Long range B values: refined atoms             1737     7.957   165.661
Long range B values: others                    1738     7.973   165.692
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale = 4418.763, B  = 115.499
Overall anisotropic scale factors
   B11 =  1.53 B22 =  3.84 B33 = -5.37 B12 = -8.28 B13 =  0.17 B23 = -3.26
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1. M(Rfactor) v. resln :N:1,6,7:
:Cycle    1. M(Fobs) and M(Fc) v. resln :N:1,4,5:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used $$
$$
 0.001       9 100.00  1574.3  1591.5  0.04  0.04
 0.001       6 100.00   525.9   499.8  0.12  0.12
 0.001      21 100.00   272.9   297.5  0.14  0.14
 0.002       6 100.00   291.1   292.1  0.10  0.10
 0.002      18 100.00   277.8   266.5  0.06  0.06
 0.003      17 100.00   261.9   234.4  0.12  0.12
 0.003      16 100.00   194.4   180.5  0.13  0.13
 0.004      24 100.00   122.2   121.3  0.14  0.14
 0.004      14 100.00   155.6   139.4  0.14  0.14
 0.005      22 100.00   141.9   132.4  0.11  0.11
 0.005      21 100.00   111.4   109.0  0.12  0.12
 0.006      32 100.00   110.5   109.7  0.14  0.14
 0.006      16 100.00   108.1   105.4  0.10  0.10
 0.007      22 100.00   113.4   106.6  0.11  0.11
 0.007      32 100.00    79.7    85.4  0.18  0.18
 0.008      28 100.00    87.0    89.7  0.15  0.15
 0.008      41 100.00    84.5    88.5  0.16  0.16
 0.009      14 100.00    57.0    63.3  0.23  0.23
 0.009      20 100.00    60.2    65.2  0.26  0.26
 0.010      42 100.00    53.6    57.1  0.22  0.22
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle    1. FSC and  Fom(<cos(DelPhi)>-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCwork CorrFofcWork$$
 $$
  0.0005      9   0.998      0   0.000      9   0.998  0.919  0.9976  0.9990
  0.0010      6   0.992      0   0.000      6   0.992  0.877  0.9435  0.9553
  0.0015     21   0.990      0   0.000     21   0.990  0.837  0.9433  0.9653
  0.0020      6   0.990      0   0.000      6   0.990  0.813  0.9149  0.9630
  0.0025     18   0.990      0   0.000     18   0.990  0.784  0.8849  0.9919
  0.0029     17   0.990      0   0.000     17   0.990  0.768  0.9423  0.9750
  0.0034     16   0.989      0   0.000     16   0.989  0.745  0.7051  0.9197
  0.0039     24   0.988      0   0.000     24   0.988  0.726  0.8065  0.9542
  0.0044     14   0.989      0   0.000     14   0.989  0.708  0.8327  0.9661
  0.0049     22   0.989      0   0.000     22   0.989  0.693  0.9009  0.9777
  0.0054     21   0.988      0   0.000     21   0.988  0.677  0.6746  0.9523
  0.0059     32   0.988      0   0.000     32   0.988  0.663  0.7761  0.9594
  0.0064     16   0.988      0   0.000     16   0.988  0.645  0.5489  0.9542
  0.0068     22   0.988      0   0.000     22   0.988  0.635  0.6235  0.9611
  0.0073     32   0.988      0   0.000     32   0.988  0.620  0.8365  0.9402
  0.0078     28   0.988      0   0.000     28   0.988  0.605  0.6324  0.9369
  0.0083     41   0.988      0   0.000     41   0.988  0.592  0.7291  0.9280
  0.0088     14   0.988      0   0.000     14   0.988  0.580  0.1751  0.9009
  0.0093     20   0.988      0   0.000     20   0.988  0.569  0.5837  0.8997
  0.0098     42   0.988      0   0.000     42   0.988  0.557  0.4992  0.8895
 $$
Resolution limits                    =     60.500    10.000
Number of used reflections           =        421
Percentage observed                  =   100.0000
Percentage of free reflections       =     0.0000
Overall R factor                     =     0.1143
Average Fourier shell correlation    =     0.7244
Overall weighted R factor            =     0.1143
Overall weighted R2 factor           =     0.0880
Average correlation coefficient      =     0.9437
Overall correlation coefficient      =     0.9947
Overall figure of merit              =     0.9887
ML based su of positional parameters =    21.3880
ML based su of thermal parameters    =  3837.1514
-----------------------------------------------------------------------------
 Trying gamma equal    0.00000000    
 Trying gamma equal    5.00000007E-02
 Gamma decreased to    3.99999991E-02


 fvalues   -14140.7070       513834.844      -102353.594       372427.781    

    ****                         Bond distance outliers                         ****

Bond distance deviations from the ideal >10.000Sigma will be monitored

A     56 GLY N   . - A     56 GLY H   . mod.= 1.229 id.= 1.010 dev= -0.219 sig.= 0.020
A    186 ALA N   . - A    186 ALA H   . mod.= 1.223 id.= 1.010 dev= -0.213 sig.= 0.020

    ****                         Torsion angle outliers                         ****

Torsion angle deviations from the ideal >10.000Sigma will be monitored

A     62 GLU CA    - A     63 LEU CA    mod.= -63.46 id.=   0.00 per.= 1 dev=  63.46 sig.=   5.00
A     72 ILE CA    - A     73 ALA CA    mod.=-115.72 id.=   0.00 per.= 1 dev= 115.72 sig.=   5.00
A    195 LYS CA    - A    196 VAL CA    mod.= -64.97 id.=   0.00 per.= 1 dev=  64.97 sig.=   5.00

    ****                         Chiral volume outliers                         ****

Chiral volume deviations from the ideal >10.000Sigma will be monitored

A    168 LEU CA    mod.=   0.33 id.=  -2.50 dev= -2.829 sig.=  0.200


 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/job_data/fsc_out.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1639     0.008     0.020
Bond distances: others                         1664     0.014     0.020
Bond angles  : refined atoms                   2140     1.675     1.998
Bond angles  : others                          3800     1.182     3.000
Torsion angles, period  1. refined              172    13.992     5.000
Torsion angles, period  2. refined               75    36.961    24.533
Torsion angles, period  3. refined              313    19.750    15.000
Torsion angles, period  4. refined               13    17.640    15.000
Chiral centres: refined atoms                   254     0.200     0.200
Planar groups: refined atoms                   1600     0.006     0.021
Planar groups: others                           303     0.002     0.020
VDW repulsions: refined_atoms                   794     0.206     0.200
VDW repulsions.others                          3426     0.167     0.200
VDW; torsion: refined_atoms                    1378     0.153     0.200
VDW; torsion.others                            1598     0.078     0.200
HBOND: refined_atoms                            110     0.135     0.200
M. chain bond B values: refined atoms           814     7.194    22.807
M. chain bond B values: others                  813     7.198    22.808
M. chain angle B values: refined atoms          944    10.785    34.465
M. chain angle B values: others                 945    10.779    34.462
S. chain bond B values: refined atoms           825     5.626    23.197
S. chain bond B values: others                  825     5.625    23.197
S. chain angle B values: refined atoms         1196     7.961    34.648
S. chain angle B values: others                1196     7.960    34.648
Long range B values: refined atoms             1718    16.498   176.521
Long range B values: others                    1719    16.499   176.546
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale = 4421.735, B  =  80.880
Overall anisotropic scale factors
   B11 =  1.73 B22 =  1.36 B33 = -3.09 B12 = -9.33 B13 =  1.28 B23 = -5.21
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle    2. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    2. M(Rfactor) v. resln :N:1,6,7:
:Cycle    2. M(Fobs) and M(Fc) v. resln :N:1,4,5:
:Cycle    2. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used $$
$$
 0.001       9 100.00  1573.2  1591.0  0.04  0.04
 0.001       6 100.00   525.5   499.2  0.12  0.12
 0.001      21 100.00   272.7   297.4  0.14  0.14
 0.002       6 100.00   290.9   291.9  0.10  0.10
 0.002      18 100.00   277.6   266.1  0.06  0.06
 0.003      17 100.00   261.7   232.7  0.13  0.13
 0.003      16 100.00   194.3   180.5  0.13  0.13
 0.004      24 100.00   122.1   121.5  0.14  0.14
 0.004      14 100.00   155.5   139.9  0.14  0.14
 0.005      22 100.00   141.8   132.5  0.12  0.12
 0.005      21 100.00   111.4   109.2  0.12  0.12
 0.006      32 100.00   110.4   109.6  0.13  0.13
 0.006      16 100.00   108.1   106.2  0.10  0.10
 0.007      22 100.00   113.4   107.6  0.11  0.11
 0.007      32 100.00    79.7    85.5  0.18  0.18
 0.008      28 100.00    86.9    89.4  0.15  0.15
 0.008      41 100.00    84.4    88.5  0.15  0.15
 0.009      14 100.00    57.0    64.4  0.22  0.22
 0.009      20 100.00    60.2    65.3  0.25  0.25
 0.010      42 100.00    53.5    56.5  0.23  0.23
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle    2. FSC and  Fom(<cos(DelPhi)>-acentric, centric, overall v resln:
 $GRAPHS:Cycle    2. M(Fom) v. resln :N:1,3,5,7,8,9,10:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCwork CorrFofcWork$$
 $$
  0.0005      9   0.998      0   0.000      9   0.998  0.920  0.9976  0.9990
  0.0010      6   0.992      0   0.000      6   0.992  0.879  0.9436  0.9554
  0.0015     21   0.990      0   0.000     21   0.990  0.840  0.9436  0.9648
  0.0020      6   0.990      0   0.000      6   0.990  0.816  0.9160  0.9615
  0.0025     18   0.990      0   0.000     18   0.990  0.788  0.8859  0.9909
  0.0029     17   0.990      0   0.000     17   0.990  0.772  0.9436  0.9749
  0.0034     16   0.989      0   0.000     16   0.989  0.750  0.7076  0.9188
  0.0039     24   0.988      0   0.000     24   0.988  0.731  0.8074  0.9521
  0.0044     14   0.989      0   0.000     14   0.989  0.714  0.8340  0.9648
  0.0049     22   0.989      0   0.000     22   0.989  0.699  0.9029  0.9788
  0.0054     21   0.988      0   0.000     21   0.988  0.684  0.6817  0.9508
  0.0059     32   0.988      0   0.000     32   0.988  0.670  0.7803  0.9613
  0.0064     16   0.988      0   0.000     16   0.988  0.652  0.5664  0.9541
  0.0068     22   0.988      0   0.000     22   0.988  0.643  0.6371  0.9641
  0.0073     32   0.988      0   0.000     32   0.988  0.628  0.8379  0.9447
  0.0078     28   0.988      0   0.000     28   0.988  0.613  0.6458  0.9422
  0.0083     41   0.988      0   0.000     41   0.988  0.601  0.7337  0.9294
  0.0088     14   0.988      0   0.000     14   0.988  0.589  0.2016  0.9169
  0.0093     20   0.988      0   0.000     20   0.988  0.578  0.6045  0.9092
  0.0098     42   0.988      0   0.000     42   0.988  0.567  0.5116  0.8867
 $$
Resolution limits                    =     60.500    10.000
Number of used reflections           =        421
Percentage observed                  =   100.0000
Percentage of free reflections       =     0.0000
Overall R factor                     =     0.1137
Average Fourier shell correlation    =     0.7314
Overall weighted R factor            =     0.1137
Overall weighted R2 factor           =     0.0882
Average correlation coefficient      =     0.9452
Overall correlation coefficient      =     0.9946
Overall figure of merit              =     0.9887
ML based su of positional parameters =    21.3880
ML based su of thermal parameters    =  3837.1514
-----------------------------------------------------------------------------
  Time in seconds: CPU =         4.07
             Elapsed =           0.00

    ****           Things for loggraph, R factor and others vs cycle            ****


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS:<Rfactor> vs cycle :N:1,2,3:
:FOM vs cycle :N:1,4:
:-LL vs cycle :N:1,5:
:-LLfree vs cycle :N:1,6:
:Geometry vs cycle:N:1,7,8,9,10,11:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1143   0.0      0.989      -14137.       0.0   0.0086  0.434   1.692  0.773   0.234
       1   0.1137   0.0      0.989      -14144.       0.0   0.0081  0.404   1.675  0.772   0.200
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1143   0.1137
     Rms BondLength    0.0086   0.0081
      Rms BondAngle    1.6918   1.6746
     Rms ChirVolume    0.2338   0.2002
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
 Refmac_5.8.0131:  End of Refmac_5.8.0131  
Times: User:      10.0s System:    0.1s Elapsed:     0:10  
</pre>
</html>
<!--SUMMARY_END--></FONT></B>


CCP-EM job finished: Wednesday, 12. August 2015 10:33AM ______________________
_______________________________________________________________________________

_________ CCP-EM Job launch/home/tom/Code/devtools/install/bin/refmac5 ________



CCP-EM pipeline job 10 of 10 __________________________________________________

__ Command ____________________________________________________________________
/home/tom/Code/devtools/install/bin/refmac5 mapin1 /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc mapin2 /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc mapref /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc atomsf /home/tom/Code/devtools/checkout/refmac5.8/data/atomsf_electron.lib << eof
/home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/refmac5_job_24/job_data/stdin_map_fsc.txt
eof
_______________________________________________________________________________
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<html> <!-- CCP4 HTML LOGFILE -->
<hr>
<!--SUMMARY_END--></FONT></B>
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<pre>
 
 ###############################################################
 ###############################################################
 ###############################################################
 ### CCP4 6.5.011: Refmac_5.8.0131 version 5.8.0131 : 06/08/15##
 ###############################################################
 User: unknown  Run date: 12/ 8/2015 Run time: 10:33:40 


 Please reference: Collaborative Computational Project, Number 4. 2011.
 "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242.
 as well as any specific reference in the program write-up.

<!--SUMMARY_END--></FONT></B>
 $TEXT:Reference1: $$ Main reference $$ 
   "REFMAC5 for the refinement of macromolecular crystal structures:"
   G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011) 
   Acta Crystallogr. D67, 355-367

 $$
 $SUMMARY :Reference1:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference2: $$ Secondary reference $$ 
   "Refinement of Macromolecular Structures by the  Maximum-Likelihood Method:"
   G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
   Acta Crystallogr. D53, 240-255
   EU  Validation contract: BIO2CT-92-0524

 $$
 $SUMMARY :Reference2:  $$ Refmac: $$
 :TEXT:Reference2: $$

 Data line--- labin FP=Fout0 PHIB=Pout0
 Data line--- weight auto 10
 Data line--- RESO 10.0
 Data line--- solvent no
 Data line--- source EM
 Data line--- mode sfcalc
 Data line--- sfcalc fsc
 Data line--- end
  Data line--- labin FP=Fout0 PHIB=Pout0
  Data line--- weight auto 10
  Data line--- RESO 10.0
  Data line--- solvent no
  Data line--- source EM
  Data line--- mode sfcalc
  Data line--- sfcalc fsc
  Data line--- END
===> Warning: Reflections file has not been defined
===> Warning: Switching to the idealisation mode

    ****                     Input and Default parameters#                      ****


Input coordinate file.  Logical name - XYZIN actual file name  - XYZIN
Output coordinate file. Logical name - XYZOUT actual file name - XYZOUT

  Refinement type                        : Idealisation
  Refinement type                        : NONE
  SF calculation from MAP: /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc


    ****                           Makecif parameters                           ****

Dictionary files for restraints : /usr/local/sci_local/mx/ccp4-6.5/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /usr/local/sci_local/mx/ccp4-6.5/lib/data/monomers/ener_lib.cif
    Apart from amino acids and DNA/RNA all monomers will be checked to see if atom names and connectivity is correct
    Hydrogens will be restored in their riding positions
    Links between monomers will be checked. Only those links present in the coordinate file will be used
    Standard sugar links will be analysed and used
    For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
    Symmetry related links will be analysed and used
    Cis peptides will be found and used automatically




Monitoring style is "MEDIUM". Complete information will be printed out in the
first and last cycle. In all other cycles minimum information will be printed out
Sigma cutoffs for printing out outliers
If deviation of restraint parameter > alpha*sigma then information will be printed out
Distance outliers      10.000
Angle outliers         10.000
Torsion outliers       10.000
Chiral volume outliers 10.000
Plane outliers         10.000
Non-bonding outliers   10.000
---------------------------------------------------------------

 Map file here /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc

 Logical Name: /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc   Filename: /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc 

File name for input map file on unit  10 : /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc
file size 56320 ; logical name /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc



           Number of columns, rows, sections ...............   24   24   24
           Map mode ........................................    2
           Start and stop points on columns, rows, sections     0   23    0   23    0   23
           Grid sampling on x, y, z ........................   24   24   24
           Cell dimensions .................................   66.0000    66.0000    66.0000    90.0000    90.0000    90.0000
           Fast, medium, slow axes .........................    X    Y    Z
           Minimum density .................................     0.00000
           Maximum density .................................    43.92188
           Mean density ....................................     3.79930
           Rms deviation from mean density .................     9.01953
           Space-group .....................................    1
           Number of titles ................................    1


     Labels:                            
  MODIM M CCP4    Chimera 1.3.2570 Mon Sep  7 14:1                    ?    ?


 nsym 1           1
 res max nominal    5.50000000      res max used    9.99979973    
 Map manupilation mode = M
 reference map

  Reference structure factors will be calculated from the map: /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc

 Logical Name: /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc   Filename: /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc 

File name for input map file on unit  10 : /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc
file size 56320 ; logical name /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc



           Number of columns, rows, sections ...............   24   24   24
           Map mode ........................................    2
           Start and stop points on columns, rows, sections     0   23    0   23    0   23
           Grid sampling on x, y, z ........................   24   24   24
           Cell dimensions .................................   66.0000    66.0000    66.0000    90.0000    90.0000    90.0000
           Fast, medium, slow axes .........................    X    Y    Z
           Minimum density .................................     0.00000
           Maximum density .................................    43.92188
           Mean density ....................................     3.79930
           Rms deviation from mean density .................     9.01953
           Space-group .....................................    1
           Number of titles ................................    1


     Labels:                            
  MODIM M CCP4    Chimera 1.3.2570 Mon Sep  7 14:1                    ?    ?


 nsym            1
 Start reading            0           0           0          23          23          23
 After map_reader_0           24          24          24           1           1
 After redalli
 Starting reso    5.00009991E-02   9.99979973    
 RelVol    20.7968750    
 Number of resolution bins            2

  The number of bins for reference SF :           2

 Logical Name: /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc   Filename: /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc 

File name for input map file on unit  10 : /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc
file size 56320 ; logical name /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc



           Number of columns, rows, sections ...............   24   24   24
           Map mode ........................................    2
           Start and stop points on columns, rows, sections     0   23    0   23    0   23
           Grid sampling on x, y, z ........................   24   24   24
           Cell dimensions .................................   66.0000    66.0000    66.0000    90.0000    90.0000    90.0000
           Fast, medium, slow axes .........................    X    Y    Z
           Minimum density .................................     0.00000
           Maximum density .................................    43.92188
           Mean density ....................................     3.79930
           Rms deviation from mean density .................     9.01953
           Space-group .....................................    1
           Number of titles ................................    1


     Labels:                            
  MODIM M CCP4    Chimera 1.3.2570 Mon Sep  7 14:1                    ?    ?


 Starting (nominal) resolution    5.00009991E-02   9.99979973    
 Number of all maps for SF calculation :           2
 Map file number 1 /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc
 File number            1 /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc
 nsym            1
 Start reading            0           0           0          23          23          23
 logname : MAPIN2 file name: /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc
 File number            2 /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/refmac/test_data/1ake_10A_molrep.mrc
 nsym            1
 Start reading            0           0           0          23          23          23
 logname : MAPIN3 file name: 
 Number of maps            2
 Number of resolution bins            2

    ****         FSC and other statistics: Without accounting for mask          ****

 $TABLE: FSC and other statistics
 $GRAPH: FSC cos(deltaPHI), cor(|F1|,|F2|) vs resolutions: 1,5,7,11
 $$
 2sin(th)/l 2sin(th)/l NREF sigma  FSC PHdiff cos(PHdiff) sigmaSig ZZ TT cor(|F1|,|F2|)
 $$
   2.29568410E-04   5.05050598E-03         230   0.00000000      0.999999940       0.00000000       1.00000000       31986636.0       92.9974976       43733.3086       1.00000012    
   5.05050598E-03   9.87145398E-03         376   0.00000000      0.999999881       0.00000000       1.00000000       874238.438       97.5392761       39606.4297      0.999999940    
 $$
 resolution limit            0         Infinity           1   14.0712471    
 Starting B value for sharpening               NaN

 Structure factors will be sharpened using reference map/curveR 

   Map maximum =    856.547424    
   Map minimum =   -124.204338    
   Map mean    =   -3.06069851E-05
   Map rmsd    =    186.517349    

 Print stats of the original data to the file: orig_data_rescut.txt
 Number of resolution bins            2

    ****      Mean(|F|) and other statistics: Without accounting for mask       ****

 $TABLE: Mean(|F|) and other statistics
 $GRAPH: Mean(|F|), Mean(|F|^2), Mean(|F|^4) vs resolutions: 1,6,7,8
 $$
 2sin(th)/l 2sin(th)/l dmin dmax NREF Mn(|F|) Mn(|F|^2) Mn(|F|^4) Mn(A) Mn(B) Mn(A^2) Mn(B^2) cor(A,B)
 $$
   2.29558413E-04   5.05050598E-03   66.0014420       14.0712471             230   65217.3906       1.38345380E+10   3.62911598E+21  -2341.04736       913.007812       1.18420767E+10   1.99245619E+09 -0.470917672    
   5.05050598E-03   9.88145359E-03   14.0712471       10.0598059             376   16493.1055       378116448.       3.96082777E+17   78.6627350      -450.494598       169967216.       208149152.      -2.58570500E-02
 $$
 sharpening things:            7           4              NaN              NaN
LWASSN: duplicate column labels in output file, columns 12 and 18 both have the label Fout1_NaN 
 Refmac_5.8.0131:  Duplicate column labels in output file
Times: User:       0.0s System:    0.0s Elapsed:     0:00  
</pre>
</html>
<!--SUMMARY_END--></FONT></B>


CCP-EM job finished: Wednesday, 12. August 2015 10:33AM ______________________
_______________________________________________________________________________


CCP-EM pipeline finished: Wednesday, 12. August 2015 10:33AM _________________
_______________________________________________________________________________
