
________________________________________________________________________________

______________________ CCP-EM Process | Buccaneer pipeline _____________________

__ Command _____________________________________________________________________
/home/tom/Code/devtools/install/bin/ccp4-python -u /home/tom/Code/devtools/install/bin/buccaneer_pipeline -stdin  << eof

title None
pdbin-ref /home/tom/Code/devtools/install/lib/data/reference_structures/reference-1tqw.pdb
mtzin-ref /home/tom/Code/devtools/install/lib/data/reference_structures/reference-1tqw.mtz
colin-ref-fo FP.F_sigF.F,FP.F_sigF.sigF
colin-ref-hl FC.ABCD.A,FC.ABCD.B,FC.ABCD.C,FC.ABCD.D
seqin /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/buccaneer/test_data/1ake.seq
mtzin /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/buccaneer/Buccaneer_12/buccaneer.mtz
colin-fo FemSHARP0,SIGFemSHARP0
colin-free FreeR_flag
colin-phifom PHIem,FOMem
pdbout /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/buccaneer/Buccaneer_12/buccaneer.pdb
cycles 1
buccaneer-anisotropy-correction
buccaneer-fast
buccaneer-1st-cycles 1
buccaneer-1st-sequence-reliability 0.95
buccaneer-1st-correlation-mode
buccaneer-nth-cycles 2
buccaneer-nth-sequence-reliability 0.95
buccaneer-nth-correlation-mode
buccaneer-new-residue-name UNK
buccaneer-resolution 2.0
buccaneer-keyword model-filter-sigma 3.0
buccaneer-keyword mr-model-filter-sigma 3.0
refmac-mlhl 1
refmac-twin 0
prefix /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/buccaneer/Buccaneer_12/

eof
________________________________________________________________________________
################################################################
### buccaneer-pipeline v1.5                                  ###
################################################################
----------------------  INPUT PARAMETERS  ----------------------
title None
pdbin-ref /home/tom/Code/devtools/install/lib/data/reference_structures/reference-1tqw.pdb
mtzin-ref /home/tom/Code/devtools/install/lib/data/reference_structures/reference-1tqw.mtz
colin-ref-fo FP.F_sigF.F,FP.F_sigF.sigF
colin-ref-hl FC.ABCD.A,FC.ABCD.B,FC.ABCD.C,FC.ABCD.D
seqin /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/buccaneer/test_data/1ake.seq
mtzin /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/buccaneer/Buccaneer_12/buccaneer.mtz
colin-fo FemSHARP0,SIGFemSHARP0
colin-free FreeR_flag
colin-phifom PHIem,FOMem
pdbout /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/buccaneer/Buccaneer_12/buccaneer.pdb
cycles 1
buccaneer-anisotropy-correction 
buccaneer-fast 
buccaneer-1st-cycles 1
buccaneer-1st-sequence-reliability 0.95
buccaneer-1st-correlation-mode 
buccaneer-nth-cycles 2
buccaneer-nth-sequence-reliability 0.95
buccaneer-nth-correlation-mode 
buccaneer-new-residue-name UNK
buccaneer-resolution 2.0
buccaneer-keyword model-filter-sigma 3.0
buccaneer-keyword mr-model-filter-sigma 3.0
refmac-mlhl 1
refmac-twin 0
prefix /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/buccaneer/Buccaneer_12/
---------------------- DEFAULT PARAMETERS ----------------------
----------------------------------------------------------------

<B><FONT COLOR='#FF0000'><!--SUMMARY_BEGIN-->
<html> <!-- CCP4 HTML LOGFILE -->
<hr>
<pre>
 
 ###############################################################
 ###############################################################
 ###############################################################
 ### CCP4 7.0: cbuccaneer             version 1.6.3 : 17/05/16##
 ###############################################################
 User: unknown  Run date:  8/ 3/2017 Run time: 12:44:56 


 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>

Copyright 2002-2010 Kevin Cowtan and University of York.

<B><FONT COLOR='#FF0000'><!--SUMMARY_BEGIN-->
$TEXT:Reference: $$ Please reference $$

 'Fitting molecular fragments into electron density'
 Cowtan K. (2008) Acta Cryst. D64, 83-89.

$$
$TEXT:Reference: $$ Please reference $$

 'The Buccaneer software for automated model building'
 Cowtan K. (2006) Acta Cryst. D62, 1002-1011.

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

title 	None
pdbin-ref 	/home/tom/Code/devtools/install/lib/data/reference_structures/reference-1tqw.pdb
mtzin-ref 	/home/tom/Code/devtools/install/lib/data/reference_structures/reference-1tqw.mtz
colin-ref-fo 	FP.F_sigF.F,FP.F_sigF.sigF
colin-ref-hl 	FC.ABCD.A,FC.ABCD.B,FC.ABCD.C,FC.ABCD.D
seqin 	/home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/buccaneer/test_data/1ake.seq
mtzin 	/home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/buccaneer/Buccaneer_12/buccaneer.mtz
colin-fo 	FemSHARP0,SIGFemSHARP0
colin-phifom 	PHIem,FOMem
colin-free 	FreeR_flag
pdbout 	/home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/buccaneer/Buccaneer_12/build.pdb
anisotropy-correction
fast
cycles 	1
sequence-reliability 	0.95
correlation-mode
new-residue-name 	UNK
resolution 	2.0
model-filter-sigma 	3.0
mr-model-filter-sigma 	3.0

Correlation mode selected

MTZ file: /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/buccaneer/Buccaneer_12/buccaneer.mtz
  Number of reflections:      9690        Number of columns:  10

Applying anisotropy correction:
|  -0.05272,  -0.04214,    -0.057|
|  -0.04214,   -0.1237,   -0.0403|
|    -0.057,   -0.0403,  -0.06193|


Cycle: 1

 C-alphas after finding:    187
 C-alphas after growing:    1593
 C-alphas after joining:    658
 C-alphas linked:           2
 C-alphas sequenced:        127
 C-alphas corrected:        1
 C-alphas after filtering:  570
 C-alphas after NCS build:  570
 C-alphas after pruning:    168
 C-alphas after rebuilding: 168

<B><FONT COLOR='#FF0000'><!--SUMMARY_BEGIN-->
Internal cycle   1
    168 residues were built in  12 fragments, the longest having   26 residues.
     85 residues were sequenced, after pruning.
     64 residues were uniquely allocated to   1 chains.
  Completeness by residues built:    38.1%
  Completeness of chains (number):   29.9%    (1)

<!--SUMMARY_END--></FONT></B>
$TEXT:Result: $$ $$
    168 residues were built in  12 fragments, the longest having   26 residues.
     85 residues were sequenced, after pruning.
     64 residues were uniquely allocated to   1 chains.
  Completeness by residues built:    38.1%
  Completeness of chains (number):   29.9%    (1)
$$

<B><FONT COLOR='#FF0000'><!--SUMMARY_BEGIN-->
cbuccaneer: Normal termination
Times: User:      51.9s System:    0.0s Elapsed:     0:52  
</pre>
</html>
<!--SUMMARY_END--></FONT></B>
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<html> <!-- CCP4 HTML LOGFILE -->
<hr>
<!--SUMMARY_END--></FONT></B>
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<pre>
 
 ###############################################################
 ###############################################################
 ###############################################################
 ### CCP4 7.0: Refmac              version 5.8.0158 : 03/10/16##
 ###############################################################
 User: unknown  Run date:  8/ 3/2017 Run time: 12:45:48 


 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--- title  None
  Data line--- ncyc 10
  Data line--- labin                    PHIB=PHIem FOM=FOMem                FREE=FreeR_flag   FP=FemSHARP0 SIGFP=SIGFemSHARP0
  Data line--- weight AUTO
  Data line--- make check NONE
  Data line--- make hydrogen NO hout NO peptide NO cispeptide YES ssbridge YES symmetry YES sugar YES connectivity NO link NO
  Data line--- refi type REST PHASE resi MLKF meth CGMAT bref ISOT
  Data line--- scal type SIMP LSSC ANISO EXPE
  Data line--- solvent YES VDWProb 1.4 IONProb 0.8 RSHRink 0.8
  Data line--- PHOUT
  Data line--- PNAME buccaneer
  Data line--- DNAME buccaneer
  Data line--- END

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN   Filename: /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/buccaneer/Buccaneer_12/buccaneer.mtz 


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


Input coordinate file.  Logical name - XYZIN actual file name  - /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/buccaneer/Buccaneer_12/build.pdb
Output coordinate file. Logical name - XYZOUT actual file name - /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/buccaneer/Buccaneer_12/refine.pdb
Input reflection file.  Logical name - HKLIN actual file name  - /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/buccaneer/Buccaneer_12/buccaneer.mtz
Output reflection file. Logical name - HKLOUT actual file name - /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/buccaneer/Buccaneer_12/refine.mtz

Cell from mtz :    75.000    75.000    75.000    90.000    90.000    90.000
Space group from mtz: number -    1; name - P 1

  Refinement type                        : Restrained

    ****                           Makecif parameters                           ****

Dictionary files for restraints : /home/tom/Code/devtools/install/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /home/tom/Code/devtools/install/lib/data/monomers/ener_lib.cif
    Program will rely on residue and atom names. No checking
    If this option is used then monomers should be checked carefully before using
    Hydrogens will not be used
    Links between monomers will be checked. Only those links present in the coordinate file will be used
    All links to sugar 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
Constant bulk solvent in non protein region
Probe radii for non-ions     1.400
Probe radii for ions         0.800
Shrinkage of the mask  by    0.800


    ****                 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       0.0025
  Refinement of individual isotropic Bfactors
  Refinement resln        :    75.0000  4.5063
  Estimated number of reflections :      13756
  Free R exclusion - flag equals:     0
  Auto weighting. An attempt
  Refinement cycles       :    10
  Scaling type                           :
          Wilson using 1 Gaussian

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

  Scaling and SigmaA resln:    75.0000  4.5063

  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/bu
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.44
 _lib_update       30/05/14
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 13482
                with complete description    : 13482
  NUMBER OF MODIFICATIONS                    :    63
  NUMBER OF LINKS                            :    73
  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/install/lib/data/atomsf.lib
<!--SUMMARY_END--></FONT></B>

  Number of atoms    :    1010
  Number of residues :     168
  Number of chains   :      10
  I am reading library. Please wait.
                mon_lib.cif
  WARNING : CIS peptide bond is found, angle =     62.46
            ch:AA   res: 138  ASN              --> 139  PRO
  INFO:     link is found (not be used) dist=   1.625 ideal_dist=   1.240
            ch:AA   res: 123  ARG              at:O   .->ch:AA   res: 125  VAL              at:N   .
  INFO:     link is found (not be used) dist=   1.182 ideal_dist=   1.500
            ch:AA   res: 129  SER              at:C   .->ch:AA   res: 148  VAL              at:CB  .
  INFO:     link is found (not be used) dist=   1.567 ideal_dist=   1.420
            ch:AA   res: 129  SER              at:O   .->ch:AA   res: 148  VAL              at:CA  .
  INFO:     link is found (not be used) dist=   1.499 ideal_dist=   1.330
            ch:AA   res: 129  SER              at:O   .->ch:AA   res: 148  VAL              at:C   .
  INFO:     link is found (not be used) dist=   1.336 ideal_dist=   1.080
            ch:AA   res: 129  SER              at:O   .->ch:AA   res: 148  VAL              at:O   .
  INFO:     link is found (not be used) dist=   1.234 ideal_dist=   1.420
            ch:AA   res: 129  SER              at:O   .->ch:AA   res: 148  VAL              at:CB  .
  INFO:     link is found (not be used) dist=   1.778 ideal_dist=   1.450
            ch:AA   res: 138  ASN              at:N   .->ch:AA   res: 140  PRO              at:CD  .
  INFO:     link is found (not be used) dist=   1.853 ideal_dist=   1.500
            ch:AA   res: 140  PRO              at:CA  .->ch:AA   res: 143  GLU              at:CD  .
  INFO:     link is found (not be used) dist=   1.604 ideal_dist=   1.420
            ch:AA   res: 140  PRO              at:CA  .->ch:AA   res: 143  GLU              at:OE2 .
  INFO:     link is found (not be used) dist=   1.680 ideal_dist=   1.460
            ch:AA   res: 140  PRO              at:C   .->ch:AA   res: 143  GLU              at:CD  .
  INFO:     link is found (not be used) dist=   1.591 ideal_dist=   1.250
            ch:AA   res: 140  PRO              at:C   .->ch:AA   res: 143  GLU              at:OE2 .
  INFO:     link is found (not be used) dist=   1.507 ideal_dist=   1.330
            ch:AA   res: 140  PRO              at:O   .->ch:AA   res: 143  GLU              at:CD  .
  INFO:     link is found (not be used) dist=   1.455 ideal_dist=   1.115
            ch:AA   res: 140  PRO              at:O   .->ch:AA   res: 143  GLU              at:OE2 .
  INFO:     link is found (not be used) dist=   1.483 ideal_dist=   1.337
            ch:AA   res: 145  LYS              at:CB  .->ch:AA   res: 152  GLU              at:OE2 .
  INFO:     link is found (not be used) dist=   1.329 ideal_dist=   1.337
            ch:AA   res: 145  LYS              at:CG  .->ch:AA   res: 152  GLU              at:OE2 .
  INFO:     link is found (not be used) dist=   1.750 ideal_dist=   1.488
            ch:AA   res: 145  LYS              at:NZ  .->ch:BB   res:  22  UNK              at:CB  .
  INFO:     link is found (not be used) dist=   1.506 ideal_dist=   1.513
            ch:AA   res: 149  THR              at:CG2 .->ch:AA   res: 152  GLU              at:CB  .
  INFO:     link is found (not be used) dist=   1.727 ideal_dist=   1.432
            ch:AA   res: 151  GLU              at:CB  .->ch:AA   res: 154  THR              at:OG1 .
  INFO:     link is found (not be used) dist=   1.642 ideal_dist=   1.513
            ch:AA   res: 153  LEU              at:CD2 .->ch:BB   res:  19  UNK              at:CB  .
  INFO:     link is found (not be used) dist=   1.597 ideal_dist=   1.457
            ch:AA   res: 156  ARG              at:NH2 .->ch:BB   res:  26  UNK              at:CB  .
  INFO:     link is found (not be used) dist=   1.266 ideal_dist=   1.420
            ch:AA   res: 157  LYS              at:O   .->ch:AA   res: 160  GLN              at:CG  .
  INFO:     link is found (not be used) dist=   1.460 ideal_dist=   1.450
            ch:AA   res: 157  LYS              at:CE  .->ch:CC   res:   1  UNK              at:N   .
  INFO:     link is found (not be used) dist=   1.276 ideal_dist=   1.410
            ch:AA   res: 157  LYS              at:NZ  .->ch:CC   res:   1  UNK              at:N   .
  INFO:     link is found (not be used) dist=   1.522 ideal_dist=   1.250
            ch:AA   res: 170  GLU              at:OE2 .->ch:AA   res: 172  HIS              at:C   .
  INFO:     link is found (not be used) dist=   1.672 ideal_dist=   1.400
            ch:AA   res: 175  THR              at:O   .->ch:AA   res: 177  PRO              at:N   .
  INFO:     link is found (not be used) dist=   1.644 ideal_dist=   1.450
            ch:DD   res: 177  UNK              at:N   .->ch:DD   res: 184  LYS              at:CB  .
  INFO:     link is found (not be used) dist=   1.929 ideal_dist=   1.413
            ch:DD   res: 179  ILE              at:CG2 .->ch:DD   res: 183  SER              at:OG  .
  INFO:     link is found (not be used) dist=   1.724 ideal_dist=   1.240
            ch:DD   res: 184  LYS              at:O   .->ch:DD   res: 187  GLU              at:N   .
  INFO:     link is found (not be used) dist=   1.845 ideal_dist=   1.420
            ch:EE   res:  13  LYS              at:NZ  .->ch:II   res:   5  UNK              at:C   .
  INFO:     link is found (not be used) dist=   1.593 ideal_dist=   1.410
            ch:EE   res:  13  LYS              at:NZ  .->ch:II   res:   6  UNK              at:N   .
  INFO:     link is found (not be used) dist=   1.585 ideal_dist=   1.450
            ch:EE   res:  13  LYS              at:CE  .->ch:II   res:   7  UNK              at:N   .
  INFO:     link is found (not be used) dist=   1.711 ideal_dist=   1.410
            ch:EE   res:  13  LYS              at:NZ  .->ch:II   res:   7  UNK              at:N   .
  INFO:     link is found (not be used) dist=   1.533 ideal_dist=   1.400
            ch:FF   res:   1  UNK              at:N   .->ch:II   res:   1  UNK              at:N   .
  INFO:     link is found (not be used) dist=   1.654 ideal_dist=   1.240
            ch:FF   res:   5  UNK              at:O   .->ch:FF   res:   7  UNK              at:N   .
  INFO:     link is found (not be used) dist=   1.583 ideal_dist=   1.413
            ch:GG   res: 153  LEU              at:CD2 .->ch:JJ   res:   1  UNK              at:O   .
  INFO:     link is found (not be used) dist=   1.851 ideal_dist=   1.450
            ch:GG   res: 153  LEU              at:CD1 .->ch:JJ   res:   5  UNK              at:N   .
  INFO:     link is found (not be used) dist=   1.924 ideal_dist=   1.524
            ch:GG   res: 153  LEU              at:CD1 .->ch:JJ   res:   5  UNK              at:CA  .
  INFO:     link is found (not be used) dist=   1.976 ideal_dist=   1.513
            ch:GG   res: 153  LEU              at:CD1 .->ch:JJ   res:   5  UNK              at:CB  .
  INFO:     link is found (not be used) dist=   1.044 ideal_dist=   1.240
            ch:JJ   res:   2  UNK              at:O   .->ch:JJ   res:   4  UNK              at:N   .
  --------------------------------
  --- title of input coord file ---

  PDB_code:xxxx
  PDB_name:----
  PDB_date:XX-XXX-XX
  --------------------------------
  ATTENTION: atom:CG   UNK               113  AA   is missing in the structure
  ATTENTION: atom:CG   UNK               114  AA   is missing in the structure
  ATTENTION: atom:CG   UNK               115  AA   is missing in the structure
  ATTENTION: atom:CG   UNK               116  AA   is missing in the structure
  ATTENTION: atom:CG   UNK               117  AA   is missing in the structure
  ATTENTION: atom:CG   UNK               118  AA   is missing in the structure
  ATTENTION: atom:CG   UNK               119  AA   is missing in the structure
  ATTENTION: atom:CG   UNK               120  AA   is missing in the structure
  ATTENTION: atom:CG   UNK               121  AA   is missing in the structure
  ATTENTION: atom:CG   UNK               122  AA   is missing in the structure
  ATTENTION: atom:CG   ARG               123  AA   is missing in the structure
  ATTENTION: atom:CD   ARG               123  AA   is missing in the structure
  ATTENTION: atom:NE   ARG               123  AA   is missing in the structure
  ATTENTION: atom:CZ   ARG               123  AA   is missing in the structure
  ATTENTION: atom:NH1  ARG               123  AA   is missing in the structure
  ATTENTION: atom:NH2  ARG               123  AA   is missing in the structure
  ATTENTION: atom:CG   HIS               126  AA   is missing in the structure
  ATTENTION: atom:ND1  HIS               126  AA   is missing in the structure
  ATTENTION: atom:CE1  HIS               126  AA   is missing in the structure
  ATTENTION: atom:NE2  HIS               126  AA   is missing in the structure
   ... and more ...
  Number of chains                  :      10
  Total number of monomers          :     168
  Number of atoms                   :    1157
  Number of missing atoms           :     147
  Number of rebuilt atoms           :       0
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0

  Number of bonds restraints    :    1007
  Number of angles restraints   :    1368
  Number of torsions restraints :     616
  Number of chiralities         :     177
  Number of planar groups       :     183


 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     12.2126   0.0057   3.1322   9.8933   2.0125  28.9975   1.1663   0.5826 -11.5290
  C      2.3100  20.8439   1.0200  10.2075   1.5886   0.5687   0.8650  51.6512   0.2156
  O      3.0485  13.2771   2.2868   5.7011   1.5463   0.3239   0.8670  32.9089   0.2508
  S      6.9053   1.4679   5.2034  22.2151   1.4379   0.2536   1.5863  56.1720   0.8669


 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:      1007         0      1007
               Angles:      1368         0      1368
              Chirals:       177         0       177
               Planes:       183         0       183
             Torsions:       616         0       616
            Intervals:         0         0         0
--------------------------------------------------------------------------------


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


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

FreeR flag                            0
Number of "free" reflections        533
Number of   all  reflections       9690
--------------------------------------------------------------------------------
 Number of reflections in file       9690
 Number of reflections read           9690


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



     CGMAT cycle number =      1

    ****                         Bond distance outliers                         ****

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

A    113 UNK C   . - A    114 UNK N   . mod.= 1.081 id.= 1.329 dev=  0.248 sig.= 0.014
A    115 UNK C   . - A    116 UNK N   . mod.= 0.971 id.= 1.329 dev=  0.358 sig.= 0.014
A    118 UNK C   . - A    119 UNK N   . mod.= 0.878 id.= 1.329 dev=  0.451 sig.= 0.014
A    119 UNK C   . - A    120 UNK N   . mod.= 1.187 id.= 1.329 dev=  0.142 sig.= 0.014
A    123 ARG C   . - A    124 ARG N   . mod.= 1.074 id.= 1.329 dev=  0.255 sig.= 0.014
A    124 ARG C   . - A    125 VAL N   . mod.= 1.179 id.= 1.329 dev=  0.150 sig.= 0.014
A    125 VAL C   . - A    126 HIS N   . mod.= 1.107 id.= 1.329 dev=  0.222 sig.= 0.014
A    126 HIS C   . - A    127 ALA N   . mod.= 1.072 id.= 1.329 dev=  0.257 sig.= 0.014
A    127 ALA C   . - A    128 PRO N   . mod.= 0.923 id.= 1.341 dev=  0.418 sig.= 0.016
A    128 PRO C   . - A    129 SER N   . mod.= 1.088 id.= 1.329 dev=  0.241 sig.= 0.014
A    138 ASN CA  . - A    138 ASN C   . mod.= 1.122 id.= 1.525 dev=  0.403 sig.= 0.021
A    138 ASN C   . - A    139 PRO N   . mod.= 1.026 id.= 1.341 dev=  0.315 sig.= 0.016
A    140 PRO C   . - A    141 LYS N   . mod.= 1.163 id.= 1.329 dev=  0.166 sig.= 0.014
A    144 GLY C   . - A    145 LYS N   . mod.= 1.095 id.= 1.329 dev=  0.234 sig.= 0.014
A    147 ASP C   . - A    148 VAL N   . mod.= 1.140 id.= 1.329 dev=  0.189 sig.= 0.014
A    150 GLY C   . - A    151 GLU N   . mod.= 1.114 id.= 1.329 dev=  0.215 sig.= 0.014
A    151 GLU N   . - A    151 GLU CA  . mod.= 1.245 id.= 1.458 dev=  0.213 sig.= 0.021
A    151 GLU C   . - A    152 GLU N   . mod.= 0.918 id.= 1.329 dev=  0.411 sig.= 0.014
A    152 GLU C   . - A    153 LEU N   . mod.= 1.174 id.= 1.329 dev=  0.155 sig.= 0.014
A    154 THR C   . - A    155 THR N   . mod.= 1.188 id.= 1.329 dev=  0.141 sig.= 0.014
A    155 THR C   . - A    156 ARG N   . mod.= 0.981 id.= 1.329 dev=  0.348 sig.= 0.014
A    160 GLN C   . - A    161 GLU N   . mod.= 1.026 id.= 1.329 dev=  0.303 sig.= 0.014
A    173 GLN C   . - A    174 MET N   . mod.= 1.085 id.= 1.329 dev=  0.244 sig.= 0.014
A    174 MET CA  . - A    174 MET C   . mod.= 1.243 id.= 1.525 dev=  0.282 sig.= 0.020
A    175 THR N   . - A    175 THR CA  . mod.= 1.165 id.= 1.458 dev=  0.293 sig.= 0.021
A    176 ALA N   . - A    176 ALA CA  . mod.= 1.043 id.= 1.458 dev=  0.415 sig.= 0.021
A    177 PRO C   . - A    178 LEU N   . mod.= 1.157 id.= 1.329 dev=  0.172 sig.= 0.014
A    178 LEU C   . - A    179 ILE N   . mod.= 1.176 id.= 1.329 dev=  0.153 sig.= 0.014
A    182 TYR C   . - A    183 SER N   . mod.= 1.166 id.= 1.329 dev=  0.163 sig.= 0.014
B      6 UNK C   . - B      7 UNK N   . mod.= 1.168 id.= 1.329 dev=  0.161 sig.= 0.014
B     11 UNK C   . - B     12 UNK N   . mod.= 0.850 id.= 1.329 dev=  0.479 sig.= 0.014
B     12 UNK C   . - B     13 UNK N   . mod.= 0.935 id.= 1.329 dev=  0.394 sig.= 0.014
B     17 UNK C   . - B     18 UNK N   . mod.= 1.183 id.= 1.329 dev=  0.146 sig.= 0.014
B     20 UNK C   . - B     21 UNK N   . mod.= 1.134 id.= 1.329 dev=  0.195 sig.= 0.014
B     22 UNK C   . - B     23 UNK N   . mod.= 0.831 id.= 1.329 dev=  0.498 sig.= 0.014
B     24 UNK C   . - B     25 UNK N   . mod.= 1.155 id.= 1.329 dev=  0.174 sig.= 0.014
C      5 UNK C   . - C      6 UNK N   . mod.= 1.070 id.= 1.329 dev=  0.259 sig.= 0.014
C     12 UNK N   . - C     12 UNK CA  . mod.= 1.195 id.= 1.458 dev=  0.263 sig.= 0.021
C     12 UNK C   . - C     13 UNK N   . mod.= 1.078 id.= 1.329 dev=  0.251 sig.= 0.014
C     13 UNK C   . - C     14 UNK N   . mod.= 1.145 id.= 1.329 dev=  0.184 sig.= 0.014
C     14 UNK C   . - C     15 UNK N   . mod.= 0.704 id.= 1.329 dev=  0.625 sig.= 0.014
C     15 UNK C   . - C     16 UNK N   . mod.= 1.125 id.= 1.329 dev=  0.204 sig.= 0.014
C     16 UNK C   . - C     17 UNK N   . mod.= 0.867 id.= 1.329 dev=  0.462 sig.= 0.014
D    179 ILE C   . - D    180 GLY N   . mod.= 1.042 id.= 1.329 dev=  0.287 sig.= 0.014
D    190 ASN C   . - D    191 THR N   . mod.= 1.063 id.= 1.329 dev=  0.266 sig.= 0.014
F      1 UNK C   . - F      2 UNK N   . mod.= 1.071 id.= 1.329 dev=  0.258 sig.= 0.014
F      2 UNK C   . - F      3 UNK N   . mod.= 1.018 id.= 1.329 dev=  0.311 sig.= 0.014
F      3 UNK C   . - F      4 UNK N   . mod.= 1.164 id.= 1.329 dev=  0.165 sig.= 0.014
F      5 UNK C   . - F      6 UNK N   . mod.= 0.701 id.= 1.329 dev=  0.628 sig.= 0.014
F      8 UNK C   . - F      9 UNK N   . mod.= 1.078 id.= 1.329 dev=  0.251 sig.= 0.014
G    150 GLY N   . - G    150 GLY CA  . mod.= 1.213 id.= 1.491 dev=  0.278 sig.= 0.021
G    152 GLU C   . - G    153 LEU N   . mod.= 1.095 id.= 1.329 dev=  0.234 sig.= 0.014
G    153 LEU C   . - G    154 THR N   . mod.= 0.871 id.= 1.329 dev=  0.458 sig.= 0.014
H      1 UNK C   . - H      2 UNK N   . mod.= 0.721 id.= 1.329 dev=  0.608 sig.= 0.014
J      1 UNK C   . - J      2 UNK N   . mod.= 0.832 id.= 1.329 dev=  0.497 sig.= 0.014
J      2 UNK C   . - J      3 UNK N   . mod.= 0.785 id.= 1.329 dev=  0.544 sig.= 0.014
J      3 UNK CA  . - J      3 UNK C   . mod.= 1.767 id.= 1.500 dev= -0.267 sig.= 0.020
J      4 UNK N   . - J      4 UNK CA  . mod.= 1.727 id.= 1.458 dev= -0.269 sig.= 0.021

    ****                         Torsion angle outliers                         ****

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

A    138 ASN CA    - A    139 PRO CA    mod.=  62.46 id.=   0.00 per.= 1 dev= -62.46 sig.=   5.00
B     11 UNK CA    - B     12 UNK CA    mod.= 126.65 id.= 180.00 per.= 1 dev=  53.35 sig.=   5.00

    ****                              VDW outliers                              ****

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

A    129 SER C   . - A    148 VAL CB  . mod.= 1.182 id.= 3.700 dev= -2.52 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1
A    129 SER C   . - A    148 VAL CB  . mod.= 1.182 id.= 3.700 dev= -2.52 sig.= 0.20 sym.=  1  0  0  0 ncs  -1 type =  1
A    129 SER O   . - A    148 VAL CB  . mod.= 1.234 id.= 3.470 dev= -2.24 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1
A    129 SER O   . - A    148 VAL CB  . mod.= 1.234 id.= 3.470 dev= -2.24 sig.= 0.20 sym.=  1  0  0  0 ncs  -1 type =  1
A    145 LYS CG  . - A    152 GLU OE2 . mod.= 1.329 id.= 3.440 dev= -2.11 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1
A    145 LYS CG  . - A    152 GLU OE2 . mod.= 1.329 id.= 3.440 dev= -2.11 sig.= 0.20 sym.=  1  0  0  0 ncs  -1 type =  1
A    149 THR CG2 . - A    152 GLU CB  . mod.= 1.506 id.= 3.860 dev= -2.35 sig.= 0.20 sym.=  1  0  0  0 ncs  -1 type =  1
A    149 THR CG2 . - A    152 GLU CB  . mod.= 1.506 id.= 3.860 dev= -2.35 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1
A    153 LEU CD2 . - B     19 UNK CB  . mod.= 1.642 id.= 3.860 dev= -2.22 sig.= 0.20 sym.=  1  0  0  0 ncs  -1 type =  1
A    153 LEU CD2 . - B     19 UNK CB  . mod.= 1.642 id.= 3.860 dev= -2.22 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1
A    157 LYS CE  . - C      1 UNK N   . mod.= 1.460 id.= 3.520 dev= -2.06 sig.= 0.20 sym.=  1  0  0  0 ncs  -1 type =  1
A    157 LYS CE  . - C      1 UNK N   . mod.= 1.460 id.= 3.520 dev= -2.06 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1
A    157 LYS O   . - A    160 GLN CG  . mod.= 1.266 id.= 3.440 dev= -2.17 sig.= 0.20 sym.=  1  0  0  0 ncs  -1 type =  1
A    157 LYS O   . - A    160 GLN CG  . mod.= 1.266 id.= 3.440 dev= -2.17 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 1.00
 Grid spacing to be used        :    88   88   88
 Maximuum H,K,L                 :    17   17   17
 Minimum acceptable grid spacing:    58   58   58
 Limits of asymmetric unit      : 1.00 1.00 1.00
 Grid spacing to be used        :    88   88   88
 Maximuum H,K,L                 :    17   17   17
 Minimum acceptable grid spacing:    58   58   58
 Weight matrix    4.31707129E-03
 Actual weight    10.0000000      is applied to the X-ray term
Norm of X_ray positional gradient                18.9
Norm of Geom. positional gradient                398.
Norm of X_ray B-factor gradient                  20.6
Norm of Geom. B-factor gradient                  0.00
Product of X_ray and Geom posit. gradients     -0.532E+06
 Cosine of angle between them                      -0.023
Product of X_ray and Geom B-fact gradients       0.00
 Cosine of angle between them                       0.000


Residuals: XRAY=     0.5165E+06 GEOM=     0.4284E+05 TOTAL=     0.5594E+06
 function value    559376.500    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1007     0.086     0.019
Bond angles  : refined atoms                   1368     7.214     2.122
Torsion angles, period  1. refined              156     8.291     5.000
Torsion angles, period  2. refined               23    29.706    25.217
Torsion angles, period  3. refined               86    16.949    15.000
Torsion angles, period  4. refined                3    10.672    15.000
Chiral centres: refined atoms                   177     0.223     0.200
Planar groups: refined atoms                    753     0.028     0.021
VDW repulsions: refined_atoms                  1848     0.711     0.200
VDW; torsion: refined_atoms                    1678     0.401     0.200
HBOND: refined_atoms                            190     0.513     0.200
M. chain bond B values: refined atoms           660     0.000     3.948
M. chain angle B values: refined atoms          804     0.000     5.922
S. chain bond B values: refined atoms           347     0.000     3.948
S. chain angle B values: refined atoms          564     0.000     5.922
Long range B values: refined atoms             2073     0.000    58.152
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.243, B  = -10.895
Partial structure    1: scale =    0.000, B  = -10.000
Overall anisotropic scale factors
   B11 =  0.70 B22 = -0.18 B33 = -0.52 B12 =  2.77 B13 =  1.59 B23 = -0.72
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1. <Rfactor> v. resln :N:1,6,7,11,12:
:Cycle    1. <Fobs> and <Fc> v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.001     125 100.00  1688.7  1045.6  0.46  0.46       0     0.0     0.0******  0.00
 0.004     184 100.00   645.5   546.2  0.41  0.41       0     0.0     0.0******  0.00
 0.006     279 100.00   512.9   455.2  0.39  0.39       6   634.2   452.0  0.35  0.35
 0.009     265 100.00   443.1   407.5  0.38  0.38      36   393.0   372.3  0.38  0.38
 0.011     322 100.00   348.6   362.3  0.43  0.43      24   335.2   358.2  0.55  0.55
 0.014     337 100.00   298.3   296.7  0.45  0.45      24   383.3   313.2  0.42  0.42
 0.016     372 100.00   268.1   254.2  0.46  0.46      12   221.4   307.9  0.44  0.44
 0.019     481 100.00   240.1   238.5  0.47  0.47      12   223.9   195.0  0.48  0.48
 0.021     459 100.00   227.1   210.9  0.46  0.46      12   216.9   203.2  0.56  0.56
 0.023     450 100.00   200.2   194.6  0.50  0.50      36   239.9   157.3  0.44  0.44
 0.026     439 100.00   191.1   179.6  0.48  0.48      72   217.3   195.6  0.48  0.48
 0.028     582 100.00   185.7   170.5  0.51  0.51       0     0.0     0.0******  0.00
 0.031     516 100.00   187.0   170.5  0.46  0.46      27   198.5   169.1  0.55  0.55
 0.033     612 100.00   192.0   163.0  0.44  0.44       4   141.7   108.7  0.36  0.36
 0.036     565 100.00   195.1   159.0  0.46  0.46      24   178.8   155.2  0.46  0.46
 0.038     612 100.00   199.0   157.0  0.45  0.45      24   178.9   162.4  0.47  0.47
 0.041     675 100.00   193.7   150.9  0.48  0.48      24   184.1   165.9  0.55  0.55
 0.043     570 100.00   196.4   153.7  0.47  0.47      88   202.3   145.7  0.51  0.51
 0.046     639 100.00   195.1   144.9  0.51  0.51      24   185.5   126.6  0.53  0.53
 0.048     664 100.00   193.5   139.1  0.49  0.49      84   191.1   124.0  0.52  0.52
$$

    ****                      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:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0014    125   0.918      0   0.000    125   0.918  1.179  0.0000  0.9606  0.0000  0.9318
  0.0039    184   0.852      0   0.000    184   0.852  1.023  0.0000  0.8262  0.0000  0.4846
  0.0063    279   0.798      0   0.000    279   0.798  0.906  0.8302  0.8016  0.4071  0.5532
  0.0088    265   0.766      0   0.000    265   0.766  0.810  0.7422  0.7851  0.3540  0.5800
  0.0112    315   0.740      0   0.000    315   0.740  0.726  0.6414  0.7399  0.3205  0.4787
  0.0137    337   0.681      0   0.000    337   0.681  0.655  0.6657  0.6534  0.2672  0.4380
  0.0161    372   0.645      0   0.000    372   0.645  0.629  0.6171  0.6001  0.6595  0.3737
  0.0186    481   0.640      0   0.000    481   0.640  0.624  0.5123  0.5882  0.1369  0.3524
  0.0210    459   0.645      0   0.000    459   0.645  0.619  0.4975  0.5883 -0.0627  0.3288
  0.0235    450   0.628      0   0.000    450   0.628  0.615  0.5096  0.5525  0.3874  0.2733
  0.0259    439   0.616      0   0.000    439   0.616  0.638  0.5625  0.5395  0.1331  0.2971
  0.0284    582   0.627      0   0.000    582   0.627  0.678  0.0000  0.5438  0.0000  0.2280
  0.0308    516   0.658      0   0.000    516   0.658  0.718  0.4907  0.6075  0.0768  0.3251
  0.0333    612   0.679      0   0.000    612   0.679  0.753  0.4468  0.6505 -0.4207  0.4028
  0.0358    561   0.689      0   0.000    561   0.689  0.767  0.6561  0.6543  0.4049  0.3458
  0.0382    612   0.685      0   0.000    612   0.685  0.765  0.6251  0.6522  0.3670  0.3653
  0.0407    675   0.664      0   0.000    675   0.664  0.763  0.6218  0.6141  0.1488  0.3029
  0.0431    570   0.667      0   0.000    570   0.667  0.761  0.6064  0.6120  0.1840  0.2945
  0.0456    639   0.646      0   0.000    639   0.646  0.759  0.4915  0.5651 -0.0547  0.2011
  0.0480    684   0.642      0   0.000    684   0.642  0.757  0.5172  0.5599  0.2028  0.2006
 $$
Resolution limits                    =     75.000     4.506
Number of used reflections           =       9137
Percentage observed                  =   100.0000
Percentage of free reflections       =     5.5119
Overall R factor                     =     0.4570
Free R factor                        =     0.4787
Average Fourier shell correlation    =     0.6247
AverageFree Fourier shell correlation=     0.5830
Overall weighted R factor            =     0.4570
Free weighted R factor               =     0.4787
Overall weighted R2 factor           =     0.5016
Free weighted R2 factor              =     0.5382
Average correlation coefficient      =     0.3416
Overall correlation coefficient      =     0.7913
Free correlation coefficient         =     0.4726
Cruickshanks DPI for coordinate error=     0.9342
DPI based on free R factor           =     0.7309
Overall figure of merit              =     0.6730
ML based su of positional parameters =     1.1815
ML based su of thermal parameters    =    90.3169
-----------------------------------------------------------------------------
 Trying gamma equal    0.00000000    
 Convergence reached with no gamma cycles 


 fvalues    51686.1016       42843.3750       531121.312       559704.375    


     CGMAT cycle number =      2

 Weight matrix    5.43910312E-03
 Actual weight    10.0000000      is applied to the X-ray term


 function value    526698.500    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1007     0.056     0.019
Bond angles  : refined atoms                   1368     4.782     2.122
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.251, B  =  -6.898
Partial structure    1: scale =    0.000, B  = -10.000
Overall anisotropic scale factors
   B11 =  0.63 B22 = -0.04 B33 = -0.60 B12 =  2.76 B13 =  1.52 B23 = -0.55
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.4308
Free R factor                        =     0.4550
Average Fourier shell correlation    =     0.6597
AverageFree Fourier shell correlation=     0.6209
Average correlation coefficient      =     0.4325
Overall figure of merit              =     0.6866
-----------------------------------------------------------------------------
 Trying gamma equal    0.00000000    
 Convergence reached with no gamma cycles 


 fvalues    50803.7539       19141.8867       516390.062       527179.438    


     CGMAT cycle number =      3

 Weight matrix    6.77685346E-03
 Actual weight    10.0000000      is applied to the X-ray term


 function value    513913.625    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1007     0.043     0.019
Bond angles  : refined atoms                   1368     3.471     2.122
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.254, B  =   1.290
Partial structure    1: scale =    0.000, B  = -10.000
Overall anisotropic scale factors
   B11 =  0.21 B22 = -0.07 B33 = -0.14 B12 =  2.48 B13 =  1.56 B23 = -0.48
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.4194
Free R factor                        =     0.4413
Average Fourier shell correlation    =     0.6813
AverageFree Fourier shell correlation=     0.6442
Average correlation coefficient      =     0.4722
Overall figure of merit              =     0.6976
-----------------------------------------------------------------------------
 Trying gamma equal    0.00000000    
 Convergence reached with no gamma cycles 


 fvalues    50262.6758       11219.1992       508970.406       513845.938    


     CGMAT cycle number =      4

 Weight matrix    7.84028042E-03
 Actual weight    10.0000000      is applied to the X-ray term


 function value    504898.312    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1007     0.039     0.019
Bond angles  : refined atoms                   1368     3.366     2.122
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.262, B  =   4.661
Partial structure    1: scale =    0.000, B  = -10.000
Overall anisotropic scale factors
   B11 = -0.54 B22 =  0.01 B33 =  0.53 B12 =  2.36 B13 =  1.46 B23 = -0.25
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.4100
Free R factor                        =     0.4330
Average Fourier shell correlation    =     0.6976
AverageFree Fourier shell correlation=     0.6607
Average correlation coefficient      =     0.5025
Overall figure of merit              =     0.7058
-----------------------------------------------------------------------------
 Trying gamma equal    0.00000000    
 Convergence reached with no gamma cycles 


 fvalues    49630.9219       8316.11328       501948.406       504625.344    


     CGMAT cycle number =      5

 Weight matrix    8.07645917E-03
 Actual weight    10.0000000      is applied to the X-ray term


 function value    502250.531    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1007     0.028     0.019
Bond angles  : refined atoms                   1368     3.035     2.122
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.262, B  =   6.859
Partial structure    1: scale =    0.000, B  = -10.000
Overall anisotropic scale factors
   B11 = -0.96 B22 =  0.10 B33 =  0.86 B12 =  2.31 B13 =  1.64 B23 = -0.32
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.4064
Free R factor                        =     0.4313
Average Fourier shell correlation    =     0.7034
AverageFree Fourier shell correlation=     0.6669
Average correlation coefficient      =     0.5135
Overall figure of merit              =     0.7089
-----------------------------------------------------------------------------
 Trying gamma equal    0.00000000    
 Trying gamma equal    5.00000007E-02
 Gamma decreased to    3.99999991E-02


 fvalues    49539.7656       6527.87402       500667.375       501925.531    


     CGMAT cycle number =      6

 Weight matrix    8.38645920E-03
 Actual weight    10.0000000      is applied to the X-ray term


 function value    500492.781    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1007     0.018     0.019
Bond angles  : refined atoms                   1368     2.975     2.122
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.262, B  =   0.801
Partial structure    1: scale =    0.000, B  = -10.000
Overall anisotropic scale factors
   B11 = -1.03 B22 =  0.13 B33 =  0.90 B12 =  2.33 B13 =  1.73 B23 = -0.26
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.4046
Free R factor                        =     0.4299
Average Fourier shell correlation    =     0.7074
AverageFree Fourier shell correlation=     0.6717
Average correlation coefficient      =     0.5195
Overall figure of merit              =     0.7114
-----------------------------------------------------------------------------
 Trying gamma equal    3.99999991E-02
 Gamma decreased to    3.09090894E-02


 fvalues    49497.3555       5467.80176       499949.375       500441.375    


     CGMAT cycle number =      7

 Weight matrix    8.72089434E-03
 Actual weight    10.0000000      is applied to the X-ray term


 function value    500053.375    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1007     0.017     0.019
Bond angles  : refined atoms                   1368     2.990     2.122
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.262, B  =   0.201
Partial structure    1: scale =    0.000, B  = -10.000
Overall anisotropic scale factors
   B11 = -1.16 B22 =  0.10 B33 =  1.06 B12 =  2.36 B13 =  1.67 B23 = -0.20
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.4022
Free R factor                        =     0.4284
Average Fourier shell correlation    =     0.7121
AverageFree Fourier shell correlation=     0.6768
Average correlation coefficient      =     0.5272
Overall figure of merit              =     0.7141
-----------------------------------------------------------------------------
 Trying gamma equal    3.09090894E-02
 Gamma decreased to    2.26446278E-02


 fvalues    49444.2383       5595.68848       499640.500       500038.062    


     CGMAT cycle number =      8

 Weight matrix    8.95596296E-03
 Actual weight    10.0000000      is applied to the X-ray term


 function value    499279.562    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1007     0.019     0.019
Bond angles  : refined atoms                   1368     3.028     2.122
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.262, B  =   0.860
Partial structure    1: scale =    0.000, B  = -10.000
Overall anisotropic scale factors
   B11 = -1.27 B22 = -0.02 B33 =  1.29 B12 =  2.51 B13 =  1.57 B23 = -0.08
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.4003
Free R factor                        =     0.4263
Average Fourier shell correlation    =     0.7156
AverageFree Fourier shell correlation=     0.6806
Average correlation coefficient      =     0.5331
Overall figure of merit              =     0.7160
-----------------------------------------------------------------------------
 Trying gamma equal    2.26446278E-02
 Gamma decreased to    1.51314801E-02


 fvalues    49348.6680       5727.44922       498803.531       499214.125    


     CGMAT cycle number =      9

 Weight matrix    9.31712985E-03
 Actual weight    10.0000000      is applied to the X-ray term


 function value    498647.500    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1007     0.019     0.019
Bond angles  : refined atoms                   1368     3.069     2.122
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.262, B  =   1.272
Partial structure    1: scale =    0.000, B  = -10.000
Overall anisotropic scale factors
   B11 = -1.46 B22 = -0.08 B33 =  1.55 B12 =  2.63 B13 =  1.44 B23 =  0.06
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.3986
Free R factor                        =     0.4242
Average Fourier shell correlation    =     0.7189
AverageFree Fourier shell correlation=     0.6834
Average correlation coefficient      =     0.5377
Overall figure of merit              =     0.7180
-----------------------------------------------------------------------------
 Trying gamma equal    1.51314801E-02
 Gamma decreased to    8.30134563E-03


 fvalues    49279.8906       5757.43701       498238.938       498556.344    


     CGMAT cycle number =     10

    ****                         Bond distance outliers                         ****

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

G    156 ARG C   . - G    156 ARG O   . mod.= 1.492 id.= 1.231 dev= -0.261 sig.= 0.020

 Limits of asymmetric unit      : 1.00 1.00 1.00
 Grid spacing to be used        :    88   88   88
 Maximuum H,K,L                 :    17   17   17
 Minimum acceptable grid spacing:    58   58   58
 Limits of asymmetric unit      : 1.00 1.00 1.00
 Grid spacing to be used        :    88   88   88
 Maximuum H,K,L                 :    17   17   17
 Minimum acceptable grid spacing:    58   58   58
 Weight matrix    9.58390813E-03
 Actual weight    10.0000000      is applied to the X-ray term
Norm of X_ray positional gradient                20.0
Norm of Geom. positional gradient                28.4
Norm of X_ray B-factor gradient                  24.4
Norm of Geom. B-factor gradient                  21.8
Product of X_ray and Geom posit. gradients     -0.116E+07
 Cosine of angle between them                      -0.674
Product of X_ray and Geom B-fact gradients     -0.524E+06
 Cosine of angle between them                      -0.975


Residuals: XRAY=     0.4921E+06 GEOM=      5862.     TOTAL=     0.4979E+06
 function value    497922.375    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1007     0.020     0.019
Bond angles  : refined atoms                   1368     3.118     2.122
Torsion angles, period  1. refined              156    13.061     5.000
Torsion angles, period  2. refined               23    38.100    25.217
Torsion angles, period  3. refined               86    25.357    15.000
Torsion angles, period  4. refined                3    16.941    15.000
Chiral centres: refined atoms                   177     0.194     0.200
Planar groups: refined atoms                    753     0.013     0.021
VDW repulsions: refined_atoms                  1124     0.311     0.200
VDW; torsion: refined_atoms                    1344     0.295     0.200
HBOND: refined_atoms                            116     0.295     0.200
M. chain bond B values: refined atoms           660     1.250     1.955
M. chain angle B values: refined atoms          804     2.160     2.948
S. chain bond B values: refined atoms           347     3.264     2.868
S. chain angle B values: refined atoms          564     5.142     3.975
Long range B values: refined atoms             1555     9.054    34.864
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.263, B  =   1.334
Partial structure    1: scale =    0.000, B  = -10.000
Overall anisotropic scale factors
   B11 = -1.53 B22 = -0.15 B33 =  1.68 B12 =  2.76 B13 =  1.45 B23 =  0.22
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10. <Rfactor> v. resln :N:1,6,7,11,12:
:Cycle   10. <Fobs> and <Fc> v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.001     125 100.00  1559.4  1014.5  0.43  0.43       0     0.0     0.0******  0.00
 0.004     184 100.00   596.1   499.2  0.40  0.40       0     0.0     0.0******  0.00
 0.006     279 100.00   473.6   410.9  0.39  0.39       6   585.6   395.5  0.34  0.34
 0.009     265 100.00   409.1   375.9  0.36  0.36      36   362.9   362.0  0.33  0.33
 0.011     322 100.00   321.9   340.0  0.41  0.41      24   309.6   341.3  0.57  0.57
 0.014     337 100.00   275.5   283.8  0.43  0.43      24   353.9   317.0  0.37  0.37
 0.016     372 100.00   247.6   238.3  0.45  0.45      12   204.5   281.2  0.45  0.45
 0.019     481 100.00   221.7   216.4  0.45  0.45      12   206.8   155.9  0.49  0.49
 0.021     459 100.00   209.8   198.5  0.45  0.45      12   200.3   191.7  0.45  0.45
 0.023     450 100.00   184.9   182.4  0.46  0.46      36   221.5   170.4  0.36  0.36
 0.026     439 100.00   176.4   169.1  0.42  0.42      72   200.7   191.3  0.45  0.45
 0.028     582 100.00   171.5   160.1  0.42  0.42       0     0.0     0.0******  0.00
 0.031     516 100.00   172.7   156.8  0.38  0.38      27   183.3   150.1  0.43  0.43
 0.033     612 100.00   177.3   157.6  0.35  0.35       4   130.8    99.2  0.24  0.24
 0.036     565 100.00   180.2   158.6  0.34  0.34      24   165.1   156.2  0.45  0.45
 0.038     612 100.00   183.8   165.5  0.32  0.32      24   165.2   174.6  0.41  0.41
 0.041     675 100.00   178.9   155.9  0.36  0.36      24   170.0   162.6  0.39  0.39
 0.043     570 100.00   181.4   159.1  0.35  0.35      88   186.8   152.8  0.44  0.44
 0.046     639 100.00   180.1   153.2  0.41  0.41      24   171.3   142.7  0.37  0.37
 0.048     664 100.00   178.7   147.8  0.39  0.39      84   176.5   135.4  0.46  0.46
$$

    ****                      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:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0014    125   0.928      0   0.000    125   0.928  1.159  0.0000  0.9668  0.0000  0.9411
  0.0039    184   0.857      0   0.000    184   0.857  0.999  0.0000  0.8381  0.0000  0.5234
  0.0063    279   0.799      0   0.000    279   0.799  0.879  0.8452  0.8155  0.4871  0.5976
  0.0088    265   0.770      0   0.000    265   0.770  0.780  0.7794  0.8038  0.4779  0.6358
  0.0112    315   0.750      0   0.000    315   0.750  0.694  0.6578  0.7617  0.3959  0.5441
  0.0137    337   0.692      0   0.000    337   0.692  0.621  0.7210  0.6718  0.4097  0.4773
  0.0161    372   0.651      0   0.000    372   0.651  0.586  0.6806  0.6210  0.8277  0.4411
  0.0186    481   0.643      0   0.000    481   0.643  0.567  0.5312  0.5969  0.3860  0.3843
  0.0210    459   0.647      0   0.000    459   0.647  0.548  0.5891  0.5904  0.3813  0.3367
  0.0235    450   0.632      0   0.000    450   0.632  0.532  0.5854  0.5767  0.5100  0.3889
  0.0259    439   0.635      0   0.000    439   0.635  0.579  0.6170  0.6027  0.3283  0.4805
  0.0284    582   0.660      0   0.000    582   0.660  0.669  0.0000  0.6458  0.0000  0.4713
  0.0308    516   0.708      0   0.000    516   0.708  0.757  0.6940  0.7291  0.6179  0.5825
  0.0333    612   0.758      0   0.000    612   0.758  0.835  0.6282  0.7927 -0.4634  0.6562
  0.0358    561   0.777      0   0.000    561   0.777  0.863  0.7567  0.8120  0.4382  0.6604
  0.0382    612   0.775      0   0.000    612   0.775  0.852  0.7767  0.8152  0.6080  0.6838
  0.0407    675   0.752      0   0.000    675   0.752  0.840  0.7587  0.7781  0.4971  0.6080
  0.0431    570   0.741      0   0.000    570   0.741  0.829  0.7268  0.7760  0.4021  0.6306
  0.0456    639   0.727      0   0.000    639   0.727  0.819  0.7549  0.7295  0.5814  0.4997
  0.0480    684   0.717      0   0.000    684   0.717  0.809  0.6465  0.7165  0.3345  0.5050
 $$
Resolution limits                    =     75.000     4.506
Number of used reflections           =       9137
Percentage observed                  =   100.0000
Percentage of free reflections       =     5.5119
Overall R factor                     =     0.3969
Free R factor                        =     0.4213
Average Fourier shell correlation    =     0.7219
AverageFree Fourier shell correlation=     0.6866
Overall weighted R factor            =     0.3969
Free weighted R factor               =     0.4213
Overall weighted R2 factor           =     0.4561
Free weighted R2 factor              =     0.4794
Average correlation coefficient      =     0.5430
Overall correlation coefficient      =     0.8355
Free correlation coefficient         =     0.5821
Cruickshanks DPI for coordinate error=     0.8114
DPI based on free R factor           =     0.6433
Overall figure of merit              =     0.7197
ML based su of positional parameters =     0.8057
ML based su of thermal parameters    =    60.2449
-----------------------------------------------------------------------------
 Trying gamma equal    8.30134563E-03
 Gamma decreased to    2.09213281E-03


 fvalues    49196.1953       5861.87061       497398.844       497823.812    

 LABOUT FreeR_flag=FreeR_flag FemSHARP0=FemSHARP0 SIGFemSHARP0=SIGFemSHARP0 FC=FC PHIC=PHIC FC_ALL=FC_ALL PHIC_ALL=PHIC_ALL FWT=FWT PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM PHCOMB=PHCOMB HLACOMB=HLACOMB HLBCOMB=HLBCOMB HLCCOMB=HLCCOMB HLDCOMB=HLDCOMB FC_ALL_LS=FC_ALL_LS PHIC_ALL_LS=PHIC_ALL_LS

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: /home/tom/Code/devtools/checkout/ccpem/src/ccpem_core/gui/tasks/buccaneer/Buccaneer_12/refine.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1007     0.020     0.019
Bond angles  : refined atoms                   1368     3.168     2.122
Torsion angles, period  1. refined              156    13.240     5.000
Torsion angles, period  2. refined               23    38.577    25.217
Torsion angles, period  3. refined               86    25.407    15.000
Torsion angles, period  4. refined                3    14.491    15.000
Chiral centres: refined atoms                   177     0.201     0.200
Planar groups: refined atoms                    753     0.013     0.021
VDW repulsions: refined_atoms                  1112     0.311     0.200
VDW; torsion: refined_atoms                    1330     0.296     0.200
HBOND: refined_atoms                            114     0.301     0.200
M. chain bond B values: refined atoms           660     1.207     1.820
M. chain angle B values: refined atoms          804     2.090     2.745
S. chain bond B values: refined atoms           347     3.137     2.713
S. chain angle B values: refined atoms          564     5.002     3.750
Long range B values: refined atoms             1542     8.776    32.535
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.261, B  =   1.623
Partial structure    1: scale =    0.000, B  = 950.751
Overall anisotropic scale factors
   B11 = -1.69 B22 = -0.11 B33 =  1.81 B12 =  2.87 B13 =  1.29 B23 = -0.15
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11. <Rfactor> v. resln :N:1,6,7,11,12:
:Cycle   11. <Fobs> and <Fc> v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.001     125 100.00  1568.1  1014.1  0.43  0.43       0     0.0     0.0******  0.00
 0.004     184 100.00   599.4   498.5  0.40  0.40       0     0.0     0.0******  0.00
 0.006     279 100.00   476.3   410.5  0.38  0.38       6   588.9   391.2  0.35  0.35
 0.009     265 100.00   411.4   376.8  0.36  0.36      36   364.9   362.2  0.33  0.33
 0.011     322 100.00   323.7   340.9  0.41  0.41      24   311.3   340.2  0.57  0.57
 0.014     337 100.00   277.0   284.9  0.43  0.43      24   355.9   319.8  0.37  0.37
 0.016     372 100.00   249.0   239.5  0.45  0.45      12   205.6   283.1  0.45  0.45
 0.019     481 100.00   223.0   217.8  0.45  0.45      12   207.9   156.8  0.49  0.49
 0.021     459 100.00   210.9   200.2  0.45  0.45      12   201.4   193.2  0.45  0.45
 0.023     450 100.00   185.9   183.8  0.46  0.46      36   222.7   171.0  0.37  0.37
 0.026     439 100.00   177.4   170.6  0.42  0.42      72   201.8   192.1  0.45  0.45
 0.028     582 100.00   172.4   161.1  0.41  0.41       0     0.0     0.0******  0.00
 0.031     516 100.00   173.7   158.1  0.37  0.37      27   184.3   151.9  0.41  0.41
 0.033     612 100.00   178.3   159.2  0.35  0.35       4   131.5    98.1  0.25  0.25
 0.036     565 100.00   181.2   160.6  0.34  0.34      24   166.0   157.8  0.45  0.45
 0.038     612 100.00   184.8   167.3  0.32  0.32      24   166.1   176.5  0.40  0.40
 0.041     675 100.00   179.9   157.5  0.36  0.36      24   171.0   162.5  0.40  0.40
 0.043     570 100.00   182.4   161.0  0.35  0.35      88   187.9   155.3  0.44  0.44
 0.046     639 100.00   181.1   155.0  0.41  0.41      24   172.3   144.5  0.37  0.37
 0.048     664 100.00   179.7   149.4  0.39  0.39      84   177.5   137.1  0.46  0.46
$$

    ****                      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:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0014    125   0.928      0   0.000    125   0.928  1.171  0.0000  0.9670  0.0000  0.9415
  0.0039    184   0.857      0   0.000    184   0.857  1.007  0.0000  0.8389  0.0000  0.5279
  0.0063    279   0.799      0   0.000    279   0.799  0.885  0.8450  0.8160  0.5005  0.6006
  0.0088    265   0.770      0   0.000    265   0.770  0.784  0.7795  0.8044  0.4806  0.6375
  0.0112    315   0.750      0   0.000    315   0.750  0.696  0.6567  0.7621  0.3938  0.5468
  0.0137    337   0.692      0   0.000    337   0.692  0.622  0.7251  0.6728  0.4266  0.4778
  0.0161    372   0.652      0   0.000    372   0.652  0.586  0.6824  0.6221  0.8293  0.4436
  0.0186    481   0.643      0   0.000    481   0.643  0.567  0.5277  0.5969  0.3916  0.3820
  0.0210    459   0.647      0   0.000    459   0.647  0.548  0.5888  0.5910  0.3856  0.3360
  0.0235    450   0.632      0   0.000    450   0.632  0.532  0.5869  0.5768  0.5050  0.3878
  0.0259    439   0.635      0   0.000    439   0.635  0.579  0.6194  0.6053  0.3386  0.4842
  0.0284    582   0.662      0   0.000    582   0.662  0.669  0.0000  0.6496  0.0000  0.4797
  0.0308    516   0.712      0   0.000    516   0.712  0.757  0.7057  0.7353  0.6442  0.5929
  0.0333    612   0.762      0   0.000    612   0.762  0.835  0.6290  0.7990 -0.5619  0.6671
  0.0358    561   0.782      0   0.000    561   0.782  0.863  0.7633  0.8174  0.4535  0.6671
  0.0382    612   0.778      0   0.000    612   0.778  0.852  0.7858  0.8200  0.6329  0.6924
  0.0407    675   0.754      0   0.000    675   0.754  0.840  0.7559  0.7815  0.4831  0.6114
  0.0431    570   0.743      0   0.000    570   0.743  0.829  0.7284  0.7789  0.4003  0.6369
  0.0456    639   0.728      0   0.000    639   0.728  0.819  0.7535  0.7322  0.5705  0.5035
  0.0480    684   0.717      0   0.000    684   0.717  0.809  0.6492  0.7179  0.3380  0.5054
 $$
Resolution limits                    =     75.000     4.506
Number of used reflections           =       9137
Percentage observed                  =   100.0000
Percentage of free reflections       =     5.5119
Overall R factor                     =     0.3956
Free R factor                        =     0.4193
Average Fourier shell correlation    =     0.7246
AverageFree Fourier shell correlation=     0.6890
Overall weighted R factor            =     0.3956
Free weighted R factor               =     0.4193
Overall weighted R2 factor           =     0.4566
Free weighted R2 factor              =     0.4770
Average correlation coefficient      =     0.5472
Overall correlation coefficient      =     0.8359
Free correlation coefficient         =     0.5844
Cruickshanks DPI for coordinate error=     0.8086
DPI based on free R factor           =     0.6403
Overall figure of merit              =     0.7211
ML based su of positional parameters =     0.8057
ML based su of thermal parameters    =    60.2449
-----------------------------------------------------------------------------
  Time in seconds: CPU =        53.44
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.4570   0.4787   0.673       51653.    2980.5   0.0863  5.710   7.214  3.849   0.223
       1   0.4308   0.4550   0.687       50756.    2934.5   0.0559  3.338   4.782  2.457   0.211
       2   0.4194   0.4413   0.698       50269.    2909.7   0.0427  2.292   3.471  1.665   0.167
       3   0.4100   0.4330   0.706       49658.    2881.2   0.0386  1.975   3.366  1.564   0.231
       4   0.4064   0.4313   0.709       49572.    2875.1   0.0279  1.424   3.035  1.295   0.189
       5   0.4046   0.4299   0.711       49502.    2871.4   0.0176  0.884   2.975  1.206   0.178
       6   0.4022   0.4284   0.714       49446.    2868.3   0.0174  0.874   2.990  1.209   0.179
       7   0.4003   0.4263   0.716       49355.    2863.6   0.0185  0.930   3.028  1.223   0.186
       8   0.3986   0.4242   0.718       49289.    2860.5   0.0186  0.930   3.069  1.242   0.189
       9   0.3969   0.4213   0.720       49206.    2856.2   0.0201  1.011   3.118  1.260   0.194
      10   0.3956   0.4193   0.721       49181.    2857.0   0.0203  1.020   3.168  1.278   0.201
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.4570   0.3956
             R free    0.4787   0.4193
     Rms BondLength    0.0863   0.0203
      Rms BondAngle    7.2140   3.1684
     Rms ChirVolume    0.2229   0.2014
 $$
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 Refmac:  End of Refmac_5.8.0158  
Times: User:      56.5s System:    0.2s Elapsed:     0:57  
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CCP-EM process finished Wednesday, 08. March 2017 12:46pm ______________________
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