
________________________________________________________________________________

____________________ CCP-EM Process | Refmac refine (global) ___________________

__ Command _____________________________________________________________________
/Applications/ccp4-7.0/bin/refmac5 xyzin /Users/tom/ccpem_project/Refmac5_171/in_map.pdb hklin /Users/tom/ccpem_project/Refmac5_171/starting_map.mtz xyzout /Users/tom/ccpem_project/Refmac5_171/refined.pdb  << eof
labin FP=Fout0 PHIB=Pout0
make hydr no
solvent no
source EM MB
ncycle 3
weight auto
ncsr global
BFACtor SET 40.0
reso 4.5
ridge dist sigma 0.01
ridge dist dmax 4.2

end
eof
________________________________________________________________________________
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<hr>
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<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<pre>
 
 ###############################################################
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 ### CCP4 7.0.067: Refmac          version 5.8.0238 : 10/15/18##
 ###############################################################
 User: tom  Run date:  4/ 3/2019 Run time: 13:17:04 


 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: $$ Primary reference $$ 
   "Overview of refinement procedures within REFMAC5: utilizing data from different sources"
   O.Kovalevskiy, R.A.Nicholls, F.Long, G.N.Murshudov,(2018) 
   Acta Crystallogr. D74, 492-505

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

 $TEXT:Reference1: $$ Primary reference for EM $$ 
   "Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM
   R.A. Nicholls, M. Tykac, O.Kovalevskiy, G.N.Murshudov,(2018) 
   Acta Crystallogr. D74, 215-227

 $$
 $SUMMARY :Reference2:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference1: $$ Secondary reference $$ 
   "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

 $$
 $SUMMARY :Reference3:  $$ 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

 $$
 $SUMMARY :Reference4:  $$ Refmac: $$
 :TEXT:Reference2: $$

  Data line--- labin FP=Fout0 PHIB=Pout0
  Data line--- make hydr no
  Data line--- solvent no
  Data line--- source EM MB
  Data line--- ncycle 3
  Data line--- weight auto
  Data line--- ncsr global
  Data line--- BFACtor SET 40.0
  Data line--- reso 4.5
  Data line--- ridge dist sigma 0.01
  Data line--- ridge dist dmax 4.2
  Data line--- END

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN   Filename: /Users/tom/ccpem_project/Refmac5_171/starting_map.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  - /Users/tom/ccpem_project/Refmac5_171/in_map.pdb
Output coordinate file. Logical name - XYZOUT actual file name - /Users/tom/ccpem_project/Refmac5_171/refined.pdb
Input reflection file.  Logical name - HKLIN actual file name  - /Users/tom/ccpem_project/Refmac5_171/starting_map.mtz
Output reflection file. Logical name - HKLOUT actual file name - HKLOUT

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

Initial B values of all atoms will be set to     40.000


    ****                           Makecif parameters                           ****

Dictionary files for restraints : /Applications/ccp4-7.0/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /Applications/ccp4-7.0/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 not be used
    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       0.0025
  Refinement of individual isotropic Bfactors
  Refinement resln        :    75.0000  4.5063
  Estimated number of reflections :      13756
  Auto weighting. An attempt
  Refinement cycles       :     3
  Scaling type                           :
          Wilson scaling type with Guassians

  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:    75.0000  4.5063

  Damping factors:     1.0000  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
 
 NCS will defined automatically and applied

    ****                          Alignment parameters                          ****

     Alignment leve                   80.000%
     Aligment cut                    2.000A
     Iterative aligment              N

 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:           0.0100
     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 :/Users/tom/ccpem_project/Refmac5_171/in_map.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.51
 _lib_update       11/07/18
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 24613
                with complete description    : 24613
  NUMBER OF MODIFICATIONS                    :    69
  NUMBER OF LINKS                            :    76
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  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 =      1.90
            ch:AAA  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                   :    1656
  Number of missing atoms           :       0
  Number of rebuilt atoms           :       0
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0
 
  Number of bonds restraints    :    1680
  Number of angles restraints   :    2264
  Number of torsions restraints :    1357
  Number of chiralities         :     219
  Number of planar groups       :     300

_ccp4_form_factor.scat_method    'Mott-Bethe'
_ccp4_form_factor.scat_data_source  electron


 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     12.2220   0.0057   3.1346   9.8933   2.0141  28.9975   1.1672   0.5826 -11.5379
  C      2.3103  20.8439   1.0201  10.2075   1.5888   0.5687   0.8651  51.6512   0.2156
  S      6.9054   1.4679   5.2035  22.2151   1.4379   0.2536   1.5863  56.1720   0.8669
  O      3.0487  13.2771   2.2870   5.7011   1.5464   0.3239   0.8671  32.9089   0.2508


 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:      1680         0      1680
               Angles:      2264         0      2264
              Chirals:       219         0       219
               Planes:       300         0       300
             Torsions:      1357         0      1357
            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       9690
 Warning ==>The number of free reflections with flag         -999  is zero
 Warning ==> Switching off use of free R
--------------------------------------------------------------------------------
 Number of reflections in file       9690
 Number of reflections read           9690
 
   Current auto weighting coefficient =    13.76578    
 
 mode : HKRF


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



     CGMAT cycle number =      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
 Weight matrix   1.3574869E-03
 Actual weight    13.76578      is applied to the X-ray term
Norm of X_ray positional gradient                87.7
Norm of Geom. positional gradient                65.5
Norm of X_ray B-factor gradient                  72.7
Norm of Geom. B-factor gradient                  0.00
Product of X_ray and Geom posit. gradients     -0.551E+06
 Cosine of angle between them                      -0.019
Product of X_ray and Geom B-fact gradients       0.00
 Cosine of angle between them                       0.000


Residuals: XRAY=    -0.4601E+07 GEOM=      5545.     TOTAL=    -0.4595E+07
 function value   -4595328.    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1680     0.010     0.012
Bond angles  : refined atoms                   2264     1.495     1.648
Torsion angles, period  1. refined              213     3.886     5.000
Torsion angles, period  2. refined               88    29.870    22.386
Torsion angles, period  3. refined              313    13.237    15.000
Torsion angles, period  4. refined               13    10.393    15.000
Chiral centres: refined atoms                   219     0.066     0.200
Planar groups: refined atoms                   1275     0.006     0.020
VDW repulsions: refined_atoms                  1028     0.198     0.200
VDW; torsion: refined_atoms                    2202     0.339     0.200
HBOND: refined_atoms                             46     0.212     0.200
M. chain bond B values: refined atoms           855     0.000     4.000
M. chain angle B values: refined atoms         1067     0.000     6.000
S. chain bond B values: refined atoms           825     0.000     4.000
S. chain angle B values: refined atoms         1197     0.000     6.000
Long range B values: refined atoms             5762     0.000    74.747
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.8865, B  =   48.9574
Overall anisotropic scale factors
   B11 =  -0.90 B22 =  -1.32 B33 =   2.22 B12 =   1.57 B13 =  -1.34 B23 =  -0.21
-----------------------------------------------------------------------------

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

    ****                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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used $$
$$
 0.001     125 100.00   462.1   464.4  0.08  0.08
 0.004     184 100.00   176.6   165.5  0.19  0.19
 0.006     285 100.00   141.0   132.5  0.19  0.19
 0.009     301 100.00   119.6   111.0  0.25  0.25
 0.011     351 100.00    95.1    87.7  0.29  0.29
 0.014     361 100.00    83.3    77.8  0.30  0.30
 0.016     384 100.00    73.0    67.0  0.32  0.32
 0.019     493 100.00    65.6    60.5  0.37  0.37
 0.021     471 100.00    62.1    57.8  0.36  0.36
 0.023     486 100.00    55.6    52.2  0.40  0.40
 0.026     511 100.00    53.3    53.3  0.42  0.42
 0.028     582 100.00    50.8    50.5  0.41  0.41
 0.031     543 100.00    51.3    52.6  0.40  0.40
 0.033     616 100.00    52.5    52.8  0.41  0.41
 0.036     589 100.00    53.2    51.6  0.40  0.40
 0.038     636 100.00    54.2    52.0  0.35  0.35
 0.041     699 100.00    52.9    48.0  0.36  0.36
 0.043     658 100.00    54.0    45.5  0.35  0.35
 0.046     663 100.00    53.3    44.3  0.35  0.35
 0.048     749 100.00    52.9    40.9  0.38  0.38
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCwork CorrFofcWork$$
 $$
  0.0014    125   0.995      0   0.000    125   0.995  1.006  0.9975  0.9972
  0.0039    184   0.992      0   0.000    184   0.992  1.034  0.9669  0.9101
  0.0063    285   0.991      0   0.000    285   0.991  1.017  0.9552  0.9089
  0.0088    301   0.990      0   0.000    301   0.990  0.998  0.9230  0.8252
  0.0112    339   0.989      0   0.000    339   0.989  0.961  0.8944  0.7856
  0.0137    361   0.989      0   0.000    361   0.989  0.905  0.8684  0.7324
  0.0161    384   0.989      0   0.000    384   0.989  0.892  0.8315  0.6910
  0.0186    493   0.989      0   0.000    493   0.989  0.883  0.8152  0.6104
  0.0210    471   0.989      0   0.000    471   0.989  0.868  0.8107  0.5749
  0.0235    486   0.988      0   0.000    486   0.988  0.804  0.7683  0.5536
  0.0259    511   0.988      0   0.000    511   0.988  0.746  0.7579  0.4869
  0.0284    582   0.988      0   0.000    582   0.988  0.734  0.7325  0.4945
  0.0308    543   0.988      0   0.000    543   0.988  0.758  0.7759  0.5374
  0.0333    616   0.988      0   0.000    616   0.988  0.767  0.7686  0.5502
  0.0358    585   0.989      0   0.000    585   0.989  0.804  0.7804  0.5528
  0.0382    636   0.989      0   0.000    636   0.989  0.839  0.8057  0.5977
  0.0407    699   0.989      0   0.000    699   0.989  0.901  0.8034  0.5916
  0.0431    658   0.989      0   0.000    658   0.989  0.970  0.8271  0.6463
  0.0456    663   0.989      0   0.000    663   0.989  0.984  0.8126  0.6290
  0.0480    768   0.989      0   0.000    768   0.989  1.038  0.8071  0.5966
 $$
Resolution limits                    =     75.000     4.506
Number of used reflections           =       9671
Percentage observed                  =   100.0000
Percentage of free reflections       =     0.0000
Overall R factor                     =     0.3168
Average Fourier shell correlation    =     0.8140
Overall weighted R factor            =     0.3168
Overall weighted R2 factor           =     0.2553
Average correlation coefficient      =     0.6215
Overall correlation coefficient      =     0.9483
Cruickshanks DPI for coordinate error=     1.0524
Overall figure of merit              =     0.9889
ML based su of positional parameters =     0.6867
ML based su of thermal parameters    =    56.2011
-----------------------------------------------------------------------------
 Trying gamma equal   0.0000000E+00
 Convergence reached with no gamma cycles 
 fvalues   -334225.2       5544.603      -4595328.      1.0000000E+32


     CGMAT cycle number =      2

 Weight matrix   1.6559978E-03
 Actual weight    13.76578      is applied to the X-ray term


 function value   -4621752.    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1680     0.055     0.012
Bond angles  : refined atoms                   2264     3.608     1.648
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.8952, B  =   43.7289
Overall anisotropic scale factors
   B11 =  -0.59 B22 =  -1.38 B33 =   1.96 B12 =   0.97 B13 =  -1.05 B23 =  -0.07
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2697
Average Fourier shell correlation    =     0.8749
Average correlation coefficient      =     0.7311
Overall figure of merit              =     0.9894
-----------------------------------------------------------------------------
 Trying gamma equal   0.0000000E+00
 Convergence reached with no gamma cycles 
 fvalues   -337689.1       26803.18      -4621752.      -4595328.    


     CGMAT cycle number =      3

    ****                         Bond distance outliers                         ****

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

A     40 LYS CG  . - A     40 LYS CD  . mod.= 1.269 id.= 1.514 dev=  0.245 sig.= 0.020
A     40 LYS CD  . - A     40 LYS CE  . mod.= 1.758 id.= 1.514 dev= -0.244 sig.= 0.012
A     42 GLY CA  . - A     42 GLY C   . mod.= 1.633 id.= 1.526 dev= -0.107 sig.= 0.010
A     50 LYS CD  . - A     50 LYS CE  . mod.= 1.357 id.= 1.514 dev=  0.157 sig.= 0.012
A     69 LYS CE  . - A     69 LYS NZ  . mod.= 1.654 id.= 1.482 dev= -0.172 sig.= 0.012
A     75 GLU CG  . - A     75 GLU CD  . mod.= 2.024 id.= 1.519 dev= -0.505 sig.= 0.012
A     75 GLU CD  . - A     75 GLU OE2 . mod.= 0.828 id.= 1.247 dev=  0.419 sig.= 0.019
A     97 LYS CB  . - A     97 LYS CG  . mod.= 1.701 id.= 1.523 dev= -0.178 sig.= 0.012
A    114 GLU CD  . - A    114 GLU OE1 . mod.= 1.029 id.= 1.247 dev=  0.218 sig.= 0.019
A    115 LEU CB  . - A    115 LEU CG  . mod.= 1.673 id.= 1.528 dev= -0.145 sig.= 0.011
A    118 ASP CA  . - A    118 ASP CB  . mod.= 1.664 id.= 1.531 dev= -0.133 sig.= 0.011
A    118 ASP CG  . - A    118 ASP OD2 . mod.= 1.562 id.= 1.247 dev= -0.315 sig.= 0.019
A    122 GLY C   . - A    122 GLY O   . mod.= 1.074 id.= 1.229 dev=  0.155 sig.= 0.012
A    136 LYS CG  . - A    136 LYS CD  . mod.= 1.780 id.= 1.514 dev= -0.266 sig.= 0.020
A    141 LYS CG  . - A    141 LYS CD  . mod.= 2.142 id.= 1.514 dev= -0.628 sig.= 0.020
A    143 GLU CG  . - A    143 GLU CD  . mod.= 1.318 id.= 1.519 dev=  0.201 sig.= 0.012
A    151 GLU CD  . - A    151 GLU OE2 . mod.= 0.967 id.= 1.247 dev=  0.280 sig.= 0.019
A    157 LYS CE  . - A    157 LYS NZ  . mod.= 1.710 id.= 1.482 dev= -0.228 sig.= 0.012
A    160 GLN CG  . - A    160 GLN CD  . mod.= 1.935 id.= 1.509 dev= -0.426 sig.= 0.010
A    160 GLN CD  . - A    160 GLN OE1 . mod.= 1.399 id.= 1.229 dev= -0.170 sig.= 0.012
A    160 GLN CD  . - A    160 GLN NE2 . mod.= 1.207 id.= 1.323 dev=  0.116 sig.= 0.011
A    162 GLU CB  . - A    162 GLU CG  . mod.= 1.831 id.= 1.518 dev= -0.313 sig.= 0.015
A    165 ARG CA  . - A    165 ARG CB  . mod.= 1.732 id.= 1.532 dev= -0.200 sig.= 0.010
A    166 LYS CE  . - A    166 LYS NZ  . mod.= 1.629 id.= 1.482 dev= -0.147 sig.= 0.012
A    184 LYS CE  . - A    184 LYS NZ  . mod.= 1.981 id.= 1.482 dev= -0.499 sig.= 0.012
A    212 ILE CG1 . - A    212 ILE CD1 . mod.= 1.301 id.= 1.511 dev=  0.210 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
 Weight matrix   2.4061229E-03
 Actual weight    12.51435      is applied to the X-ray term
Norm of X_ray positional gradient                112.
Norm of Geom. positional gradient                248.
Norm of X_ray B-factor gradient                  89.1
Norm of Geom. B-factor gradient                  23.0
Product of X_ray and Geom posit. gradients     -0.190E+07
 Cosine of angle between them                      -0.014
Product of X_ray and Geom B-fact gradients     -0.106E+07
 Cosine of angle between them                      -0.313


Residuals: XRAY=    -0.4255E+07 GEOM=     0.2209E+05 TOTAL=    -0.4233E+07
 function value   -4233261.    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1680     0.047     0.012
Bond angles  : refined atoms                   2264     3.780     1.648
Torsion angles, period  1. refined              213     7.572     5.000
Torsion angles, period  2. refined               88    31.291    22.386
Torsion angles, period  3. refined              313    15.954    15.000
Torsion angles, period  4. refined               13     9.237    15.000
Chiral centres: refined atoms                   219     0.192     0.200
Planar groups: refined atoms                   1275     0.022     0.020
VDW repulsions: refined_atoms                  1030     0.206     0.200
VDW; torsion: refined_atoms                    2192     0.338     0.200
HBOND: refined_atoms                             46     0.215     0.200
M. chain bond B values: refined atoms           855     3.309     7.748
M. chain angle B values: refined atoms         1067     5.012    11.617
S. chain bond B values: refined atoms           825     4.939     7.540
S. chain angle B values: refined atoms         1197     7.458    11.360
Long range B values: refined atoms             6135     9.486   145.300
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.8998, B  =   13.2324
Overall anisotropic scale factors
   B11 =  -0.51 B22 =  -1.40 B33 =   1.92 B12 =   0.63 B13 =  -1.04 B23 =  -0.24
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle    3. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    3. M(Rfactor) v. resln :N:1,6,7:
:Cycle    3. M(Fobs) and M(Fc) v. resln :N:1,4,5:
:Cycle    3. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used $$
$$
 0.001     125 100.00   455.3   468.3  0.06  0.06
 0.004     184 100.00   174.0   166.8  0.12  0.12
 0.006     285 100.00   139.0   131.0  0.15  0.15
 0.009     301 100.00   117.8   109.3  0.20  0.20
 0.011     351 100.00    93.7    87.3  0.23  0.23
 0.014     361 100.00    82.1    77.3  0.23  0.23
 0.016     384 100.00    71.9    66.0  0.26  0.26
 0.019     493 100.00    64.6    60.6  0.29  0.29
 0.021     471 100.00    61.2    57.9  0.30  0.30
 0.023     486 100.00    54.8    53.9  0.30  0.30
 0.026     511 100.00    52.5    54.1  0.32  0.32
 0.028     582 100.00    50.1    51.3  0.31  0.31
 0.031     543 100.00    50.6    53.6  0.31  0.31
 0.033     616 100.00    51.7    53.4  0.31  0.31
 0.036     589 100.00    52.4    53.1  0.30  0.30
 0.038     636 100.00    53.4    53.4  0.26  0.26
 0.041     699 100.00    52.1    50.1  0.27  0.27
 0.043     658 100.00    53.2    48.4  0.26  0.26
 0.046     663 100.00    52.5    47.0  0.27  0.27
 0.048     749 100.00    52.1    44.4  0.28  0.28
$$

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

 $TABLE: Cycle    3. FSC and  Fom(<cos(DelPhi)>-acentric, centric, overall v resln:
 $GRAPHS:Cycle    3. M(Fom) v. resln :N:1,3,5,7,8,9,10:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCwork CorrFofcWork$$
 $$
  0.0014    125   0.997      0   0.000    125   0.997  0.997  0.9990  0.9990
  0.0039    184   0.994      0   0.000    184   0.994  1.033  0.9858  0.9629
  0.0063    285   0.992      0   0.000    285   0.992  1.037  0.9740  0.9456
  0.0088    301   0.991      0   0.000    301   0.991  1.033  0.9563  0.8976
  0.0112    339   0.991      0   0.000    339   0.991  1.012  0.9432  0.8688
  0.0137    361   0.990      0   0.000    361   0.990  0.977  0.9260  0.8407
  0.0161    384   0.990      0   0.000    384   0.990  0.966  0.9033  0.8097
  0.0186    493   0.989      0   0.000    493   0.989  0.958  0.8971  0.7633
  0.0210    471   0.989      0   0.000    471   0.989  0.935  0.8920  0.7317
  0.0235    486   0.989      0   0.000    486   0.989  0.886  0.8795  0.7545
  0.0259    511   0.989      0   0.000    511   0.989  0.836  0.8653  0.7021
  0.0284    582   0.989      0   0.000    582   0.989  0.834  0.8649  0.7271
  0.0308    543   0.989      0   0.000    543   0.989  0.834  0.8795  0.7481
  0.0333    616   0.989      0   0.000    616   0.989  0.855  0.8853  0.7543
  0.0358    585   0.989      0   0.000    585   0.989  0.883  0.8935  0.7545
  0.0382    636   0.990      0   0.000    636   0.990  0.912  0.9077  0.7832
  0.0407    699   0.990      0   0.000    699   0.990  0.945  0.9082  0.7892
  0.0431    658   0.990      0   0.000    658   0.990  0.995  0.9144  0.8083
  0.0456    663   0.990      0   0.000    663   0.990  1.022  0.9102  0.7982
  0.0480    768   0.990      0   0.000    768   0.990  1.054  0.9051  0.7787
 $$
Resolution limits                    =     75.000     4.506
Number of used reflections           =       9671
Percentage observed                  =   100.0000
Percentage of free reflections       =     0.0000
Overall R factor                     =     0.2419
Average Fourier shell correlation    =     0.9046
Overall weighted R factor            =     0.2419
Overall weighted R2 factor           =     0.1951
Average correlation coefficient      =     0.7886
Overall correlation coefficient      =     0.9699
Cruickshanks DPI for coordinate error=     0.8037
Overall figure of merit              =     0.9898
ML based su of positional parameters =     0.4741
ML based su of thermal parameters    =    38.7824
-----------------------------------------------------------------------------
 Trying gamma equal   0.0000000E+00
 Convergence reached with no gamma cycles 


 fvalues   -340040.5       22090.07      -4264903.      -4621752.    
 fvalues   -340040.5       22090.07      -4264903.      -4233296.    

    ****                         Bond distance outliers                         ****

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

A     40 LYS CG  . - A     40 LYS CD  . mod.= 1.041 id.= 1.514 dev=  0.473 sig.= 0.020
A     40 LYS CD  . - A     40 LYS CE  . mod.= 1.970 id.= 1.514 dev= -0.456 sig.= 0.012
A     75 GLU CG  . - A     75 GLU CD  . mod.= 1.854 id.= 1.519 dev= -0.335 sig.= 0.012
A     75 GLU CD  . - A     75 GLU OE1 . mod.= 1.590 id.= 1.247 dev= -0.343 sig.= 0.019
A     75 GLU CD  . - A     75 GLU OE2 . mod.= 0.810 id.= 1.247 dev=  0.437 sig.= 0.019
A     97 LYS CG  . - A     97 LYS CD  . mod.= 1.722 id.= 1.514 dev= -0.208 sig.= 0.020
A     97 LYS CD  . - A     97 LYS CE  . mod.= 1.648 id.= 1.514 dev= -0.134 sig.= 0.012
A    114 GLU CD  . - A    114 GLU OE1 . mod.= 1.045 id.= 1.247 dev=  0.202 sig.= 0.019
A    118 ASP CA  . - A    118 ASP CB  . mod.= 1.646 id.= 1.531 dev= -0.115 sig.= 0.011
A    118 ASP CG  . - A    118 ASP OD2 . mod.= 1.508 id.= 1.247 dev= -0.261 sig.= 0.019
A    122 GLY C   . - A    122 GLY O   . mod.= 1.069 id.= 1.229 dev=  0.160 sig.= 0.012
A    141 LYS CG  . - A    141 LYS CD  . mod.= 2.330 id.= 1.514 dev= -0.816 sig.= 0.020
A    157 LYS CE  . - A    157 LYS NZ  . mod.= 1.805 id.= 1.482 dev= -0.323 sig.= 0.012
A    162 GLU CB  . - A    162 GLU CG  . mod.= 1.713 id.= 1.518 dev= -0.195 sig.= 0.015
A    162 GLU CG  . - A    162 GLU CD  . mod.= 1.773 id.= 1.519 dev= -0.254 sig.= 0.012
A    165 ARG CA  . - A    165 ARG CB  . mod.= 1.677 id.= 1.532 dev= -0.145 sig.= 0.010
A    166 LYS CE  . - A    166 LYS NZ  . mod.= 1.697 id.= 1.482 dev= -0.215 sig.= 0.012
A    184 LYS CD  . - A    184 LYS CE  . mod.= 1.891 id.= 1.514 dev= -0.377 sig.= 0.012
A    192 LYS CE  . - A    192 LYS NZ  . mod.= 1.624 id.= 1.482 dev= -0.142 sig.= 0.012
A    211 LYS CE  . - A    211 LYS NZ  . mod.= 1.795 id.= 1.482 dev= -0.313 sig.= 0.012
A    212 ILE CG1 . - A    212 ILE CD1 . mod.= 1.302 id.= 1.511 dev=  0.209 sig.= 0.020

 LABOUT FP=FP SIGFP=SIGFP FC=FC PHIC=PHIC FC_ALL=FC_ALL PHIC_ALL=PHIC_ALL FWT=FW
 T PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM PHCOMB=PHCOMB FC_ALL_LS=FC_AL
 L_LS PHIC_ALL_LS=PHIC_ALL_LS

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: HKLOUT 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1680     0.047     0.012
Bond angles  : refined atoms                   2264     3.792     1.648
Torsion angles, period  1. refined              213     7.851     5.000
Torsion angles, period  2. refined               88    30.900    22.386
Torsion angles, period  3. refined              313    17.353    15.000
Torsion angles, period  4. refined               13     9.941    15.000
Chiral centres: refined atoms                   219     0.184     0.200
Planar groups: refined atoms                   1275     0.023     0.020
VDW repulsions: refined_atoms                  1032     0.210     0.200
VDW; torsion: refined_atoms                    2196     0.340     0.200
HBOND: refined_atoms                             46     0.214     0.200
M. chain bond B values: refined atoms           855     9.786     8.313
M. chain angle B values: refined atoms         1067    14.990    12.457
S. chain bond B values: refined atoms           825    11.412     8.335
S. chain angle B values: refined atoms         1197    17.253    12.499
Long range B values: refined atoms             6120    22.259   156.402
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.8969, B  =    8.6741
Overall anisotropic scale factors
   B11 =  -0.62 B22 =  -1.27 B33 =   1.89 B12 =   0.28 B13 =  -0.92 B23 =  -0.40
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle    4. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    4. M(Rfactor) v. resln :N:1,6,7:
:Cycle    4. M(Fobs) and M(Fc) v. resln :N:1,4,5:
:Cycle    4. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used $$
$$
 0.001     125 100.00   456.7   470.4  0.06  0.06
 0.004     184 100.00   174.6   167.7  0.12  0.12
 0.006     285 100.00   139.4   131.1  0.15  0.15
 0.009     301 100.00   118.2   109.8  0.19  0.19
 0.011     351 100.00    94.0    87.5  0.21  0.21
 0.014     361 100.00    82.3    77.3  0.21  0.21
 0.016     384 100.00    72.1    66.6  0.23  0.23
 0.019     493 100.00    64.8    61.3  0.26  0.26
 0.021     471 100.00    61.4    58.1  0.27  0.27
 0.023     486 100.00    55.0    54.1  0.26  0.26
 0.026     511 100.00    52.7    54.4  0.29  0.29
 0.028     582 100.00    50.2    52.0  0.27  0.27
 0.031     543 100.00    50.7    54.0  0.27  0.27
 0.033     616 100.00    51.8    53.9  0.27  0.27
 0.036     589 100.00    52.6    53.8  0.25  0.25
 0.038     636 100.00    53.6    54.3  0.21  0.21
 0.041     699 100.00    52.3    51.2  0.22  0.22
 0.043     658 100.00    53.3    49.6  0.22  0.22
 0.046     663 100.00    52.7    47.9  0.22  0.22
 0.048     749 100.00    52.3    45.7  0.24  0.24
$$

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

 $TABLE: Cycle    4. FSC and  Fom(<cos(DelPhi)>-acentric, centric, overall v resln:
 $GRAPHS:Cycle    4. M(Fom) v. resln :N:1,3,5,7,8,9,10:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCwork CorrFofcWork$$
 $$
  0.0014    125   0.997      0   0.000    125   0.997  0.997  0.9992  0.9991
  0.0039    184   0.994      0   0.000    184   0.994  1.034  0.9872  0.9666
  0.0063    285   0.992      0   0.000    285   0.992  1.041  0.9762  0.9516
  0.0088    301   0.991      0   0.000    301   0.991  1.038  0.9612  0.9092
  0.0112    339   0.991      0   0.000    339   0.991  1.024  0.9532  0.8894
  0.0137    361   0.990      0   0.000    361   0.990  0.994  0.9397  0.8685
  0.0161    384   0.990      0   0.000    384   0.990  0.983  0.9194  0.8435
  0.0186    493   0.990      0   0.000    493   0.990  0.973  0.9170  0.8069
  0.0210    471   0.990      0   0.000    471   0.990  0.955  0.9153  0.7835
  0.0235    486   0.990      0   0.000    486   0.990  0.915  0.9101  0.8132
  0.0259    511   0.989      0   0.000    511   0.989  0.868  0.8987  0.7713
  0.0284    582   0.990      0   0.000    582   0.990  0.863  0.9048  0.8060
  0.0308    543   0.990      0   0.000    543   0.990  0.864  0.9155  0.8117
  0.0333    616   0.990      0   0.000    616   0.990  0.884  0.9238  0.8249
  0.0358    585   0.990      0   0.000    585   0.990  0.910  0.9305  0.8327
  0.0382    636   0.990      0   0.000    636   0.990  0.931  0.9415  0.8603
  0.0407    699   0.990      0   0.000    699   0.990  0.966  0.9405  0.8586
  0.0431    658   0.990      0   0.000    658   0.990  1.011  0.9448  0.8693
  0.0456    663   0.990      0   0.000    663   0.990  1.033  0.9405  0.8677
  0.0480    768   0.990      0   0.000    768   0.990  1.057  0.9313  0.8353
 $$
Resolution limits                    =     75.000     4.506
Number of used reflections           =       9671
Percentage observed                  =   100.0000
Percentage of free reflections       =     0.0000
Overall R factor                     =     0.2122
Average Fourier shell correlation    =     0.9317
Overall weighted R factor            =     0.2122
Overall weighted R2 factor           =     0.1733
Average correlation coefficient      =     0.8446
Overall correlation coefficient      =     0.9763
Cruickshanks DPI for coordinate error=     0.7050
Overall figure of merit              =     0.9903
ML based su of positional parameters =     0.4741
ML based su of thermal parameters    =    38.7824
-----------------------------------------------------------------------------
  Time in seconds: CPU =         2.68
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.3168   0.0      0.989     -334225.       0.0   0.0098  0.803   1.495  0.930   0.066
       1   0.2697   0.0      0.989     -337689.       0.0   0.0552  4.364   3.608  2.211   0.178
       2   0.2419   0.0      0.990     -340038.       0.0   0.0465  3.476   3.780  2.264   0.192
       3   0.2122   0.0      0.990     -342780.       0.0   0.0466  3.263   3.792  2.305   0.184
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.3168   0.2122
     Rms BondLength    0.0098   0.0466
      Rms BondAngle    1.4955   3.7924
     Rms ChirVolume    0.0663   0.1837
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
 Refmac:  End of Refmac_5.8.0238  
Times: User:       6.8s System:    0.5s Elapsed:     0:09  
</pre>
</html>
<!--SUMMARY_END--></FONT></B>

CCP-EM version dev 1.2.0-42-g243bc59 ___________________________________________

CCP-EM process finished Monday, 04. March 2019 01:17pm _________________________
________________________________________________________________________________
