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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 26/ 5/2020 Run time: 13:19:36 


 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.


 $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--- make     check NONE
  Data line--- refi     type REST reso 41.96 1.94     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- bins 4
  Data line--- ncyc 10
  Data line--- monitor MEDIum
  Data line--- free 0
  Data line--- END

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

 LABIN FP=FP SIGFP=SIGFP FREE=FreeR_flag

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


Input coordinate file.  Logical name - XYZIN actual file name  - CDO_step0-01A_R00_1-95A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-94A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_step0-01A_R00_1-94A.mtz

Cell from mtz :    57.632    57.632   122.391    90.000    90.000    90.000
Space group from mtz: number -   96; name - P 43 21 2

  Refinement type                        : Restrained

    ****                           Makecif parameters                           ****

Dictionary files for restraints : /protein2/ccp4/ccp4-7.0/ccp4-7.0/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /protein2/ccp4/ccp4-7.0/ccp4-7.0/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 be restored in their riding positions
    Links between monomers will be checked. Only those links present in the coordinate file will be used
    Standard sugar links will be analysed and used
    For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
    Symmetry related links will be analysed and used
    Cis peptides will be found and used automatically


  Residual                               : Rice Maximum Likelihood for Fs

    ****                    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     1.200
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:     4       0.0664
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.9400
  Estimated number of reflections :      20160
  Free R exclusion - flag equals:     0
  Auto weighting. An attempt
  Refinement cycles       :    10
  Scaling type                           :
          Wilson scaling type with Guassians

  Estimation of D/Sigma in resolution bins
  using  free set of reflns with experimental sigmas
  using  free set of reflns with experimental sigmas

  Scaling and SigmaA resln:    41.9635  1.9400

  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

 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
Rigid bond outliers    10.000
Sphericity outliers    10.000
---------------------------------------------------------------

 Input file :CDO_step0-01A_R00_1-95A.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.51
 _lib_update       11/07/18
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 24624
                with complete description    : 24624
  NUMBER OF MODIFICATIONS                    :    70
  NUMBER OF LINKS                            :    77
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  Number of atoms    :    1836
  Number of residues :     502
  Number of chains   :       4
  I am reading library. Please wait.
                mon_lib.cif
  INFO:     link is found (not be used) dist=   1.983 ideal_dist=   2.090
            ch:AAA  res:  86  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.207 ideal_dist=   2.090
            ch:AAA  res:  88  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   1.846 ideal_dist=   1.720
            ch:AAA  res:  93  CYS              at:SG  .->ch:AAA  res: 157  TYR              at:CE1 .
  INFO:     link is found (not be used) dist=   2.199 ideal_dist=   2.090
            ch:AAA  res: 140  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.357 ideal_dist=   1.945
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:N   .
  INFO:     link is found (not be used) dist=   2.433 ideal_dist=   2.235
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:SG  .
  INFO:     link is found (not be used) dist=   2.056 ideal_dist=   1.870
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:OD  .
  --------------------------------
  --- title of input coord file ---

  PDB_code:xxxx
  PDB_name:----
  PDB_date:22-OCT-19
  --------------------------------
  ATTENTION: atom:OXT  PRO               190  AAA  is missing in the structure
  Number of chains                  :       4
  Total number of monomers          :     502
  Number of atoms                   :    3945
  Number of missing atoms           :       1
  Number of rebuilt atoms           :    1480
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0

_ccp4_form_factor.scat_method    'Sum of Gaussians'
_ccp4_form_factor.scat_data_source  X-ray


 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
  H      0.4930  10.5109   0.3229  26.1257   0.1402   3.1424   0.0408  57.7997   0.0030
  C      2.3103  20.8439   1.0201  10.2075   1.5888   0.5687   0.8651  51.6512   0.2156
  O      3.0487  13.2771   2.2870   5.7011   1.5464   0.3239   0.8671  32.9089   0.2508
  S      6.9054   1.4679   5.2035  22.2151   1.4379   0.2536   1.5863  56.1720   1.0490
  FE    11.7738   4.7611   7.3600   0.3072   3.5235  15.3535   2.3054  76.8805   1.2805


 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:      2949         0      2949
               Angles:      5344         0      5344
              Chirals:       196         0       196
               Planes:       453         0       453
             Torsions:      1556         0      1556
            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        817
Number of   all  reflections      15982
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          15982

   Current auto weighting coefficient =    7.3495216    

 mode : HKRF


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



     CGMAT cycle number =      1

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.912 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    30   30   64
 Minimum acceptable grid spacing:    72   72  151
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    30   30   64
 Minimum acceptable grid spacing:    72   72  151
 Weight matrix   0.20045231    
 Actual weight    7.3495216      is applied to the X-ray term
Norm of X_ray positional gradient                31.3
Norm of Geom. positional gradient                77.4
Norm of X_ray B-factor gradient                  104.
Norm of Geom. B-factor gradient                  104.
Product of X_ray and Geom posit. gradients     -0.851E+07
 Cosine of angle between them                      -0.363
Product of X_ray and Geom B-fact gradients     -0.320E+08
 Cosine of angle between them                      -0.922


Residuals: XRAY=     0.6125E+06 GEOM=     0.1247E+05 TOTAL=     0.6250E+06
 function value    624958.00    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.035     0.017
Bond angles  : refined atoms                   2106     1.687     1.644
Bond angles  : others                          3238     2.342     1.580
Torsion angles, period  1. refined              185     7.073     5.000
Torsion angles, period  2. refined               90    36.668    22.778
Torsion angles, period  3. refined              268    14.491    15.000
Torsion angles, period  4. refined                9    11.107    15.000
Chiral centres: refined atoms                   196     0.082     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.015     0.020
VDW repulsions: refined_atoms                   302     0.243     0.200
VDW repulsions.others                          1329     0.220     0.200
VDW; torsion: refined_atoms                     716     0.170     0.200
VDW; torsion.others                             699     0.079     0.200
HBOND: refined_atoms                            234     0.207     0.200
Metal-ion: refined_atoms                          1     0.017     0.200
VDW repulsions: symmetry: refined_atoms           9     0.232     0.200
VDW repulsions: symmetry: others                 25     0.195     0.200
HBOND: symmetry: refined_atoms                   19     0.220     0.200
M. chain bond B values: refined atoms           746     1.506     1.197
M. chain bond B values: others                  746     1.506     1.197
M. chain angle B values: refined atoms          929     2.449     1.781
M. chain angle B values: others                 930     2.448     1.781
S. chain bond B values: refined atoms           811     2.368     1.514
S. chain bond B values: others                  810     2.365     1.514
S. chain angle B values: refined atoms         1177     3.780     2.130
S. chain angle B values: others                1178     3.778     2.130
Long range B values: refined atoms             1860     6.681    16.768
Long range B values: others                    1762     6.354    15.357
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0399, B  =   -0.1108
Partial structure    1: scale =     0.3748, B  =   46.3028
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.55 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.034    2083 100.00   485.1   487.9  0.16  0.17      93   475.0   486.6  0.20  0.22
 0.100    3512 100.00   402.1   383.9  0.16  0.15     175   399.9   370.3  0.22  0.21
 0.166    4412  99.96   254.9   251.9  0.16  0.14     258   272.2   263.7  0.22  0.19
 0.233    5154 100.00   202.2   201.0  0.16  0.13     291   208.2   209.5  0.22  0.18
$$

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

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0337   1426   0.906    657   0.806   2083   0.874  0.959  0.9608  0.9689  0.9172  0.9441
  0.1000   2841   0.883    671   0.765   3512   0.860  1.000  0.9448  0.9617  0.8799  0.9425
  0.1663   3747   0.855    665   0.766   4412   0.842  0.967  0.9423  0.9544  0.8822  0.9377
  0.2326   4493   0.869    663   0.747   5156   0.853  0.964  0.9449  0.9578  0.8778  0.9398
 $$
Resolution limits                    =     41.964     1.940
Number of used reflections           =      15163
Percentage observed                  =    99.9812
Percentage of free reflections       =     5.1126
Overall R factor                     =     0.1591
Free R factor                        =     0.2169
Average Fourier shell correlation    =     0.9593
AverageFree Fourier shell correlation=     0.9459
Overall weighted R factor            =     0.1494
Free weighted R factor               =     0.2020
Overall weighted R2 factor           =     0.1813
Free weighted R2 factor              =     0.2435
Average correlation coefficient      =     0.9404
Overall correlation coefficient      =     0.9545
Free correlation coefficient         =     0.9101
Cruickshanks DPI for coordinate error=     0.1522
DPI based on free R factor           =     0.1490
Overall figure of merit              =     0.8546
ML based su of positional parameters =     0.0928
ML based su of thermal parameters    =     3.1264
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    83336.797       12472.443       624958.00      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.20710836    
 Actual weight    7.3495216      is applied to the X-ray term


 function value    619066.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0399, B  =   -0.1402
Partial structure    1: scale =     0.3749, B  =   46.4962
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1588
Free R factor                        =     0.2158
Average Fourier shell correlation    =     0.9604
AverageFree Fourier shell correlation=     0.9470
Average correlation coefficient      =     0.9410
Overall figure of merit              =     0.8583
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    83143.586       8000.6992       619066.25       624958.00    


     CGMAT cycle number =      3

 Weight matrix   0.20765363    
 Actual weight    7.3495216      is applied to the X-ray term


 function value    618941.94    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0399, B  =   -0.1407
Partial structure    1: scale =     0.3750, B  =   46.3456
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1585
Free R factor                        =     0.2156
Average Fourier shell correlation    =     0.9605
AverageFree Fourier shell correlation=     0.9472
Average correlation coefficient      =     0.9412
Overall figure of merit              =     0.8585
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    83122.352       8032.4575       618941.94       619066.25    


     CGMAT cycle number =      4

 Weight matrix   0.20762573    
 Actual weight    7.3495216      is applied to the X-ray term


 function value    618924.75    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0399, B  =   -0.1398
Partial structure    1: scale =     0.3748, B  =   46.3596
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1584
Free R factor                        =     0.2155
Average Fourier shell correlation    =     0.9605
AverageFree Fourier shell correlation=     0.9472
Average correlation coefficient      =     0.9413
Overall figure of merit              =     0.8586
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    83117.953       8047.5771       618924.75       618941.94    


     CGMAT cycle number =      5

 Weight matrix   0.20762715    
 Actual weight    7.3495216      is applied to the X-ray term


 function value    618912.56    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0399, B  =   -0.1462
Partial structure    1: scale =     0.3747, B  =   46.3754
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1583
Free R factor                        =     0.2156
Average Fourier shell correlation    =     0.9605
AverageFree Fourier shell correlation=     0.9472
Average correlation coefficient      =     0.9413
Overall figure of merit              =     0.8586
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    83116.258       8047.8232       618912.56       618924.75    


     CGMAT cycle number =      6

 Weight matrix   0.20751683    
 Actual weight    7.3495216      is applied to the X-ray term


 function value    618917.63    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0399, B  =   -0.1497
Partial structure    1: scale =     0.3748, B  =   46.4398
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1583
Free R factor                        =     0.2156
Average Fourier shell correlation    =     0.9605
AverageFree Fourier shell correlation=     0.9471
Average correlation coefficient      =     0.9414
Overall figure of merit              =     0.8585
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    83118.258       8042.8418       618904.06       618912.56    
 fvalues    83118.258       8042.8418       618904.06       618922.25    


     CGMAT cycle number =      7

 Weight matrix   0.20746247    
 Actual weight    7.3495216      is applied to the X-ray term


 function value    618883.63    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0399, B  =   -0.1503
Partial structure    1: scale =     0.3749, B  =   46.3236
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1583
Free R factor                        =     0.2157
Average Fourier shell correlation    =     0.9605
AverageFree Fourier shell correlation=     0.9471
Average correlation coefficient      =     0.9414
Overall figure of merit              =     0.8585
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    83114.063       8035.0127       618883.63       618922.25    


     CGMAT cycle number =      8

 Weight matrix   0.20699871    
 Actual weight    7.3495216      is applied to the X-ray term


 function value    618934.13    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0399, B  =   -0.1595
Partial structure    1: scale =     0.3747, B  =   46.4144
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1583
Free R factor                        =     0.2157
Average Fourier shell correlation    =     0.9605
AverageFree Fourier shell correlation=     0.9471
Average correlation coefficient      =     0.9414
Overall figure of merit              =     0.8583
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    83118.680       8025.5342       618900.56       618883.63    
 fvalues    83118.680       8025.5342       618900.56       618908.13    


     CGMAT cycle number =      9

 Weight matrix   0.20711836    
 Actual weight    7.3495216      is applied to the X-ray term


 function value    618914.06    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0399, B  =   -0.1415
Partial structure    1: scale =     0.3743, B  =   46.3085
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1583
Free R factor                        =     0.2157
Average Fourier shell correlation    =     0.9605
AverageFree Fourier shell correlation=     0.9471
Average correlation coefficient      =     0.9414
Overall figure of merit              =     0.8583
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02

 fvalues    83118.445       8024.0190       618904.81       618908.13    


     CGMAT cycle number =     10

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.922 id.= 3.000 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    30   30   64
 Minimum acceptable grid spacing:    72   72  151
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    30   30   64
 Minimum acceptable grid spacing:    72   72  151
 Weight matrix   0.20708154    
 Actual weight    7.3495216      is applied to the X-ray term
Norm of X_ray positional gradient                30.8
Norm of Geom. positional gradient                30.8
Norm of X_ray B-factor gradient                  103.
Norm of Geom. B-factor gradient                  108.
Product of X_ray and Geom posit. gradients     -0.917E+07
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.350E+08
 Cosine of angle between them                      -0.980


Residuals: XRAY=     0.6109E+06 GEOM=      8019.     TOTAL=     0.6189E+06
 function value    618931.81    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.693     1.644
Bond angles  : others                          3238     1.415     1.580
Torsion angles, period  1. refined              185     7.078     5.000
Torsion angles, period  2. refined               90    36.838    22.778
Torsion angles, period  3. refined              268    14.297    15.000
Torsion angles, period  4. refined                9    11.002    15.000
Chiral centres: refined atoms                   196     0.083     0.200
Planar groups: refined atoms                   1743     0.009     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   305     0.241     0.200
VDW repulsions.others                          1366     0.192     0.200
VDW; torsion: refined_atoms                     709     0.170     0.200
VDW; torsion.others                             777     0.083     0.200
HBOND: refined_atoms                            229     0.207     0.200
Metal-ion: refined_atoms                          1     0.004     0.200
VDW repulsions: symmetry: refined_atoms           9     0.225     0.200
VDW repulsions: symmetry: others                 25     0.185     0.200
HBOND: symmetry: refined_atoms                   19     0.225     0.200
M. chain bond B values: refined atoms           746     1.522     1.198
M. chain bond B values: others                  746     1.521     1.198
M. chain angle B values: refined atoms          929     2.459     1.783
M. chain angle B values: others                 930     2.458     1.783
S. chain bond B values: refined atoms           811     2.411     1.520
S. chain bond B values: others                  810     2.408     1.519
S. chain angle B values: refined atoms         1177     3.824     2.138
S. chain angle B values: others                1178     3.823     2.138
Long range B values: refined atoms             1853     6.642    16.734
Long range B values: others                    1753     6.313    15.335
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0399, B  =   -0.1476
Partial structure    1: scale =     0.3743, B  =   46.2636
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10.  v. resln :N:1,6,7,11,12:
:Cycle   10.  and  v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.034    2083 100.00   485.6   488.6  0.16  0.17      93   475.5   486.6  0.20  0.22
 0.100    3512 100.00   402.5   384.0  0.16  0.15     175   400.3   371.1  0.22  0.21
 0.166    4412  99.96   255.1   252.1  0.16  0.14     258   272.5   263.3  0.22  0.19
 0.233    5154 100.00   202.4   201.2  0.16  0.13     291   208.4   208.9  0.22  0.18
$$

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

 $TABLE: Cycle   10. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0337   1426   0.918    657   0.820   2083   0.887  0.959  0.9633  0.9712  0.9168  0.9430
  0.1000   2841   0.886    671   0.769   3512   0.864  1.000  0.9465  0.9632  0.8819  0.9438
  0.1663   3747   0.857    665   0.766   4412   0.843  0.967  0.9431  0.9550  0.8843  0.9385
  0.2326   4493   0.872    663   0.750   5156   0.856  0.964  0.9458  0.9591  0.8780  0.9416
 $$
Resolution limits                    =     41.964     1.940
Number of used reflections           =      15163
Percentage observed                  =    99.9812
Percentage of free reflections       =     5.1126
Overall R factor                     =     0.1583
Free R factor                        =     0.2157
Average Fourier shell correlation    =     0.9605
AverageFree Fourier shell correlation=     0.9471
Overall weighted R factor            =     0.1491
Free weighted R factor               =     0.2007
Overall weighted R2 factor           =     0.1815
Free weighted R2 factor              =     0.2426
Average correlation coefficient      =     0.9414
Overall correlation coefficient      =     0.9548
Free correlation coefficient         =     0.9109
Cruickshanks DPI for coordinate error=     0.1515
DPI based on free R factor           =     0.1482
Overall figure of merit              =     0.8583
ML based su of positional parameters =     0.0912
ML based su of thermal parameters    =     3.0836
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    83121.398       8018.5234       618931.13       618904.81    

 fvalues    83121.398       8018.5234       618911.63       618921.00    
 fvalues    83121.398       8018.5234       618911.63       618921.00    

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.922 id.= 3.000 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 LABOUT FreeR_flag=FreeR_flag FP=FP SIGFP=SIGFP FC=FC PHIC=PHIC FC_ALL=FC_ALL PHIC_ALL=PHIC_ALL FWT=FWT PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM FC_ALL_LS=FC_ALL_LS PHIC_ALL_LS=PHIC_ALL_LS

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_step0-01A_R00_1-94A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.693     1.644
Bond angles  : others                          3238     1.415     1.580
Torsion angles, period  1. refined              185     7.078     5.000
Torsion angles, period  2. refined               90    36.842    22.778
Torsion angles, period  3. refined              268    14.293    15.000
Torsion angles, period  4. refined                9    10.997    15.000
Chiral centres: refined atoms                   196     0.083     0.200
Planar groups: refined atoms                   1743     0.009     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   306     0.241     0.200
VDW repulsions.others                          1365     0.192     0.200
VDW; torsion: refined_atoms                     709     0.170     0.200
VDW; torsion.others                             776     0.083     0.200
HBOND: refined_atoms                            228     0.207     0.200
Metal-ion: refined_atoms                          1     0.004     0.200
VDW repulsions: symmetry: refined_atoms           9     0.225     0.200
VDW repulsions: symmetry: others                 25     0.185     0.200
HBOND: symmetry: refined_atoms                   19     0.225     0.200
M. chain bond B values: refined atoms           746     1.522     1.198
M. chain bond B values: others                  746     1.521     1.198
M. chain angle B values: refined atoms          929     2.460     1.783
M. chain angle B values: others                 930     2.458     1.783
S. chain bond B values: refined atoms           811     2.411     1.520
S. chain bond B values: others                  810     2.408     1.519
S. chain angle B values: refined atoms         1177     3.824     2.138
S. chain angle B values: others                1178     3.822     2.138
Long range B values: refined atoms             1854     6.651    16.755
Long range B values: others                    1754     6.324    15.359
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0399, B  =   -0.1459
Partial structure    1: scale =     0.3743, B  =   46.2636
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.034    2083 100.00   485.4   488.5  0.16  0.17      93   475.3   486.7  0.20  0.22
 0.100    3512 100.00   402.4   384.0  0.16  0.15     175   400.2   371.0  0.22  0.21
 0.166    4412  99.96   255.0   252.0  0.16  0.14     258   272.4   263.3  0.22  0.19
 0.233    5154 100.00   202.4   201.2  0.16  0.13     291   208.4   208.9  0.22  0.18
$$

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

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0337   1426   0.918    657   0.820   2083   0.887  0.959  0.9633  0.9711  0.9167  0.9429
  0.1000   2841   0.886    671   0.769   3512   0.864  1.000  0.9466  0.9632  0.8820  0.9438
  0.1663   3747   0.857    665   0.766   4412   0.843  0.967  0.9431  0.9550  0.8844  0.9385
  0.2326   4493   0.872    663   0.750   5156   0.856  0.964  0.9458  0.9591  0.8779  0.9417
 $$
Resolution limits                    =     41.964     1.940
Number of used reflections           =      15163
Percentage observed                  =    99.9812
Percentage of free reflections       =     5.1126
Overall R factor                     =     0.1583
Free R factor                        =     0.2157
Average Fourier shell correlation    =     0.9605
AverageFree Fourier shell correlation=     0.9471
Overall weighted R factor            =     0.1491
Free weighted R factor               =     0.2007
Overall weighted R2 factor           =     0.1815
Free weighted R2 factor              =     0.2428
Average correlation coefficient      =     0.9414
Overall correlation coefficient      =     0.9548
Free correlation coefficient         =     0.9109
Cruickshanks DPI for coordinate error=     0.1515
DPI based on free R factor           =     0.1482
Overall figure of merit              =     0.8583
ML based su of positional parameters =     0.0912
ML based su of thermal parameters    =     3.0836
-----------------------------------------------------------------------------
  Time in seconds: CPU =        15.96
             Elapsed =           0.00

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


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS: 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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1591   0.2169   0.855       83337.    4651.3   0.0111  0.816   1.687  0.983   0.082
       1   0.1588   0.2158   0.858       83144.    4647.8   0.0109  0.800   1.671  0.973   0.083
       2   0.1585   0.2156   0.859       83122.    4647.0   0.0111  0.818   1.684  0.980   0.083
       3   0.1584   0.2155   0.859       83118.    4646.8   0.0111  0.819   1.688  0.983   0.083
       4   0.1583   0.2156   0.859       83116.    4646.9   0.0111  0.819   1.691  0.984   0.083
       5   0.1583   0.2156   0.859       83118.    4647.0   0.0111  0.819   1.692  0.984   0.083
       6   0.1583   0.2157   0.858       83114.    4647.0   0.0111  0.819   1.692  0.984   0.083
       7   0.1583   0.2157   0.858       83122.    4647.4   0.0111  0.818   1.692  0.985   0.083
       8   0.1583   0.2157   0.858       83120.    4647.2   0.0111  0.817   1.693  0.985   0.083
       9   0.1583   0.2157   0.858       83123.    4647.4   0.0111  0.817   1.693  0.985   0.083
      10   0.1583   0.2157   0.858       83119.    4647.3   0.0111  0.817   1.693  0.985   0.083
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1591   0.1583
             R free    0.2169   0.2157
     Rms BondLength    0.0111   0.0111
      Rms BondAngle    1.6866   1.6930
     Rms ChirVolume    0.0823   0.0834
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      48.0s System:    0.1s Elapsed:     0:48