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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: 22:24:55 


 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 1.58     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_1-59A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-58A.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_1-58A.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       0.1001
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.5800
  Estimated number of reflections :      37373
  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  1.5800

  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_1-59A.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=   2.056 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=   2.193 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=   1.821 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=   2.218 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=   2.410 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=   2.393 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=   2.140 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       1486
Number of   all  reflections      29123
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          29123

   Current auto weighting coefficient =    6.4496012    

 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.= 0.886 id.= 3.000 dev= -2.11 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        :   128  128  280
 Maximuum H,K,L                 :    37   37   78
 Minimum acceptable grid spacing:    83   83  177
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  280
 Maximuum H,K,L                 :    37   37   78
 Minimum acceptable grid spacing:    83   83  177
 Weight matrix   0.29041547    
 Actual weight    6.4496012      is applied to the X-ray term
Norm of X_ray positional gradient                36.7
Norm of Geom. positional gradient                82.8
Norm of X_ray B-factor gradient                  103.
Norm of Geom. B-factor gradient                  113.
Product of X_ray and Geom posit. gradients     -0.146E+08
 Cosine of angle between them                      -0.497
Product of X_ray and Geom B-fact gradients     -0.331E+08
 Cosine of angle between them                      -0.879


Residuals: XRAY=     0.8929E+06 GEOM=     0.1354E+05 TOTAL=     0.9064E+06
 function value    906442.06    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.035     0.017
Bond angles  : refined atoms                   2106     1.868     1.644
Bond angles  : others                          3238     2.369     1.580
Torsion angles, period  1. refined              185     6.797     5.000
Torsion angles, period  2. refined               90    34.875    22.778
Torsion angles, period  3. refined              268    13.257    15.000
Torsion angles, period  4. refined                9    12.467    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.018     0.020
VDW repulsions: refined_atoms                   301     0.247     0.200
VDW repulsions.others                          1341     0.220     0.200
VDW; torsion: refined_atoms                     727     0.174     0.200
VDW; torsion.others                             724     0.082     0.200
HBOND: refined_atoms                            210     0.202     0.200
HBOND.others                                      1     0.056     0.200
VDW repulsions: symmetry: refined_atoms           8     0.206     0.200
VDW repulsions: symmetry: others                 23     0.204     0.200
HBOND: symmetry: refined_atoms                   22     0.228     0.200
M. chain bond B values: refined atoms           746     1.759     1.517
M. chain bond B values: others                  746     1.755     1.517
M. chain angle B values: refined atoms          929     2.733     2.266
M. chain angle B values: others                 930     2.733     2.266
S. chain bond B values: refined atoms           811     3.157     1.919
S. chain bond B values: others                  810     3.153     1.918
S. chain angle B values: refined atoms         1177     4.797     2.710
S. chain angle B values: others                1178     4.795     2.710
Long range B values: refined atoms             1841     7.209    20.899
Long range B values: others                    1753     6.949    19.501
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0445, B  =    0.1160
Partial structure    1: scale =     0.3873, B  =   40.6648
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.051    3739 100.00   427.9   437.5  0.17  0.17     180   421.2   428.8  0.20  0.21
 0.151    6342  99.97   252.6   236.4  0.17  0.15     352   260.1   237.6  0.22  0.20
 0.251    8091 100.00   158.0   143.0  0.19  0.17     432   162.4   148.5  0.23  0.20
 0.351    9452 100.00    66.4    80.4  0.33  0.27     522    64.5    79.2  0.38  0.31
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0506   2743   0.909    996   0.802   3739   0.881  0.948  0.9615  0.9688  0.9096  0.9366
  0.1506   5334   0.865   1008   0.768   6342   0.850  1.026  0.9412  0.9547  0.8748  0.9368
  0.2506   7083   0.857   1008   0.754   8091   0.844  1.049  0.9462  0.9539  0.8984  0.9365
  0.3506   8456   0.652   1007   0.577   9463   0.644  0.683  0.8424  0.8605  0.8001  0.8585
 $$
Resolution limits                    =     41.964     1.580
Number of used reflections           =      27635
Percentage observed                  =    99.9897
Percentage of free reflections       =     5.1028
Overall R factor                     =     0.1953
Free R factor                        =     0.2381
Average Fourier shell correlation    =     0.9241
AverageFree Fourier shell correlation=     0.9104
Overall weighted R factor            =     0.1697
Free weighted R factor               =     0.2092
Overall weighted R2 factor           =     0.2003
Free weighted R2 factor              =     0.2459
Average correlation coefficient      =     0.9099
Overall correlation coefficient      =     0.9584
Free correlation coefficient         =     0.9354
Cruickshanks DPI for coordinate error=     0.0945
DPI based on free R factor           =     0.0987
Overall figure of merit              =     0.7820
ML based su of positional parameters =     0.0722
ML based su of thermal parameters    =     2.1435
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    138442.28       13544.592       906442.06      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.37473550    
 Actual weight    6.4496012      is applied to the X-ray term


 function value    893706.38    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0444, B  =   -0.0666
Partial structure    1: scale =     0.3869, B  =   40.7585
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1956
Free R factor                        =     0.2373
Average Fourier shell correlation    =     0.9372
AverageFree Fourier shell correlation=     0.9251
Average correlation coefficient      =     0.9085
Overall figure of merit              =     0.8214
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    137254.72       8468.1953       893706.38       906442.06    


     CGMAT cycle number =      3

 Weight matrix   0.38691825    
 Actual weight    6.4496012      is applied to the X-ray term


 function value    892556.75    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0444, B  =   -0.0035
Partial structure    1: scale =     0.3869, B  =   40.7372
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1950
Free R factor                        =     0.2372
Average Fourier shell correlation    =     0.9400
AverageFree Fourier shell correlation=     0.9278
Average correlation coefficient      =     0.9096
Overall figure of merit              =     0.8303
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    137016.44       8855.3730       892556.75       893706.38    


     CGMAT cycle number =      4

 Weight matrix   0.38952085    
 Actual weight    6.4496012      is applied to the X-ray term


 function value    892303.50    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0444, B  =    0.0003
Partial structure    1: scale =     0.3869, B  =   40.7284
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1950
Free R factor                        =     0.2373
Average Fourier shell correlation    =     0.9405
AverageFree Fourier shell correlation=     0.9283
Average correlation coefficient      =     0.9100
Overall figure of merit              =     0.8322
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    136960.69       8961.7070       892303.50       892556.75    


     CGMAT cycle number =      5

 Weight matrix   0.38951924    
 Actual weight    6.4496012      is applied to the X-ray term


 function value    892311.13    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0444, B  =    0.0091
Partial structure    1: scale =     0.3867, B  =   40.7327
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1950
Free R factor                        =     0.2373
Average Fourier shell correlation    =     0.9406
AverageFree Fourier shell correlation=     0.9283
Average correlation coefficient      =     0.9102
Overall figure of merit              =     0.8323
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03


 fvalues    136955.19       9012.3496       892347.56       892303.50    

 fvalues    136955.19       9012.3496       892329.69       892318.69    
 fvalues    136955.19       9012.3496       892329.69       892318.69    


     CGMAT cycle number =      6

 Weight matrix   0.38939291    
 Actual weight    6.4496012      is applied to the X-ray term


 function value    892323.31    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0444, B  =    0.0093
Partial structure    1: scale =     0.3866, B  =   40.7319
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1950
Free R factor                        =     0.2373
Average Fourier shell correlation    =     0.9406
AverageFree Fourier shell correlation=     0.9283
Average correlation coefficient      =     0.9102
Overall figure of merit              =     0.8322
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    136955.67       9015.9531       892369.44       892318.69    

 fvalues    136955.67       9015.9531       892352.75       892325.38    
 fvalues    136955.67       9015.9531       892352.75       892325.38    


     CGMAT cycle number =      7

 Weight matrix   0.38927034    
 Actual weight    6.4496012      is applied to the X-ray term


 function value    892329.63    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0444, B  =    0.0103
Partial structure    1: scale =     0.3865, B  =   40.7469
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1950
Free R factor                        =     0.2373
Average Fourier shell correlation    =     0.9406
AverageFree Fourier shell correlation=     0.9283
Average correlation coefficient      =     0.9102
Overall figure of merit              =     0.8322
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    136956.44       9016.8057       892326.50       892325.38    
 fvalues    136956.44       9016.8057       892326.50       892331.19    


     CGMAT cycle number =      8

 Weight matrix   0.38883552    
 Actual weight    6.4496012      is applied to the X-ray term


 function value    892360.13    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0444, B  =    0.0138
Partial structure    1: scale =     0.3866, B  =   40.7918
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1950
Free R factor                        =     0.2373
Average Fourier shell correlation    =     0.9406
AverageFree Fourier shell correlation=     0.9282
Average correlation coefficient      =     0.9102
Overall figure of merit              =     0.8321
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    136958.84       9015.6563       892360.50       892331.19    

 fvalues    136958.84       9015.6563       892345.75       892345.63    
 fvalues    136958.84       9015.6563       892345.75       892345.63    


     CGMAT cycle number =      9

 Weight matrix   0.38893524    
 Actual weight    6.4496012      is applied to the X-ray term


 function value    892349.63    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0444, B  =    0.0131
Partial structure    1: scale =     0.3866, B  =   40.7914
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1950
Free R factor                        =     0.2373
Average Fourier shell correlation    =     0.9406
AverageFree Fourier shell correlation=     0.9283
Average correlation coefficient      =     0.9102
Overall figure of merit              =     0.8322
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    136960.06       9016.1865       892339.00       892345.63    
 fvalues    136960.06       9016.1865       892339.00       892353.94    


     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.= 0.904 id.= 3.000 dev= -2.10 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        :   128  128  280
 Maximuum H,K,L                 :    37   37   78
 Minimum acceptable grid spacing:    83   83  177
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  280
 Maximuum H,K,L                 :    37   37   78
 Minimum acceptable grid spacing:    83   83  177
 Weight matrix   0.38892022    
 Actual weight    6.4496012      is applied to the X-ray term
Norm of X_ray positional gradient                44.2
Norm of Geom. positional gradient                44.1
Norm of X_ray B-factor gradient                  119.
Norm of Geom. B-factor gradient                  117.
Product of X_ray and Geom posit. gradients     -0.188E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.450E+08
 Cosine of angle between them                      -0.998


Residuals: XRAY=     0.8833E+06 GEOM=      9017.     TOTAL=     0.8923E+06
 function value    892345.19    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.862     1.644
Bond angles  : others                          3238     1.523     1.580
Torsion angles, period  1. refined              185     6.793     5.000
Torsion angles, period  2. refined               90    34.883    22.778
Torsion angles, period  3. refined              268    13.260    15.000
Torsion angles, period  4. refined                9    12.358    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   303     0.246     0.200
VDW repulsions.others                          1343     0.198     0.200
VDW; torsion: refined_atoms                     730     0.174     0.200
VDW; torsion.others                             737     0.087     0.200
HBOND: refined_atoms                            208     0.202     0.200
HBOND.others                                      1     0.003     0.200
VDW repulsions: symmetry: refined_atoms           8     0.204     0.200
VDW repulsions: symmetry: others                 23     0.191     0.200
HBOND: symmetry: refined_atoms                   22     0.231     0.200
M. chain bond B values: refined atoms           746     1.769     1.528
M. chain bond B values: others                  746     1.765     1.528
M. chain angle B values: refined atoms          929     2.742     2.282
M. chain angle B values: others                 930     2.741     2.282
S. chain bond B values: refined atoms           811     3.173     1.931
S. chain bond B values: others                  810     3.168     1.931
S. chain angle B values: refined atoms         1177     4.822     2.729
S. chain angle B values: others                1178     4.820     2.728
Long range B values: refined atoms             1843     7.252    21.077
Long range B values: others                    1757     7.000    19.706
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0444, B  =    0.0132
Partial structure    1: scale =     0.3866, B  =   40.7811
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.051    3739 100.00   428.3   438.1  0.17  0.17     180   421.6   429.7  0.20  0.21
 0.151    6342  99.97   252.8   236.5  0.17  0.15     352   260.3   237.7  0.22  0.20
 0.251    8091 100.00   158.1   143.3  0.19  0.17     432   162.6   148.6  0.23  0.20
 0.351    9452 100.00    66.5    80.4  0.33  0.27     522    64.6    79.4  0.38  0.31
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0506   2743   0.924    996   0.825   3739   0.898  0.951  0.9655  0.9724  0.9104  0.9370
  0.1506   5334   0.872   1008   0.774   6342   0.856  1.026  0.9428  0.9560  0.8765  0.9370
  0.2506   7083   0.872   1008   0.770   8091   0.859  1.049  0.9506  0.9584  0.8992  0.9370
  0.3506   8456   0.775   1007   0.701   9463   0.767  0.736  0.8871  0.9023  0.8002  0.8588
 $$
Resolution limits                    =     41.964     1.580
Number of used reflections           =      27635
Percentage observed                  =    99.9897
Percentage of free reflections       =     5.1028
Overall R factor                     =     0.1950
Free R factor                        =     0.2373
Average Fourier shell correlation    =     0.9406
AverageFree Fourier shell correlation=     0.9282
Overall weighted R factor            =     0.1694
Free weighted R factor               =     0.2080
Overall weighted R2 factor           =     0.2002
Free weighted R2 factor              =     0.2443
Average correlation coefficient      =     0.9102
Overall correlation coefficient      =     0.9586
Free correlation coefficient         =     0.9360
Cruickshanks DPI for coordinate error=     0.0943
DPI based on free R factor           =     0.0983
Overall figure of merit              =     0.8321
ML based su of positional parameters =     0.0623
ML based su of thermal parameters    =     1.8021
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    136958.56       9017.0410       892345.19       892353.94    

    ****                              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.= 0.904 id.= 3.000 dev= -2.10 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_1-58A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.863     1.644
Bond angles  : others                          3238     1.523     1.580
Torsion angles, period  1. refined              185     6.794     5.000
Torsion angles, period  2. refined               90    34.882    22.778
Torsion angles, period  3. refined              268    13.261    15.000
Torsion angles, period  4. refined                9    12.357    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   303     0.246     0.200
VDW repulsions.others                          1344     0.198     0.200
VDW; torsion: refined_atoms                     730     0.174     0.200
VDW; torsion.others                             739     0.087     0.200
HBOND: refined_atoms                            208     0.202     0.200
HBOND.others                                      1     0.003     0.200
VDW repulsions: symmetry: refined_atoms           8     0.204     0.200
VDW repulsions: symmetry: others                 23     0.191     0.200
HBOND: symmetry: refined_atoms                   22     0.231     0.200
M. chain bond B values: refined atoms           746     1.770     1.528
M. chain bond B values: others                  746     1.765     1.528
M. chain angle B values: refined atoms          929     2.742     2.282
M. chain angle B values: others                 930     2.741     2.282
S. chain bond B values: refined atoms           811     3.173     1.931
S. chain bond B values: others                  810     3.168     1.931
S. chain angle B values: refined atoms         1177     4.822     2.729
S. chain angle B values: others                1178     4.820     2.728
Long range B values: refined atoms             1843     7.252    21.077
Long range B values: others                    1757     7.000    19.706
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0444, B  =    0.0147
Partial structure    1: scale =     0.3866, B  =   40.7864
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.051    3739 100.00   428.3   438.1  0.17  0.17     180   421.6   429.7  0.20  0.21
 0.151    6342  99.97   252.8   236.5  0.17  0.15     352   260.3   237.7  0.22  0.20
 0.251    8091 100.00   158.1   143.3  0.19  0.17     432   162.6   148.6  0.23  0.20
 0.351    9452 100.00    66.5    80.4  0.33  0.27     522    64.6    79.4  0.38  0.31
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0506   2743   0.924    996   0.825   3739   0.898  0.951  0.9655  0.9724  0.9105  0.9370
  0.1506   5334   0.872   1008   0.774   6342   0.856  1.026  0.9428  0.9560  0.8765  0.9370
  0.2506   7083   0.872   1008   0.770   8091   0.859  1.049  0.9506  0.9584  0.8992  0.9370
  0.3506   8456   0.775   1007   0.701   9463   0.767  0.736  0.8871  0.9023  0.8002  0.8588
 $$
Resolution limits                    =     41.964     1.580
Number of used reflections           =      27635
Percentage observed                  =    99.9897
Percentage of free reflections       =     5.1028
Overall R factor                     =     0.1950
Free R factor                        =     0.2373
Average Fourier shell correlation    =     0.9405
AverageFree Fourier shell correlation=     0.9282
Overall weighted R factor            =     0.1695
Free weighted R factor               =     0.2080
Overall weighted R2 factor           =     0.2002
Free weighted R2 factor              =     0.2442
Average correlation coefficient      =     0.9102
Overall correlation coefficient      =     0.9586
Free correlation coefficient         =     0.9360
Cruickshanks DPI for coordinate error=     0.0943
DPI based on free R factor           =     0.0983
Overall figure of merit              =     0.8321
ML based su of positional parameters =     0.0623
ML based su of thermal parameters    =     1.8021
-----------------------------------------------------------------------------
  Time in seconds: CPU =        25.89
             Elapsed =         128.00

    ****           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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1953   0.2381   0.782      138442.    7607.2   0.0133  0.997   1.868  1.087   0.090
       1   0.1956   0.2373   0.821      137255.    7564.1   0.0121  0.907   1.795  1.043   0.087
       2   0.1950   0.2372   0.830      137016.    7555.1   0.0131  0.982   1.835  1.068   0.089
       3   0.1950   0.2373   0.832      136961.    7553.2   0.0132  0.992   1.851  1.078   0.090
       4   0.1950   0.2373   0.832      136954.    7553.2   0.0133  0.996   1.860  1.083   0.090
       5   0.1950   0.2373   0.832      136955.    7553.4   0.0133  0.997   1.861  1.084   0.090
       6   0.1950   0.2373   0.832      136956.    7553.5   0.0133  0.997   1.861  1.084   0.090
       7   0.1950   0.2373   0.832      136961.    7553.8   0.0133  0.997   1.862  1.084   0.090
       8   0.1950   0.2373   0.832      136959.    7553.7   0.0133  0.997   1.862  1.085   0.090
       9   0.1950   0.2373   0.832      136959.    7553.8   0.0133  0.997   1.862  1.085   0.090
      10   0.1950   0.2373   0.832      136960.    7553.8   0.0133  0.997   1.863  1.085   0.090
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1953   0.1950
             R free    0.2381   0.2373
     Rms BondLength    0.0133   0.0133
      Rms BondAngle    1.8679   1.8627
     Rms ChirVolume    0.0902   0.0899
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      57.8s System:    0.2s Elapsed:     0:58