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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: 15:00:23 


 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 1.82     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_1-83A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-82A.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_1-82A.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       0.0755
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.8200
  Estimated number of reflections :      24371
  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  1.8200

  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_1-83A.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=   2.053 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=   2.226 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=   1.864 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=   2.211 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=   2.393 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=   2.420 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=   2.134 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        970
Number of   all  reflections      19265
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          19265

   Current auto weighting coefficient =    7.0496025    

 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.= 0.926 id.= 3.000 dev= -2.07 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                 :    32   32   68
 Minimum acceptable grid spacing:    75   75  159
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    32   32   68
 Minimum acceptable grid spacing:    75   75  159
 Weight matrix   0.24555197    
 Actual weight    7.0496025      is applied to the X-ray term
Norm of X_ray positional gradient                32.7
Norm of Geom. positional gradient                78.6
Norm of X_ray B-factor gradient                  110.
Norm of Geom. B-factor gradient                  113.
Product of X_ray and Geom posit. gradients     -0.103E+08
 Cosine of angle between them                      -0.414
Product of X_ray and Geom B-fact gradients     -0.378E+08
 Cosine of angle between them                      -0.943


Residuals: XRAY=     0.6921E+06 GEOM=     0.1303E+05 TOTAL=     0.7051E+06
 function value    705088.44    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.035     0.017
Bond angles  : refined atoms                   2106     1.764     1.644
Bond angles  : others                          3238     2.353     1.580
Torsion angles, period  1. refined              185     6.975     5.000
Torsion angles, period  2. refined               90    35.987    22.778
Torsion angles, period  3. refined              268    13.418    15.000
Torsion angles, period  4. refined                9    11.369    15.000
Chiral centres: refined atoms                   196     0.086     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.015     0.020
VDW repulsions: refined_atoms                   298     0.243     0.200
VDW repulsions.others                          1335     0.219     0.200
VDW; torsion: refined_atoms                     718     0.172     0.200
VDW; torsion.others                             716     0.080     0.200
HBOND: refined_atoms                            227     0.205     0.200
HBOND.others                                      1     0.011     0.200
VDW repulsions: symmetry: refined_atoms           9     0.217     0.200
VDW repulsions: symmetry: others                 21     0.218     0.200
HBOND: symmetry: refined_atoms                   22     0.192     0.200
M. chain bond B values: refined atoms           746     1.592     1.268
M. chain bond B values: others                  746     1.591     1.268
M. chain angle B values: refined atoms          929     2.524     1.888
M. chain angle B values: others                 930     2.522     1.887
S. chain bond B values: refined atoms           811     2.676     1.624
S. chain bond B values: others                  810     2.673     1.623
S. chain angle B values: refined atoms         1177     4.191     2.283
S. chain angle B values: others                1178     4.189     2.282
Long range B values: refined atoms             1851     6.734    17.545
Long range B values: others                    1753     6.402    16.113
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0411, B  =    0.0225
Partial structure    1: scale =     0.3776, B  =   46.5811
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.51 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.038    2508 100.00   475.7   482.4  0.16  0.17     117   471.4   481.0  0.20  0.22
 0.114    4209 100.00   349.3   334.3  0.16  0.15     226   344.1   319.6  0.22  0.20
 0.189    5314  99.96   230.0   220.5  0.16  0.14     291   243.7   230.7  0.21  0.18
 0.264    6254 100.00   155.8   160.5  0.19  0.15     335   159.7   166.2  0.25  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0382   1754   0.912    754   0.805   2508   0.880  0.956  0.9612  0.9691  0.9063  0.9406
  0.1136   3450   0.879    759   0.780   4209   0.861  0.995  0.9467  0.9621  0.8905  0.9446
  0.1889   4562   0.871    752   0.759   5314   0.855  1.003  0.9479  0.9577  0.8941  0.9392
  0.2642   5500   0.822    762   0.732   6262   0.811  0.908  0.9364  0.9466  0.8757  0.9272
 $$
Resolution limits                    =     41.964     1.820
Number of used reflections           =      18293
Percentage observed                  =    99.9844
Percentage of free reflections       =     5.0356
Overall R factor                     =     0.1660
Free R factor                        =     0.2187
Average Fourier shell correlation    =     0.9565
AverageFree Fourier shell correlation=     0.9453
Overall weighted R factor            =     0.1525
Free weighted R factor               =     0.1994
Overall weighted R2 factor           =     0.1850
Free weighted R2 factor              =     0.2382
Average correlation coefficient      =     0.9365
Overall correlation coefficient      =     0.9563
Free correlation coefficient         =     0.9204
Cruickshanks DPI for coordinate error=     0.1259
DPI based on free R factor           =     0.1283
Overall figure of merit              =     0.8449
ML based su of positional parameters =     0.0821
ML based su of thermal parameters    =     2.6608
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    98170.008       13028.855       705088.44      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.26860261    
 Actual weight    7.0496025      is applied to the X-ray term


 function value    697725.44    

-------------------------------------------------------------------------------
             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 =     0.0410, B  =   -0.0826
Partial structure    1: scale =     0.3778, B  =   46.9299
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.51 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1661
Free R factor                        =     0.2180
Average Fourier shell correlation    =     0.9591
AverageFree Fourier shell correlation=     0.9477
Average correlation coefficient      =     0.9366
Overall figure of merit              =     0.8569
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    97783.703       8389.2139       697725.44       705088.44    


     CGMAT cycle number =      3

 Weight matrix   0.26944882    
 Actual weight    7.0496025      is applied to the X-ray term


 function value    697520.38    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0410, B  =   -0.0748
Partial structure    1: scale =     0.3777, B  =   46.8340
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1657
Free R factor                        =     0.2180
Average Fourier shell correlation    =     0.9593
AverageFree Fourier shell correlation=     0.9479
Average correlation coefficient      =     0.9371
Overall figure of merit              =     0.8573
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    97734.836       8528.6357       697520.38       697725.44    


     CGMAT cycle number =      4

 Weight matrix   0.26966140    
 Actual weight    7.0496025      is applied to the X-ray term


 function value    697477.56    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0410, B  =   -0.0684
Partial structure    1: scale =     0.3780, B  =   46.8958
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1656
Free R factor                        =     0.2180
Average Fourier shell correlation    =     0.9593
AverageFree Fourier shell correlation=     0.9479
Average correlation coefficient      =     0.9372
Overall figure of merit              =     0.8575
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    97723.742       8563.9736       697477.56       697520.38    


     CGMAT cycle number =      5

 Weight matrix   0.26945376    
 Actual weight    7.0496025      is applied to the X-ray term


 function value    697466.13    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0410, B  =   -0.0615
Partial structure    1: scale =     0.3780, B  =   46.8580
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1656
Free R factor                        =     0.2180
Average Fourier shell correlation    =     0.9593
AverageFree Fourier shell correlation=     0.9479
Average correlation coefficient      =     0.9372
Overall figure of merit              =     0.8575
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    97720.617       8574.5947       697466.13       697477.56    


     CGMAT cycle number =      6

 Weight matrix   0.26982465    
 Actual weight    7.0496025      is applied to the X-ray term


 function value    697404.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0410, B  =   -0.0641
Partial structure    1: scale =     0.3780, B  =   46.6838
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1656
Free R factor                        =     0.2181
Average Fourier shell correlation    =     0.9594
AverageFree Fourier shell correlation=     0.9480
Average correlation coefficient      =     0.9372
Overall figure of merit              =     0.8576
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    97711.836       8574.6504       697404.25       697466.13    


     CGMAT cycle number =      7

 Weight matrix   0.26981488    
 Actual weight    7.0496025      is applied to the X-ray term


 function value    697387.81    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0410, B  =   -0.0695
Partial structure    1: scale =     0.3781, B  =   46.6622
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1656
Free R factor                        =     0.2181
Average Fourier shell correlation    =     0.9594
AverageFree Fourier shell correlation=     0.9480
Average correlation coefficient      =     0.9372
Overall figure of merit              =     0.8576
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    97710.219       8569.6396       697387.81       697404.25    


     CGMAT cycle number =      8

 Weight matrix   0.26952025    
 Actual weight    7.0496025      is applied to the X-ray term


 function value    697409.00    

-------------------------------------------------------------------------------
             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 =     0.0410, B  =   -0.0706
Partial structure    1: scale =     0.3781, B  =   46.7057
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1656
Free R factor                        =     0.2181
Average Fourier shell correlation    =     0.9593
AverageFree Fourier shell correlation=     0.9479
Average correlation coefficient      =     0.9372
Overall figure of merit              =     0.8575
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    97713.039       8570.4951       697403.13       697387.81    
 fvalues    97713.039       8570.4951       697403.13       697408.56    


     CGMAT cycle number =      9

 Weight matrix   0.26944950    
 Actual weight    7.0496025      is applied to the X-ray term


 function value    697430.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0410, B  =   -0.0701
Partial structure    1: scale =     0.3781, B  =   46.8377
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1656
Free R factor                        =     0.2181
Average Fourier shell correlation    =     0.9593
AverageFree Fourier shell correlation=     0.9479
Average correlation coefficient      =     0.9372
Overall figure of merit              =     0.8575
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    97717.391       8561.5586       697412.06       697408.56    
 fvalues    97717.391       8561.5586       697412.06       697430.31    


     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.= 0.941 id.= 3.000 dev= -2.06 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                 :    32   32   68
 Minimum acceptable grid spacing:    75   75  159
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    32   32   68
 Minimum acceptable grid spacing:    75   75  159
 Weight matrix   0.26956499    
 Actual weight    7.0496025      is applied to the X-ray term
Norm of X_ray positional gradient                34.8
Norm of Geom. positional gradient                34.8
Norm of X_ray B-factor gradient                  115.
Norm of Geom. B-factor gradient                  118.
Product of X_ray and Geom posit. gradients     -0.117E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.435E+08
 Cosine of angle between them                      -0.992


Residuals: XRAY=     0.6889E+06 GEOM=      8563.     TOTAL=     0.6974E+06
 function value    697420.63    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.777     1.644
Bond angles  : others                          3238     1.458     1.580
Torsion angles, period  1. refined              185     6.961     5.000
Torsion angles, period  2. refined               90    35.958    22.778
Torsion angles, period  3. refined              268    13.415    15.000
Torsion angles, period  4. refined                9    11.302    15.000
Chiral centres: refined atoms                   196     0.086     0.200
Planar groups: refined atoms                   1743     0.009     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   299     0.243     0.200
VDW repulsions.others                          1361     0.191     0.200
VDW; torsion: refined_atoms                     713     0.172     0.200
VDW; torsion.others                             794     0.083     0.200
HBOND: refined_atoms                            222     0.207     0.200
VDW repulsions: symmetry: refined_atoms           9     0.218     0.200
VDW repulsions: symmetry: others                 23     0.192     0.200
HBOND: symmetry: refined_atoms                   23     0.185     0.200
M. chain bond B values: refined atoms           746     1.603     1.276
M. chain bond B values: others                  746     1.601     1.277
M. chain angle B values: refined atoms          929     2.531     1.901
M. chain angle B values: others                 930     2.530     1.900
S. chain bond B values: refined atoms           811     2.703     1.635
S. chain bond B values: others                  810     2.700     1.635
S. chain angle B values: refined atoms         1177     4.226     2.298
S. chain angle B values: others                1178     4.224     2.298
Long range B values: refined atoms             1843     6.777    17.602
Long range B values: others                    1750     6.476    16.235
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0410, B  =   -0.0683
Partial structure    1: scale =     0.3782, B  =   46.8679
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.038    2508 100.00   476.1   482.9  0.16  0.17     117   471.8   481.1  0.20  0.22
 0.114    4209 100.00   349.6   334.5  0.16  0.15     226   344.4   319.3  0.22  0.20
 0.189    5314  99.96   230.2   220.6  0.16  0.14     291   243.9   231.1  0.21  0.18
 0.264    6254 100.00   155.9   160.7  0.19  0.14     335   159.8   166.3  0.24  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0382   1754   0.926    754   0.823   2508   0.895  0.958  0.9645  0.9718  0.9062  0.9402
  0.1136   3450   0.881    759   0.783   4209   0.863  0.995  0.9476  0.9630  0.8914  0.9453
  0.1889   4562   0.874    752   0.762   5314   0.858  1.003  0.9489  0.9583  0.8950  0.9387
  0.2642   5500   0.849    762   0.759   6262   0.838  0.916  0.9415  0.9528  0.8778  0.9292
 $$
Resolution limits                    =     41.964     1.820
Number of used reflections           =      18293
Percentage observed                  =    99.9844
Percentage of free reflections       =     5.0356
Overall R factor                     =     0.1656
Free R factor                        =     0.2180
Average Fourier shell correlation    =     0.9593
AverageFree Fourier shell correlation=     0.9479
Overall weighted R factor            =     0.1523
Free weighted R factor               =     0.1994
Overall weighted R2 factor           =     0.1851
Free weighted R2 factor              =     0.2380
Average correlation coefficient      =     0.9372
Overall correlation coefficient      =     0.9564
Free correlation coefficient         =     0.9209
Cruickshanks DPI for coordinate error=     0.1256
DPI based on free R factor           =     0.1279
Overall figure of merit              =     0.8576
ML based su of positional parameters =     0.0783
ML based su of thermal parameters    =     2.5177
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    97715.844       8562.7754       697420.63       697430.31    

    ****                              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.= 0.941 id.= 3.000 dev= -2.06 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_1-82A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.778     1.644
Bond angles  : others                          3238     1.458     1.580
Torsion angles, period  1. refined              185     6.959     5.000
Torsion angles, period  2. refined               90    35.956    22.778
Torsion angles, period  3. refined              268    13.418    15.000
Torsion angles, period  4. refined                9    11.296    15.000
Chiral centres: refined atoms                   196     0.086     0.200
Planar groups: refined atoms                   1743     0.009     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   299     0.243     0.200
VDW repulsions.others                          1360     0.191     0.200
VDW; torsion: refined_atoms                     715     0.172     0.200
VDW; torsion.others                             798     0.083     0.200
HBOND: refined_atoms                            221     0.207     0.200
VDW repulsions: symmetry: refined_atoms           9     0.218     0.200
VDW repulsions: symmetry: others                 23     0.191     0.200
HBOND: symmetry: refined_atoms                   23     0.186     0.200
M. chain bond B values: refined atoms           746     1.603     1.276
M. chain bond B values: others                  746     1.601     1.277
M. chain angle B values: refined atoms          929     2.530     1.901
M. chain angle B values: others                 930     2.529     1.900
S. chain bond B values: refined atoms           811     2.703     1.635
S. chain bond B values: others                  810     2.701     1.635
S. chain angle B values: refined atoms         1177     4.227     2.299
S. chain angle B values: others                1178     4.225     2.298
Long range B values: refined atoms             1844     6.772    17.599
Long range B values: others                    1752     6.474    16.243
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0410, B  =   -0.0657
Partial structure    1: scale =     0.3782, B  =   46.7667
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.038    2508 100.00   476.1   482.9  0.16  0.17     117   471.8   481.1  0.20  0.22
 0.114    4209 100.00   349.6   334.4  0.16  0.15     226   344.4   319.3  0.22  0.20
 0.189    5314  99.96   230.2   220.6  0.16  0.14     291   243.9   231.1  0.21  0.18
 0.264    6254 100.00   155.9   160.7  0.19  0.14     335   159.8   166.3  0.24  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0382   1754   0.927    754   0.823   2508   0.895  0.958  0.9645  0.9719  0.9063  0.9402
  0.1136   3450   0.881    759   0.783   4209   0.863  0.995  0.9476  0.9630  0.8913  0.9453
  0.1889   4562   0.874    752   0.762   5314   0.858  1.003  0.9489  0.9583  0.8950  0.9387
  0.2642   5500   0.849    762   0.759   6262   0.838  0.916  0.9415  0.9528  0.8778  0.9292
 $$
Resolution limits                    =     41.964     1.820
Number of used reflections           =      18293
Percentage observed                  =    99.9844
Percentage of free reflections       =     5.0356
Overall R factor                     =     0.1656
Free R factor                        =     0.2180
Average Fourier shell correlation    =     0.9593
AverageFree Fourier shell correlation=     0.9479
Overall weighted R factor            =     0.1523
Free weighted R factor               =     0.1994
Overall weighted R2 factor           =     0.1851
Free weighted R2 factor              =     0.2379
Average correlation coefficient      =     0.9372
Overall correlation coefficient      =     0.9564
Free correlation coefficient         =     0.9209
Cruickshanks DPI for coordinate error=     0.1256
DPI based on free R factor           =     0.1279
Overall figure of merit              =     0.8576
ML based su of positional parameters =     0.0783
ML based su of thermal parameters    =     2.5177
-----------------------------------------------------------------------------
  Time in seconds: CPU =        14.88
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1660   0.2187   0.845       98170.    5381.2   0.0118  0.876   1.764  1.022   0.086
       1   0.1661   0.2180   0.857       97784.    5374.5   0.0113  0.843   1.736  1.006   0.085
       2   0.1657   0.2180   0.857       97735.    5373.6   0.0118  0.878   1.761  1.020   0.087
       3   0.1656   0.2180   0.857       97724.    5373.2   0.0118  0.881   1.768  1.024   0.087
       4   0.1656   0.2180   0.857       97721.    5373.0   0.0119  0.883   1.771  1.026   0.086
       5   0.1656   0.2181   0.858       97712.    5372.7   0.0119  0.883   1.773  1.027   0.086
       6   0.1656   0.2181   0.858       97710.    5372.6   0.0119  0.884   1.775  1.027   0.086
       7   0.1656   0.2181   0.858       97713.    5372.9   0.0119  0.884   1.776  1.028   0.086
       8   0.1656   0.2181   0.858       97717.    5373.0   0.0119  0.884   1.777  1.028   0.086
       9   0.1656   0.2180   0.858       97716.    5372.8   0.0119  0.885   1.777  1.028   0.086
      10   0.1656   0.2180   0.858       97716.    5372.8   0.0119  0.885   1.778  1.029   0.086
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1660   0.1656
             R free    0.2187   0.2180
     Rms BondLength    0.0118   0.0119
      Rms BondAngle    1.7643   1.7780
     Rms ChirVolume    0.0861   0.0864
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      46.9s System:    0.1s Elapsed:     0:48