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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: 14:17:52 


 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 1.86     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_1-87A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-86A.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_1-86A.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       0.0723
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.8600
  Estimated number of reflections :      22199
  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  1.8600

  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_1-87A.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=   2.023 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=   2.217 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=   1.866 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=   2.232 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=   2.379 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=   2.434 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=   2.131 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        916
Number of   all  reflections      18057
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          18057

   Current auto weighting coefficient =    7.1495919    

 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.= 0.928 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   66
 Minimum acceptable grid spacing:    74   74  156
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    32   32   66
 Minimum acceptable grid spacing:    74   74  156
 Weight matrix   0.23538890    
 Actual weight    7.1495919      is applied to the X-ray term
Norm of X_ray positional gradient                32.7
Norm of Geom. positional gradient                78.0
Norm of X_ray B-factor gradient                  111.
Norm of Geom. B-factor gradient                  108.
Product of X_ray and Geom posit. gradients     -0.964E+07
 Cosine of angle between them                      -0.391
Product of X_ray and Geom B-fact gradients     -0.363E+08
 Cosine of angle between them                      -0.938


Residuals: XRAY=     0.6628E+06 GEOM=     0.1278E+05 TOTAL=     0.6756E+06
 function value    675584.38    

-------------------------------------------------------------------------------
             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     1.736     1.644
Bond angles  : others                          3238     2.346     1.580
Torsion angles, period  1. refined              185     6.972     5.000
Torsion angles, period  2. refined               90    36.145    22.778
Torsion angles, period  3. refined              268    13.476    15.000
Torsion angles, period  4. refined                9    11.244    15.000
Chiral centres: refined atoms                   196     0.084     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.016     0.020
VDW repulsions: refined_atoms                   298     0.243     0.200
VDW repulsions.others                          1345     0.218     0.200
VDW; torsion: refined_atoms                     720     0.171     0.200
VDW; torsion.others                             714     0.080     0.200
HBOND: refined_atoms                            224     0.211     0.200
VDW repulsions: symmetry: refined_atoms           8     0.231     0.200
VDW repulsions: symmetry: others                 24     0.210     0.200
HBOND: symmetry: refined_atoms                   20     0.206     0.200
M. chain bond B values: refined atoms           746     1.565     1.241
M. chain bond B values: others                  746     1.564     1.241
M. chain angle B values: refined atoms          929     2.511     1.848
M. chain angle B values: others                 930     2.510     1.847
S. chain bond B values: refined atoms           811     2.540     1.582
S. chain bond B values: others                  810     2.538     1.582
S. chain angle B values: refined atoms         1177     3.987     2.225
S. chain angle B values: others                1178     3.985     2.224
Long range B values: refined atoms             1852     6.654    17.148
Long range B values: others                    1757     6.340    15.782
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0406, B  =   -0.0122
Partial structure    1: scale =     0.3769, B  =   46.7687
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.037    2347 100.00   477.4   483.7  0.16  0.17     108   477.2   485.9  0.20  0.22
 0.109    3949 100.00   369.2   353.0  0.16  0.15     205   368.0   341.3  0.21  0.19
 0.181    4983  99.96   239.9   232.6  0.16  0.13     291   251.9   240.4  0.22  0.19
 0.253    5856 100.00   172.5   175.1  0.18  0.14     312   174.3   177.3  0.23  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0366   1633   0.911    714   0.805   2347   0.879  0.955  0.9608  0.9688  0.9049  0.9409
  0.1087   3225   0.880    724   0.772   3949   0.860  0.996  0.9473  0.9619  0.8896  0.9446
  0.1809   4261   0.869    722   0.771   4983   0.855  0.991  0.9455  0.9578  0.8857  0.9389
  0.2530   5136   0.851    724   0.742   5860   0.838  0.935  0.9389  0.9524  0.8706  0.9317
 $$
Resolution limits                    =     41.964     1.860
Number of used reflections           =      17139
Percentage observed                  =    99.9834
Percentage of free reflections       =     5.0734
Overall R factor                     =     0.1630
Free R factor                        =     0.2157
Average Fourier shell correlation    =     0.9584
AverageFree Fourier shell correlation=     0.9455
Overall weighted R factor            =     0.1511
Free weighted R factor               =     0.1986
Overall weighted R2 factor           =     0.1838
Free weighted R2 factor              =     0.2394
Average correlation coefficient      =     0.9380
Overall correlation coefficient      =     0.9555
Free correlation coefficient         =     0.9169
Cruickshanks DPI for coordinate error=     0.1335
DPI based on free R factor           =     0.1336
Overall figure of merit              =     0.8535
ML based su of positional parameters =     0.0845
ML based su of thermal parameters    =     2.7661
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    92705.813       12775.619       675584.38      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.24704403    
 Actual weight    7.1495919      is applied to the X-ray term


 function value    669370.69    

-------------------------------------------------------------------------------
             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 =     0.0406, B  =   -0.1003
Partial structure    1: scale =     0.3766, B  =   46.7589
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1628
Free R factor                        =     0.2150
Average Fourier shell correlation    =     0.9599
AverageFree Fourier shell correlation=     0.9470
Average correlation coefficient      =     0.9386
Overall figure of merit              =     0.8590
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    92466.086       8275.9619       669370.69       675584.38    


     CGMAT cycle number =      3

 Weight matrix   0.24716283    
 Actual weight    7.1495919      is applied to the X-ray term


 function value    669293.38    

-------------------------------------------------------------------------------
             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 =     0.0406, B  =   -0.0810
Partial structure    1: scale =     0.3764, B  =   46.6315
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1625
Free R factor                        =     0.2151
Average Fourier shell correlation    =     0.9600
AverageFree Fourier shell correlation=     0.9471
Average correlation coefficient      =     0.9389
Overall figure of merit              =     0.8590
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    92441.555       8374.0107       669293.38       669370.69    


     CGMAT cycle number =      4

 Weight matrix   0.24714290    
 Actual weight    7.1495919      is applied to the X-ray term


 function value    669269.38    

-------------------------------------------------------------------------------
             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 =     0.0406, B  =   -0.0791
Partial structure    1: scale =     0.3764, B  =   46.5547
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1624
Free R factor                        =     0.2151
Average Fourier shell correlation    =     0.9601
AverageFree Fourier shell correlation=     0.9471
Average correlation coefficient      =     0.9390
Overall figure of merit              =     0.8591
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    92435.805       8391.0781       669269.38       669293.38    


     CGMAT cycle number =      5

 Weight matrix   0.24698982    
 Actual weight    7.1495919      is applied to the X-ray term


 function value    669271.69    

-------------------------------------------------------------------------------
             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 =     0.0406, B  =   -0.0801
Partial structure    1: scale =     0.3763, B  =   46.7456
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1624
Free R factor                        =     0.2151
Average Fourier shell correlation    =     0.9601
AverageFree Fourier shell correlation=     0.9471
Average correlation coefficient      =     0.9390
Overall figure of merit              =     0.8591
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03


 fvalues    92436.250       8392.7715       669255.63       669269.38    
 fvalues    92436.250       8392.7715       669255.63       669274.19    


     CGMAT cycle number =      6

 Weight matrix   0.24698727    
 Actual weight    7.1495919      is applied to the X-ray term


 function value    669252.94    

-------------------------------------------------------------------------------
             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 =     0.0406, B  =   -0.0808
Partial structure    1: scale =     0.3762, B  =   46.7495
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1624
Free R factor                        =     0.2150
Average Fourier shell correlation    =     0.9601
AverageFree Fourier shell correlation=     0.9471
Average correlation coefficient      =     0.9391
Overall figure of merit              =     0.8591
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    92433.563       8390.6787       669252.94       669274.19    


     CGMAT cycle number =      7

 Weight matrix   0.24691178    
 Actual weight    7.1495919      is applied to the X-ray term


 function value    669242.31    

-------------------------------------------------------------------------------
             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 =     0.0406, B  =   -0.0826
Partial structure    1: scale =     0.3761, B  =   46.6460
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1624
Free R factor                        =     0.2150
Average Fourier shell correlation    =     0.9601
AverageFree Fourier shell correlation=     0.9471
Average correlation coefficient      =     0.9391
Overall figure of merit              =     0.8591
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    92433.133       8383.1338       669242.31       669252.94    


     CGMAT cycle number =      8

 Weight matrix   0.24658813    
 Actual weight    7.1495919      is applied to the X-ray term


 function value    669274.00    

-------------------------------------------------------------------------------
             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 =     0.0406, B  =   -0.0832
Partial structure    1: scale =     0.3763, B  =   46.6847
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1624
Free R factor                        =     0.2151
Average Fourier shell correlation    =     0.9600
AverageFree Fourier shell correlation=     0.9471
Average correlation coefficient      =     0.9391
Overall figure of merit              =     0.8591
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    92438.359       8380.9941       669256.63       669242.31    
 fvalues    92438.359       8380.9941       669256.63       669277.56    


     CGMAT cycle number =      9

 Weight matrix   0.24634114    
 Actual weight    7.1495919      is applied to the X-ray term


 function value    669280.88    

-------------------------------------------------------------------------------
             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 =     0.0406, B  =   -0.0717
Partial structure    1: scale =     0.3763, B  =   46.6645
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1624
Free R factor                        =     0.2150
Average Fourier shell correlation    =     0.9600
AverageFree Fourier shell correlation=     0.9471
Average correlation coefficient      =     0.9391
Overall figure of merit              =     0.8590
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02

 fvalues    92434.578       8370.8037       669240.31       669277.56    


     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.= 0.944 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   66
 Minimum acceptable grid spacing:    74   74  156
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    32   32   66
 Minimum acceptable grid spacing:    74   74  156
 Weight matrix   0.24663803    
 Actual weight    7.1495919      is applied to the X-ray term
Norm of X_ray positional gradient                33.1
Norm of Geom. positional gradient                33.1
Norm of X_ray B-factor gradient                  111.
Norm of Geom. B-factor gradient                  115.
Product of X_ray and Geom posit. gradients     -0.106E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.410E+08
 Cosine of angle between them                      -0.991


Residuals: XRAY=     0.6609E+06 GEOM=      8368.     TOTAL=     0.6692E+06
 function value    669235.13    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2106     1.747     1.644
Bond angles  : others                          3238     1.447     1.580
Torsion angles, period  1. refined              185     6.994     5.000
Torsion angles, period  2. refined               90    35.941    22.778
Torsion angles, period  3. refined              268    13.395    15.000
Torsion angles, period  4. refined                9    11.303    15.000
Chiral centres: refined atoms                   196     0.085     0.200
Planar groups: refined atoms                   1743     0.009     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   299     0.242     0.200
VDW repulsions.others                          1365     0.191     0.200
VDW; torsion: refined_atoms                     714     0.172     0.200
VDW; torsion.others                             788     0.083     0.200
HBOND: refined_atoms                            226     0.207     0.200
VDW repulsions: symmetry: refined_atoms          10     0.206     0.200
VDW repulsions: symmetry: others                 26     0.186     0.200
HBOND: symmetry: refined_atoms                   19     0.208     0.200
HBOND: symmetry: others                           1     0.003     0.200
M. chain bond B values: refined atoms           746     1.566     1.246
M. chain bond B values: others                  746     1.565     1.246
M. chain angle B values: refined atoms          929     2.508     1.855
M. chain angle B values: others                 930     2.506     1.855
S. chain bond B values: refined atoms           811     2.573     1.592
S. chain bond B values: others                  810     2.572     1.592
S. chain angle B values: refined atoms         1177     4.047     2.238
S. chain angle B values: others                1178     4.046     2.237
Long range B values: refined atoms             1847     6.682    17.249
Long range B values: others                    1752     6.383    15.869
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0406, B  =   -0.0752
Partial structure    1: scale =     0.3764, B  =   46.6072
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.037    2347 100.00   478.0   484.4  0.16  0.17     108   477.7   486.4  0.20  0.22
 0.109    3949 100.00   369.6   353.0  0.16  0.15     205   368.4   340.9  0.21  0.19
 0.181    4983  99.96   240.2   232.8  0.16  0.14     291   252.2   240.4  0.21  0.18
 0.253    5856 100.00   172.7   175.4  0.17  0.14     312   174.5   177.7  0.23  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0366   1633   0.924    714   0.818   2347   0.892  0.955  0.9639  0.9715  0.9060  0.9410
  0.1087   3225   0.883    724   0.777   3949   0.864  0.996  0.9488  0.9631  0.8914  0.9451
  0.1809   4261   0.870    722   0.773   4983   0.856  0.991  0.9463  0.9579  0.8880  0.9381
  0.2530   5136   0.859    724   0.750   5860   0.846  0.935  0.9410  0.9552  0.8719  0.9351
 $$
Resolution limits                    =     41.964     1.860
Number of used reflections           =      17139
Percentage observed                  =    99.9834
Percentage of free reflections       =     5.0734
Overall R factor                     =     0.1624
Free R factor                        =     0.2150
Average Fourier shell correlation    =     0.9600
AverageFree Fourier shell correlation=     0.9471
Overall weighted R factor            =     0.1509
Free weighted R factor               =     0.1983
Overall weighted R2 factor           =     0.1838
Free weighted R2 factor              =     0.2386
Average correlation coefficient      =     0.9391
Overall correlation coefficient      =     0.9557
Free correlation coefficient         =     0.9179
Cruickshanks DPI for coordinate error=     0.1331
DPI based on free R factor           =     0.1332
Overall figure of merit              =     0.8591
ML based su of positional parameters =     0.0824
ML based su of thermal parameters    =     2.6985
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    92434.281       8367.7646       669235.13       669240.31    

    ****                              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.= 0.944 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_1-86A.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     1.747     1.644
Bond angles  : others                          3238     1.447     1.580
Torsion angles, period  1. refined              185     6.993     5.000
Torsion angles, period  2. refined               90    35.931    22.778
Torsion angles, period  3. refined              268    13.391    15.000
Torsion angles, period  4. refined                9    11.322    15.000
Chiral centres: refined atoms                   196     0.085     0.200
Planar groups: refined atoms                   1743     0.009     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   298     0.242     0.200
VDW repulsions.others                          1371     0.190     0.200
VDW; torsion: refined_atoms                     715     0.172     0.200
VDW; torsion.others                             791     0.083     0.200
HBOND: refined_atoms                            226     0.207     0.200
VDW repulsions: symmetry: refined_atoms          10     0.206     0.200
VDW repulsions: symmetry: others                 26     0.186     0.200
HBOND: symmetry: refined_atoms                   19     0.208     0.200
HBOND: symmetry: others                           1     0.002     0.200
M. chain bond B values: refined atoms           746     1.567     1.247
M. chain bond B values: others                  746     1.565     1.247
M. chain angle B values: refined atoms          929     2.508     1.856
M. chain angle B values: others                 930     2.506     1.855
S. chain bond B values: refined atoms           811     2.574     1.592
S. chain bond B values: others                  810     2.573     1.592
S. chain angle B values: refined atoms         1177     4.049     2.239
S. chain angle B values: others                1178     4.047     2.238
Long range B values: refined atoms             1847     6.678    17.255
Long range B values: others                    1752     6.379    15.875
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0406, B  =   -0.0809
Partial structure    1: scale =     0.3763, B  =   46.5949
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.037    2347 100.00   477.9   484.4  0.16  0.17     108   477.7   486.3  0.20  0.22
 0.109    3949 100.00   369.6   353.0  0.16  0.15     205   368.4   340.9  0.21  0.19
 0.181    4983  99.96   240.1   232.7  0.16  0.14     291   252.2   240.4  0.21  0.18
 0.253    5856 100.00   172.7   175.4  0.17  0.14     312   174.5   177.7  0.23  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0366   1633   0.924    714   0.818   2347   0.891  0.955  0.9638  0.9715  0.9059  0.9411
  0.1087   3225   0.883    724   0.777   3949   0.864  0.996  0.9488  0.9631  0.8916  0.9451
  0.1809   4261   0.870    722   0.773   4983   0.856  0.991  0.9463  0.9579  0.8881  0.9381
  0.2530   5136   0.859    724   0.751   5860   0.846  0.935  0.9410  0.9552  0.8719  0.9350
 $$
Resolution limits                    =     41.964     1.860
Number of used reflections           =      17139
Percentage observed                  =    99.9834
Percentage of free reflections       =     5.0734
Overall R factor                     =     0.1624
Free R factor                        =     0.2150
Average Fourier shell correlation    =     0.9600
AverageFree Fourier shell correlation=     0.9471
Overall weighted R factor            =     0.1508
Free weighted R factor               =     0.1983
Overall weighted R2 factor           =     0.1838
Free weighted R2 factor              =     0.2386
Average correlation coefficient      =     0.9391
Overall correlation coefficient      =     0.9557
Free correlation coefficient         =     0.9179
Cruickshanks DPI for coordinate error=     0.1330
DPI based on free R factor           =     0.1332
Overall figure of merit              =     0.8591
ML based su of positional parameters =     0.0824
ML based su of thermal parameters    =     2.6985
-----------------------------------------------------------------------------
  Time in seconds: CPU =        14.61
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1630   0.2157   0.853       92706.    5126.9   0.0115  0.855   1.736  1.007   0.084
       1   0.1628   0.2150   0.859       92466.    5122.7   0.0113  0.836   1.720  0.998   0.084
       2   0.1625   0.2151   0.859       92442.    5122.6   0.0116  0.861   1.737  1.008   0.085
       3   0.1624   0.2151   0.859       92436.    5122.6   0.0116  0.863   1.742  1.010   0.085
       4   0.1624   0.2151   0.859       92436.    5122.7   0.0116  0.864   1.744  1.012   0.085
       5   0.1624   0.2150   0.859       92434.    5122.8   0.0116  0.865   1.745  1.012   0.085
       6   0.1624   0.2150   0.859       92433.    5122.9   0.0116  0.865   1.746  1.012   0.085
       7   0.1624   0.2151   0.859       92438.    5123.4   0.0116  0.865   1.747  1.013   0.085
       8   0.1624   0.2150   0.859       92440.    5123.4   0.0116  0.865   1.747  1.013   0.085
       9   0.1624   0.2150   0.859       92434.    5123.1   0.0116  0.865   1.747  1.013   0.085
      10   0.1624   0.2150   0.859       92433.    5123.1   0.0117  0.865   1.747  1.013   0.085
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1630   0.1624
             R free    0.2157   0.2150
     Rms BondLength    0.0115   0.0117
      Rms BondAngle    1.7358   1.7473
     Rms ChirVolume    0.0840   0.0851
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      46.6s System:    0.1s Elapsed:     0:47