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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: 15:12:25 


 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 1.81     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_1-82A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-81A.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_1-81A.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       0.0763
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.8100
  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  1.8100

  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_1-82A.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=   2.057 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=   2.218 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=   1.863 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=   2.198 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=   2.396 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=   2.416 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=   2.142 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        983
Number of   all  reflections      19563
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          19563

   Current auto weighting coefficient =    7.0246310    

 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.= 0.924 id.= 3.000 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    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   0.24864650    
 Actual weight    7.0246310      is applied to the X-ray term
Norm of X_ray positional gradient                32.8
Norm of Geom. positional gradient                78.9
Norm of X_ray B-factor gradient                  110.
Norm of Geom. B-factor gradient                  113.
Product of X_ray and Geom posit. gradients     -0.106E+08
 Cosine of angle between them                      -0.421
Product of X_ray and Geom B-fact gradients     -0.379E+08
 Cosine of angle between them                      -0.945


Residuals: XRAY=     0.6986E+06 GEOM=     0.1306E+05 TOTAL=     0.7116E+06
 function value    711617.31    

-------------------------------------------------------------------------------
             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     1.778     1.644
Bond angles  : others                          3238     2.355     1.580
Torsion angles, period  1. refined              185     6.961     5.000
Torsion angles, period  2. refined               90    35.960    22.778
Torsion angles, period  3. refined              268    13.419    15.000
Torsion angles, period  4. refined                9    11.307    15.000
Chiral centres: refined atoms                   196     0.086     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.014     0.020
VDW repulsions: refined_atoms                   300     0.243     0.200
VDW repulsions.others                          1329     0.220     0.200
VDW; torsion: refined_atoms                     715     0.172     0.200
VDW; torsion.others                             717     0.080     0.200
HBOND: refined_atoms                            221     0.207     0.200
HBOND.others                                      1     0.025     0.200
VDW repulsions: symmetry: refined_atoms           9     0.219     0.200
VDW repulsions: symmetry: others                 23     0.208     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     2.528     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     4.227     2.299
S. chain angle B values: others                1178     4.225     2.298
Long range B values: refined atoms             1845     6.802    17.621
Long range B values: others                    1753     6.507    16.267
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0412, B  =    0.0237
Partial structure    1: scale =     0.3785, B  =   46.8349
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2539 100.00   474.1   481.1  0.16  0.17     118   467.8   478.3  0.21  0.22
 0.115    4279 100.00   345.1   330.7  0.16  0.15     235   341.9   317.2  0.22  0.19
 0.191    5407  99.96   228.3   217.9  0.16  0.14     291   240.4   227.5  0.21  0.18
 0.267    6350 100.00   151.3   156.8  0.19  0.15     338   155.5   162.2  0.25  0.20
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0387   1783   0.912    756   0.806   2539   0.881  0.955  0.9609  0.9690  0.9057  0.9400
  0.1148   3513   0.880    766   0.782   4279   0.863  0.995  0.9479  0.9624  0.8914  0.9452
  0.1910   4640   0.870    767   0.756   5407   0.854  1.006  0.9478  0.9575  0.8955  0.9389
  0.2672   5587   0.823    766   0.734   6353   0.812  0.904  0.9344  0.9457  0.8713  0.9257
 $$
Resolution limits                    =     41.964     1.810
Number of used reflections           =      18577
Percentage observed                  =    99.9847
Percentage of free reflections       =     5.0207
Overall R factor                     =     0.1667
Free R factor                        =     0.2186
Average Fourier shell correlation    =     0.9562
AverageFree Fourier shell correlation=     0.9448
Overall weighted R factor            =     0.1528
Free weighted R factor               =     0.1999
Overall weighted R2 factor           =     0.1855
Free weighted R2 factor              =     0.2389
Average correlation coefficient      =     0.9360
Overall correlation coefficient      =     0.9564
Free correlation coefficient         =     0.9209
Cruickshanks DPI for coordinate error=     0.1241
DPI based on free R factor           =     0.1266
Overall figure of merit              =     0.8454
ML based su of positional parameters =     0.0815
ML based su of thermal parameters    =     2.6276
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    99443.945       13060.342       711617.31      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.27478233    
 Actual weight    7.0246310      is applied to the X-ray term


 function value    704209.63    

-------------------------------------------------------------------------------
             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 =     0.0412, B  =   -0.0695
Partial structure    1: scale =     0.3783, B  =   46.9910
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                     =     0.1669
Free R factor                        =     0.2178
Average Fourier shell correlation    =     0.9589
AverageFree Fourier shell correlation=     0.9474
Average correlation coefficient      =     0.9360
Overall figure of merit              =     0.8576
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    99052.359       8403.3789       704209.63       711617.31    


     CGMAT cycle number =      3

 Weight matrix   0.27638447    
 Actual weight    7.0246310      is applied to the X-ray term


 function value    703947.00    

-------------------------------------------------------------------------------
             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 =     0.0412, B  =   -0.0539
Partial structure    1: scale =     0.3785, B  =   46.7854
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                     =     0.1664
Free R factor                        =     0.2174
Average Fourier shell correlation    =     0.9591
AverageFree Fourier shell correlation=     0.9477
Average correlation coefficient      =     0.9365
Overall figure of merit              =     0.8582
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    98990.961       8572.0098       703947.00       704209.63    


     CGMAT cycle number =      4

 Weight matrix   0.27644747    
 Actual weight    7.0246310      is applied to the X-ray term


 function value    703902.88    

-------------------------------------------------------------------------------
             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 =     0.0412, B  =   -0.0408
Partial structure    1: scale =     0.3786, B  =   46.7560
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                     =     0.1664
Free R factor                        =     0.2174
Average Fourier shell correlation    =     0.9591
AverageFree Fourier shell correlation=     0.9477
Average correlation coefficient      =     0.9366
Overall figure of merit              =     0.8583
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    98978.391       8616.1914       703902.88       703947.00    


     CGMAT cycle number =      5

 Weight matrix   0.27647963    
 Actual weight    7.0246310      is applied to the X-ray term


 function value    703878.81    

-------------------------------------------------------------------------------
             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 =     0.0412, B  =   -0.0383
Partial structure    1: scale =     0.3787, B  =   46.7446
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                     =     0.1664
Free R factor                        =     0.2174
Average Fourier shell correlation    =     0.9591
AverageFree Fourier shell correlation=     0.9478
Average correlation coefficient      =     0.9366
Overall figure of merit              =     0.8583
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    98973.453       8626.8389       703878.81       703902.88    


     CGMAT cycle number =      6

 Weight matrix   0.27641419    
 Actual weight    7.0246310      is applied to the X-ray term


 function value    703874.94    

-------------------------------------------------------------------------------
             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 =     0.0412, B  =   -0.0439
Partial structure    1: scale =     0.3787, B  =   46.7424
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                     =     0.1664
Free R factor                        =     0.2175
Average Fourier shell correlation    =     0.9591
AverageFree Fourier shell correlation=     0.9477
Average correlation coefficient      =     0.9366
Overall figure of merit              =     0.8583
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    98973.109       8625.3486       703874.94       703878.81    


     CGMAT cycle number =      7

 Weight matrix   0.27605191    
 Actual weight    7.0246310      is applied to the X-ray term


 function value    703891.31    

-------------------------------------------------------------------------------
             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 =     0.0412, B  =   -0.0404
Partial structure    1: scale =     0.3787, B  =   46.7152
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                     =     0.1664
Free R factor                        =     0.2175
Average Fourier shell correlation    =     0.9591
AverageFree Fourier shell correlation=     0.9477
Average correlation coefficient      =     0.9366
Overall figure of merit              =     0.8582
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    98974.844       8619.6016       703924.69       703874.94    

 fvalues    98974.844       8619.6016       703881.63       703881.38    
 fvalues    98974.844       8619.6016       703881.63       703881.38    


     CGMAT cycle number =      8

 Weight matrix   0.27616200    
 Actual weight    7.0246310      is applied to the X-ray term


 function value    703883.75    

-------------------------------------------------------------------------------
             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 =     0.0412, B  =   -0.0446
Partial structure    1: scale =     0.3788, B  =   46.7358
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                     =     0.1664
Free R factor                        =     0.2176
Average Fourier shell correlation    =     0.9591
AverageFree Fourier shell correlation=     0.9477
Average correlation coefficient      =     0.9366
Overall figure of merit              =     0.8582
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    98978.055       8615.7959       703877.56       703881.38    
 fvalues    98978.055       8615.7959       703877.56       703900.13    


     CGMAT cycle number =      9

 Weight matrix   0.27599028    
 Actual weight    7.0246310      is applied to the X-ray term


 function value    703901.31    

-------------------------------------------------------------------------------
             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 =     0.0412, B  =   -0.0418
Partial structure    1: scale =     0.3788, B  =   46.7638
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                     =     0.1664
Free R factor                        =     0.2176
Average Fourier shell correlation    =     0.9591
AverageFree Fourier shell correlation=     0.9477
Average correlation coefficient      =     0.9366
Overall figure of merit              =     0.8581
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    98978.422       8614.5215       703897.31       703900.13    
 fvalues    98978.422       8614.5215       703897.31       703901.38    


     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.= 0.938 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   0.27580497    
 Actual weight    7.0246310      is applied to the X-ray term
Norm of X_ray positional gradient                35.3
Norm of Geom. positional gradient                35.3
Norm of X_ray B-factor gradient                  117.
Norm of Geom. B-factor gradient                  120.
Product of X_ray and Geom posit. gradients     -0.121E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.451E+08
 Cosine of angle between them                      -0.997


Residuals: XRAY=     0.6953E+06 GEOM=      8613.     TOTAL=     0.7039E+06
 function value    703916.75    

-------------------------------------------------------------------------------
             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     1.782     1.644
Bond angles  : others                          3238     1.465     1.580
Torsion angles, period  1. refined              185     6.974     5.000
Torsion angles, period  2. refined               90    35.932    22.778
Torsion angles, period  3. refined              268    13.431    15.000
Torsion angles, period  4. refined                9    11.497    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                   295     0.245     0.200
VDW repulsions.others                          1358     0.192     0.200
VDW; torsion: refined_atoms                     720     0.171     0.200
VDW; torsion.others                             765     0.084     0.200
HBOND: refined_atoms                            220     0.206     0.200
HBOND.others                                      1     0.009     0.200
VDW repulsions: symmetry: refined_atoms           9     0.209     0.200
VDW repulsions: symmetry: others                 25     0.180     0.200
HBOND: symmetry: refined_atoms                   24     0.183     0.200
M. chain bond B values: refined atoms           746     1.613     1.284
M. chain bond B values: others                  746     1.611     1.284
M. chain angle B values: refined atoms          929     2.539     1.911
M. chain angle B values: others                 930     2.538     1.911
S. chain bond B values: refined atoms           811     2.732     1.644
S. chain bond B values: others                  810     2.729     1.644
S. chain angle B values: refined atoms         1177     4.260     2.312
S. chain angle B values: others                1178     4.258     2.312
Long range B values: refined atoms             1844     6.768    17.728
Long range B values: others                    1751     6.463    16.331
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0412, B  =   -0.0390
Partial structure    1: scale =     0.3789, B  =   46.7908
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2539 100.00   474.7   481.7  0.16  0.17     118   468.4   478.9  0.20  0.22
 0.115    4279 100.00   345.5   330.5  0.16  0.15     235   342.3   317.1  0.22  0.19
 0.191    5407  99.96   228.6   218.0  0.16  0.14     291   240.7   227.6  0.21  0.18
 0.267    6350 100.00   151.5   156.9  0.19  0.15     338   155.7   162.1  0.24  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0387   1783   0.925    756   0.821   2539   0.894  0.955  0.9639  0.9716  0.9065  0.9399
  0.1148   3513   0.882    766   0.784   4279   0.864  0.995  0.9486  0.9630  0.8916  0.9452
  0.1910   4640   0.874    767   0.760   5407   0.858  1.006  0.9491  0.9585  0.8970  0.9390
  0.2672   5587   0.851    766   0.763   6353   0.840  0.912  0.9402  0.9520  0.8740  0.9275
 $$
Resolution limits                    =     41.964     1.810
Number of used reflections           =      18577
Percentage observed                  =    99.9847
Percentage of free reflections       =     5.0207
Overall R factor                     =     0.1664
Free R factor                        =     0.2176
Average Fourier shell correlation    =     0.9591
AverageFree Fourier shell correlation=     0.9477
Overall weighted R factor            =     0.1528
Free weighted R factor               =     0.1992
Overall weighted R2 factor           =     0.1857
Free weighted R2 factor              =     0.2375
Average correlation coefficient      =     0.9366
Overall correlation coefficient      =     0.9565
Free correlation coefficient         =     0.9216
Cruickshanks DPI for coordinate error=     0.1239
DPI based on free R factor           =     0.1260
Overall figure of merit              =     0.8581
ML based su of positional parameters =     0.0773
ML based su of thermal parameters    =     2.4679
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    98978.906       8613.0469       703906.13       703901.38    

 fvalues    98978.906       8613.0469       703942.88       703903.38    
 fvalues    98978.906       8613.0469       703942.88       703903.38    

    ****                              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.= 0.938 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_1-81A.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     1.782     1.644
Bond angles  : others                          3238     1.465     1.580
Torsion angles, period  1. refined              185     6.974     5.000
Torsion angles, period  2. refined               90    35.932    22.778
Torsion angles, period  3. refined              268    13.432    15.000
Torsion angles, period  4. refined                9    11.498    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                   295     0.245     0.200
VDW repulsions.others                          1358     0.192     0.200
VDW; torsion: refined_atoms                     720     0.171     0.200
VDW; torsion.others                             769     0.084     0.200
HBOND: refined_atoms                            220     0.206     0.200
HBOND.others                                      1     0.010     0.200
VDW repulsions: symmetry: refined_atoms           9     0.209     0.200
VDW repulsions: symmetry: others                 25     0.180     0.200
HBOND: symmetry: refined_atoms                   24     0.183     0.200
M. chain bond B values: refined atoms           746     1.613     1.284
M. chain bond B values: others                  746     1.611     1.284
M. chain angle B values: refined atoms          929     2.539     1.911
M. chain angle B values: others                 930     2.538     1.911
S. chain bond B values: refined atoms           811     2.732     1.644
S. chain bond B values: others                  810     2.729     1.644
S. chain angle B values: refined atoms         1177     4.260     2.312
S. chain angle B values: others                1178     4.258     2.312
Long range B values: refined atoms             1844     6.768    17.728
Long range B values: others                    1751     6.463    16.331
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0412, B  =   -0.0423
Partial structure    1: scale =     0.3789, B  =   46.8031
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2539 100.00   474.6   481.7  0.16  0.17     118   468.3   479.0  0.20  0.22
 0.115    4279 100.00   345.5   330.6  0.16  0.15     235   342.3   317.1  0.22  0.19
 0.191    5407  99.96   228.6   218.0  0.16  0.14     291   240.7   227.6  0.21  0.18
 0.267    6350 100.00   151.5   157.0  0.19  0.15     338   155.7   162.1  0.24  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0387   1783   0.925    756   0.821   2539   0.894  0.955  0.9638  0.9715  0.9065  0.9399
  0.1148   3513   0.882    766   0.784   4279   0.864  0.995  0.9486  0.9630  0.8916  0.9452
  0.1910   4640   0.874    767   0.760   5407   0.858  1.006  0.9491  0.9585  0.8970  0.9390
  0.2672   5587   0.851    766   0.763   6353   0.840  0.912  0.9402  0.9520  0.8740  0.9275
 $$
Resolution limits                    =     41.964     1.810
Number of used reflections           =      18577
Percentage observed                  =    99.9847
Percentage of free reflections       =     5.0207
Overall R factor                     =     0.1664
Free R factor                        =     0.2176
Average Fourier shell correlation    =     0.9591
AverageFree Fourier shell correlation=     0.9477
Overall weighted R factor            =     0.1528
Free weighted R factor               =     0.1992
Overall weighted R2 factor           =     0.1857
Free weighted R2 factor              =     0.2375
Average correlation coefficient      =     0.9366
Overall correlation coefficient      =     0.9565
Free correlation coefficient         =     0.9216
Cruickshanks DPI for coordinate error=     0.1239
DPI based on free R factor           =     0.1260
Overall figure of merit              =     0.8581
ML based su of positional parameters =     0.0773
ML based su of thermal parameters    =     2.4679
-----------------------------------------------------------------------------
  Time in seconds: CPU =        20.27
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1667   0.2186   0.845       99444.    5438.4   0.0119  0.886   1.778  1.029   0.086
       1   0.1669   0.2178   0.858       99052.    5431.1   0.0114  0.845   1.744  1.009   0.085
       2   0.1664   0.2174   0.858       98991.    5429.7   0.0119  0.885   1.768  1.022   0.086
       3   0.1664   0.2174   0.858       98978.    5429.4   0.0120  0.889   1.776  1.026   0.086
       4   0.1664   0.2174   0.858       98973.    5429.3   0.0120  0.891   1.779  1.028   0.086
       5   0.1664   0.2175   0.858       98973.    5429.6   0.0120  0.891   1.781  1.029   0.086
       6   0.1664   0.2175   0.858       98976.    5429.8   0.0120  0.891   1.782  1.029   0.086
       7   0.1664   0.2176   0.858       98976.    5429.9   0.0120  0.891   1.782  1.029   0.086
       8   0.1664   0.2176   0.858       98978.    5430.0   0.0120  0.891   1.782  1.029   0.086
       9   0.1664   0.2176   0.858       98981.    5430.1   0.0120  0.891   1.782  1.029   0.086
      10   0.1664   0.2176   0.858       98980.    5430.1   0.0120  0.891   1.782  1.029   0.086
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1667   0.1664
             R free    0.2186   0.2176
     Rms BondLength    0.0119   0.0120
      Rms BondAngle    1.7784   1.7819
     Rms ChirVolume    0.0864   0.0860
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      52.3s System:    0.1s Elapsed:     0:52