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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: 14:48:59 


 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 1.83     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_1-84A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-83A.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_1-83A.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       0.0747
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.8300
  Estimated number of reflections :      24012
  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  1.8300

  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_1-84A.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=   2.050 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=   2.231 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=   1.852 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=   2.215 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=   2.401 ideal_dist=   1.945
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:N   .
  INFO:     link is found (not be used) dist=   2.420 ideal_dist=   2.235
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:SG  .
  INFO:     link is found (not be used) dist=   2.132 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        956
Number of   all  reflections      18952
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          18952

   Current auto weighting coefficient =    7.0747962    

 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.= 0.913 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    32   32   67
 Minimum acceptable grid spacing:    75   75  158
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    32   32   67
 Minimum acceptable grid spacing:    75   75  158
 Weight matrix   0.24110252    
 Actual weight    7.0747962      is applied to the X-ray term
Norm of X_ray positional gradient                32.4
Norm of Geom. positional gradient                78.7
Norm of X_ray B-factor gradient                  110.
Norm of Geom. B-factor gradient                  112.
Product of X_ray and Geom posit. gradients     -0.101E+08
 Cosine of angle between them                      -0.408
Product of X_ray and Geom B-fact gradients     -0.376E+08
 Cosine of angle between them                      -0.941


Residuals: XRAY=     0.6849E+06 GEOM=     0.1300E+05 TOTAL=     0.6979E+06
 function value    697861.13    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.035     0.017
Bond angles  : refined atoms                   2106     1.764     1.644
Bond angles  : others                          3238     2.352     1.580
Torsion angles, period  1. refined              185     6.962     5.000
Torsion angles, period  2. refined               90    35.855    22.778
Torsion angles, period  3. refined              268    13.373    15.000
Torsion angles, period  4. refined                9    11.520    15.000
Chiral centres: refined atoms                   196     0.086     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.017     0.020
VDW repulsions: refined_atoms                   300     0.242     0.200
VDW repulsions.others                          1339     0.219     0.200
VDW; torsion: refined_atoms                     722     0.171     0.200
VDW; torsion.others                             718     0.080     0.200
HBOND: refined_atoms                            229     0.204     0.200
HBOND.others                                      1     0.020     0.200
VDW repulsions: symmetry: refined_atoms           8     0.225     0.200
VDW repulsions: symmetry: others                 21     0.217     0.200
HBOND: symmetry: refined_atoms                   21     0.199     0.200
M. chain bond B values: refined atoms           746     1.580     1.260
M. chain bond B values: others                  746     1.579     1.261
M. chain angle B values: refined atoms          929     2.509     1.877
M. chain angle B values: others                 930     2.508     1.877
S. chain bond B values: refined atoms           811     2.645     1.613
S. chain bond B values: others                  810     2.643     1.613
S. chain angle B values: refined atoms         1177     4.146     2.268
S. chain angle B values: others                1178     4.144     2.267
Long range B values: refined atoms             1858     6.746    17.542
Long range B values: others                    1763     6.428    16.145
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0409, B  =    0.0005
Partial structure    1: scale =     0.3771, B  =   46.7933
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.51 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.038    2459 100.00   475.2   481.6  0.16  0.17     113   471.6   481.0  0.20  0.22
 0.112    4149 100.00   355.5   340.1  0.16  0.15     219   353.6   328.3  0.22  0.20
 0.187    5230  99.96   232.9   223.9  0.16  0.13     293   246.6   233.8  0.21  0.18
 0.261    6148 100.00   160.2   164.4  0.18  0.14     330   164.2   170.0  0.24  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0378   1717   0.913    742   0.803   2459   0.880  0.956  0.9618  0.9692  0.9087  0.9404
  0.1123   3402   0.877    747   0.776   4149   0.859  0.994  0.9464  0.9617  0.8893  0.9446
  0.1868   4481   0.871    749   0.761   5230   0.855  1.000  0.9480  0.9582  0.8928  0.9399
  0.2614   5402   0.830    754   0.734   6156   0.818  0.916  0.9364  0.9477  0.8711  0.9291
 $$
Resolution limits                    =     41.964     1.830
Number of used reflections           =      17994
Percentage observed                  =    99.9842
Percentage of free reflections       =     5.0449
Overall R factor                     =     0.1651
Free R factor                        =     0.2178
Average Fourier shell correlation    =     0.9569
AverageFree Fourier shell correlation=     0.9453
Overall weighted R factor            =     0.1521
Free weighted R factor               =     0.1996
Overall weighted R2 factor           =     0.1849
Free weighted R2 factor              =     0.2384
Average correlation coefficient      =     0.9374
Overall correlation coefficient      =     0.9561
Free correlation coefficient         =     0.9195
Cruickshanks DPI for coordinate error=     0.1276
DPI based on free R factor           =     0.1295
Overall figure of merit              =     0.8467
ML based su of positional parameters =     0.0830
ML based su of thermal parameters    =     2.6993
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    96802.500       13003.192       697861.13      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.26081041    
 Actual weight    7.0747962      is applied to the X-ray term


 function value    690777.50    

-------------------------------------------------------------------------------
             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 =     0.0409, B  =   -0.0871
Partial structure    1: scale =     0.3773, B  =   47.0214
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.51 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1651
Free R factor                        =     0.2171
Average Fourier shell correlation    =     0.9592
AverageFree Fourier shell correlation=     0.9475
Average correlation coefficient      =     0.9375
Overall figure of merit              =     0.8567
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    96457.977       8356.9980       690777.50       697861.13    


     CGMAT cycle number =      3

 Weight matrix   0.26193100    
 Actual weight    7.0747962      is applied to the X-ray term


 function value    690628.13    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0409, B  =   -0.0831
Partial structure    1: scale =     0.3772, B  =   46.9366
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.51 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1647
Free R factor                        =     0.2169
Average Fourier shell correlation    =     0.9594
AverageFree Fourier shell correlation=     0.9477
Average correlation coefficient      =     0.9379
Overall figure of merit              =     0.8572
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    96419.656       8478.6982       690628.13       690777.50    


     CGMAT cycle number =      4

 Weight matrix   0.26229838    
 Actual weight    7.0747962      is applied to the X-ray term


 function value    690566.50    

-------------------------------------------------------------------------------
             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 =     0.0409, B  =   -0.0755
Partial structure    1: scale =     0.3774, B  =   46.8241
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.51 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1646
Free R factor                        =     0.2169
Average Fourier shell correlation    =     0.9594
AverageFree Fourier shell correlation=     0.9477
Average correlation coefficient      =     0.9379
Overall figure of merit              =     0.8574
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    96406.000       8513.7168       690566.50       690628.13    


     CGMAT cycle number =      5

 Weight matrix   0.26237050    
 Actual weight    7.0747962      is applied to the X-ray term


 function value    690527.56    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0409, B  =   -0.0698
Partial structure    1: scale =     0.3774, B  =   46.7280
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.51 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1646
Free R factor                        =     0.2168
Average Fourier shell correlation    =     0.9595
AverageFree Fourier shell correlation=     0.9478
Average correlation coefficient      =     0.9380
Overall figure of merit              =     0.8575
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    96398.914       8524.9043       690527.56       690566.50    


     CGMAT cycle number =      6

 Weight matrix   0.26248965    
 Actual weight    7.0747962      is applied to the X-ray term


 function value    690495.31    

-------------------------------------------------------------------------------
             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 =     0.0409, B  =   -0.0685
Partial structure    1: scale =     0.3775, B  =   46.6950
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.51 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1646
Free R factor                        =     0.2168
Average Fourier shell correlation    =     0.9595
AverageFree Fourier shell correlation=     0.9478
Average correlation coefficient      =     0.9380
Overall figure of merit              =     0.8576
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    96393.891       8528.1787       690495.31       690527.56    


     CGMAT cycle number =      7

 Weight matrix   0.26306006    
 Actual weight    7.0747962      is applied to the X-ray term


 function value    690430.13    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0409, B  =   -0.0767
Partial structure    1: scale =     0.3777, B  =   46.6582
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.51 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1646
Free R factor                        =     0.2168
Average Fourier shell correlation    =     0.9595
AverageFree Fourier shell correlation=     0.9479
Average correlation coefficient      =     0.9380
Overall figure of merit              =     0.8577
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    96385.055       8525.5205       690430.13       690495.31    


     CGMAT cycle number =      8

 Weight matrix   0.26289234    
 Actual weight    7.0747962      is applied to the X-ray term


 function value    690435.00    

-------------------------------------------------------------------------------
             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 =     0.0409, B  =   -0.0807
Partial structure    1: scale =     0.3777, B  =   46.5682
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.51 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1646
Free R factor                        =     0.2168
Average Fourier shell correlation    =     0.9595
AverageFree Fourier shell correlation=     0.9478
Average correlation coefficient      =     0.9380
Overall figure of merit              =     0.8577
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    96386.242       8528.2568       690414.63       690430.13    
 fvalues    96386.242       8528.2568       690414.63       690441.25    


     CGMAT cycle number =      9

 Weight matrix   0.26290694    
 Actual weight    7.0747962      is applied to the X-ray term


 function value    690418.19    

-------------------------------------------------------------------------------
             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 =     0.0409, B  =   -0.0740
Partial structure    1: scale =     0.3777, B  =   46.5026
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.51 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1646
Free R factor                        =     0.2167
Average Fourier shell correlation    =     0.9595
AverageFree Fourier shell correlation=     0.9479
Average correlation coefficient      =     0.9380
Overall figure of merit              =     0.8577
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    96383.625       8523.7080       690418.19       690441.25    


     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.= 0.942 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   67
 Minimum acceptable grid spacing:    75   75  158
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    32   32   67
 Minimum acceptable grid spacing:    75   75  158
 Weight matrix   0.26315486    
 Actual weight    7.0747962      is applied to the X-ray term
Norm of X_ray positional gradient                34.3
Norm of Geom. positional gradient                34.2
Norm of X_ray B-factor gradient                  115.
Norm of Geom. B-factor gradient                  118.
Product of X_ray and Geom posit. gradients     -0.113E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.433E+08
 Cosine of angle between them                      -0.990


Residuals: XRAY=     0.6819E+06 GEOM=      8524.     TOTAL=     0.6904E+06
 function value    690380.38    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2106     1.763     1.644
Bond angles  : others                          3238     1.455     1.580
Torsion angles, period  1. refined              185     6.975     5.000
Torsion angles, period  2. refined               90    35.976    22.778
Torsion angles, period  3. refined              268    13.414    15.000
Torsion angles, period  4. refined                9    11.383    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                   297     0.244     0.200
VDW repulsions.others                          1371     0.190     0.200
VDW; torsion: refined_atoms                     719     0.171     0.200
VDW; torsion.others                             782     0.083     0.200
HBOND: refined_atoms                            227     0.205     0.200
VDW repulsions: symmetry: refined_atoms           9     0.217     0.200
VDW repulsions: symmetry: others                 24     0.189     0.200
HBOND: symmetry: refined_atoms                   22     0.191     0.200
M. chain bond B values: refined atoms           746     1.592     1.268
M. chain bond B values: others                  746     1.591     1.268
M. chain angle B values: refined atoms          929     2.524     1.887
M. chain angle B values: others                 930     2.522     1.887
S. chain bond B values: refined atoms           811     2.675     1.623
S. chain bond B values: others                  810     2.672     1.623
S. chain angle B values: refined atoms         1177     4.189     2.282
S. chain angle B values: others                1178     4.187     2.282
Long range B values: refined atoms             1851     6.731    17.524
Long range B values: others                    1753     6.400    16.092
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0409, B  =   -0.0767
Partial structure    1: scale =     0.3776, B  =   46.5425
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.51 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10.  v. resln :N:1,6,7,11,12:
:Cycle   10.  and  v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.038    2459 100.00   475.4   482.0  0.16  0.17     113   471.8   481.9  0.20  0.22
 0.112    4149 100.00   355.6   340.1  0.16  0.15     219   353.7   328.3  0.22  0.20
 0.187    5230  99.96   233.0   224.1  0.16  0.13     293   246.7   234.3  0.21  0.18
 0.261    6148 100.00   160.2   164.5  0.18  0.14     330   164.2   170.0  0.24  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0378   1717   0.926    742   0.820   2459   0.894  0.958  0.9648  0.9719  0.9091  0.9409
  0.1123   3402   0.880    747   0.780   4149   0.862  0.994  0.9479  0.9627  0.8908  0.9449
  0.1868   4481   0.874    749   0.763   5230   0.858  1.000  0.9492  0.9589  0.8946  0.9395
  0.2614   5402   0.852    754   0.755   6156   0.840  0.922  0.9410  0.9529  0.8732  0.9309
 $$
Resolution limits                    =     41.964     1.830
Number of used reflections           =      17994
Percentage observed                  =    99.9842
Percentage of free reflections       =     5.0449
Overall R factor                     =     0.1646
Free R factor                        =     0.2167
Average Fourier shell correlation    =     0.9595
AverageFree Fourier shell correlation=     0.9479
Overall weighted R factor            =     0.1518
Free weighted R factor               =     0.1985
Overall weighted R2 factor           =     0.1846
Free weighted R2 factor              =     0.2372
Average correlation coefficient      =     0.9380
Overall correlation coefficient      =     0.9563
Free correlation coefficient         =     0.9204
Cruickshanks DPI for coordinate error=     0.1272
DPI based on free R factor           =     0.1289
Overall figure of merit              =     0.8578
ML based su of positional parameters =     0.0794
ML based su of thermal parameters    =     2.5658
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    96378.250       8523.8984       690380.38       690418.19    

    ****                              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.= 0.942 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_1-83A.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     1.764     1.644
Bond angles  : others                          3238     1.455     1.580
Torsion angles, period  1. refined              185     6.973     5.000
Torsion angles, period  2. refined               90    35.982    22.778
Torsion angles, period  3. refined              268    13.417    15.000
Torsion angles, period  4. refined                9    11.368    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                   298     0.243     0.200
VDW repulsions.others                          1372     0.190     0.200
VDW; torsion: refined_atoms                     720     0.171     0.200
VDW; torsion.others                             786     0.083     0.200
HBOND: refined_atoms                            227     0.205     0.200
VDW repulsions: symmetry: refined_atoms           9     0.217     0.200
VDW repulsions: symmetry: others                 24     0.189     0.200
HBOND: symmetry: refined_atoms                   22     0.192     0.200
M. chain bond B values: refined atoms           746     1.592     1.268
M. chain bond B values: others                  746     1.591     1.268
M. chain angle B values: refined atoms          929     2.524     1.888
M. chain angle B values: others                 930     2.522     1.887
S. chain bond B values: refined atoms           811     2.676     1.624
S. chain bond B values: others                  810     2.673     1.623
S. chain angle B values: refined atoms         1177     4.191     2.283
S. chain angle B values: others                1178     4.189     2.282
Long range B values: refined atoms             1852     6.732    17.544
Long range B values: others                    1754     6.400    16.114
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0409, B  =   -0.0800
Partial structure    1: scale =     0.3776, B  =   46.5600
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.51 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.038    2459 100.00   475.4   482.0  0.16  0.17     113   471.8   481.8  0.20  0.22
 0.112    4149 100.00   355.6   340.1  0.16  0.15     219   353.7   328.3  0.22  0.20
 0.187    5230  99.96   233.0   224.1  0.16  0.13     293   246.7   234.4  0.21  0.18
 0.261    6148 100.00   160.2   164.5  0.18  0.14     330   164.3   170.0  0.24  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0378   1717   0.926    742   0.820   2459   0.894  0.958  0.9648  0.9719  0.9091  0.9409
  0.1123   3402   0.880    747   0.780   4149   0.862  0.994  0.9479  0.9627  0.8907  0.9449
  0.1868   4481   0.874    749   0.763   5230   0.858  1.000  0.9492  0.9589  0.8946  0.9395
  0.2614   5402   0.852    754   0.755   6156   0.840  0.922  0.9410  0.9529  0.8732  0.9309
 $$
Resolution limits                    =     41.964     1.830
Number of used reflections           =      17994
Percentage observed                  =    99.9842
Percentage of free reflections       =     5.0449
Overall R factor                     =     0.1646
Free R factor                        =     0.2167
Average Fourier shell correlation    =     0.9595
AverageFree Fourier shell correlation=     0.9479
Overall weighted R factor            =     0.1518
Free weighted R factor               =     0.1986
Overall weighted R2 factor           =     0.1846
Free weighted R2 factor              =     0.2373
Average correlation coefficient      =     0.9380
Overall correlation coefficient      =     0.9563
Free correlation coefficient         =     0.9203
Cruickshanks DPI for coordinate error=     0.1272
DPI based on free R factor           =     0.1289
Overall figure of merit              =     0.8578
ML based su of positional parameters =     0.0794
ML based su of thermal parameters    =     2.5658
-----------------------------------------------------------------------------
  Time in seconds: CPU =        14.12
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1651   0.2178   0.847       96803.    5316.7   0.0118  0.875   1.764  1.021   0.086
       1   0.1651   0.2171   0.857       96458.    5309.8   0.0113  0.839   1.732  1.003   0.085
       2   0.1647   0.2169   0.857       96420.    5308.7   0.0117  0.871   1.750  1.013   0.086
       3   0.1646   0.2169   0.857       96406.    5308.2   0.0117  0.874   1.755  1.017   0.086
       4   0.1646   0.2168   0.857       96399.    5307.7   0.0117  0.875   1.758  1.019   0.086
       5   0.1646   0.2168   0.858       96394.    5307.5   0.0118  0.876   1.760  1.020   0.086
       6   0.1646   0.2168   0.858       96385.    5307.1   0.0118  0.876   1.761  1.020   0.086
       7   0.1646   0.2168   0.858       96385.    5307.1   0.0118  0.877   1.762  1.021   0.086
       8   0.1646   0.2167   0.858       96384.    5307.0   0.0118  0.877   1.763  1.021   0.086
       9   0.1646   0.2167   0.858       96378.    5306.6   0.0118  0.877   1.763  1.022   0.086
      10   0.1646   0.2167   0.858       96378.    5306.5   0.0118  0.877   1.764  1.022   0.086
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1651   0.1646
             R free    0.2178   0.2167
     Rms BondLength    0.0118   0.0118
      Rms BondAngle    1.7639   1.7638
     Rms ChirVolume    0.0861   0.0860
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      46.3s System:    0.1s Elapsed:     0:46