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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: 20:03:01 


 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 1.64     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_1-65A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-64A.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_1-64A.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       0.0930
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.6400
  Estimated number of reflections :      34020
  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  1.6400

  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_1-65A.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=   2.047 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=   2.195 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=   1.834 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=   2.220 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=   2.429 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=   2.392 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=   2.130 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       1331
Number of   all  reflections      26108
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          26108

   Current auto weighting coefficient =    6.5995836    

 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.= 0.902 id.= 3.000 dev= -2.10 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    36   36   75
 Minimum acceptable grid spacing:    81   81  172
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    36   36   75
 Minimum acceptable grid spacing:    81   81  172
 Weight matrix   0.29511425    
 Actual weight    6.5995836      is applied to the X-ray term
Norm of X_ray positional gradient                37.0
Norm of Geom. positional gradient                82.2
Norm of X_ray B-factor gradient                  107.
Norm of Geom. B-factor gradient                  117.
Product of X_ray and Geom posit. gradients     -0.142E+08
 Cosine of angle between them                      -0.481
Product of X_ray and Geom B-fact gradients     -0.358E+08
 Cosine of angle between them                      -0.885


Residuals: XRAY=     0.8342E+06 GEOM=     0.1356E+05 TOTAL=     0.8477E+06
 function value    847717.75    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.035     0.017
Bond angles  : refined atoms                   2106     1.843     1.644
Bond angles  : others                          3238     2.367     1.580
Torsion angles, period  1. refined              185     6.763     5.000
Torsion angles, period  2. refined               90    34.958    22.778
Torsion angles, period  3. refined              268    13.150    15.000
Torsion angles, period  4. refined                9    12.586    15.000
Chiral centres: refined atoms                   196     0.091     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.017     0.020
VDW repulsions: refined_atoms                   298     0.248     0.200
VDW repulsions.others                          1334     0.220     0.200
VDW; torsion: refined_atoms                     728     0.174     0.200
VDW; torsion.others                             727     0.081     0.200
HBOND: refined_atoms                            214     0.205     0.200
HBOND.others                                      2     0.049     0.200
VDW repulsions: symmetry: refined_atoms           8     0.213     0.200
VDW repulsions: symmetry: others                 23     0.202     0.200
HBOND: symmetry: refined_atoms                   21     0.175     0.200
M. chain bond B values: refined atoms           746     1.733     1.452
M. chain bond B values: others                  746     1.730     1.452
M. chain angle B values: refined atoms          929     2.706     2.168
M. chain angle B values: others                 930     2.705     2.168
S. chain bond B values: refined atoms           811     3.089     1.852
S. chain bond B values: others                  810     3.084     1.851
S. chain angle B values: refined atoms         1177     4.717     2.611
S. chain angle B values: others                1178     4.715     2.610
Long range B values: refined atoms             1841     7.160    20.087
Long range B values: others                    1752     6.892    18.693
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0436, B  =    0.0830
Partial structure    1: scale =     0.3870, B  =   42.3003
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.43 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.047    3375 100.00   441.7   450.6  0.16  0.17     153   441.0   450.7  0.20  0.21
 0.140    5673  99.98   272.1   258.7  0.17  0.15     333   279.5   258.5  0.23  0.20
 0.233    7233  99.99   183.0   165.5  0.18  0.16     385   186.0   169.3  0.21  0.18
 0.325    8489 100.00    82.3    96.3  0.29  0.23     460    77.8    93.4  0.35  0.27
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0470   2446   0.911    929   0.812   3375   0.884  0.950  0.9621  0.9695  0.9061  0.9370
  0.1398   4745   0.866    928   0.758   5673   0.849  1.008  0.9419  0.9556  0.8818  0.9390
  0.2326   6296   0.877    937   0.768   7233   0.863  1.057  0.9528  0.9596  0.9086  0.9414
  0.3254   7567   0.723    927   0.652   8494   0.716  0.763  0.8787  0.8988  0.8383  0.8857
 $$
Resolution limits                    =     41.964     1.640
Number of used reflections           =      24775
Percentage observed                  =    99.9885
Percentage of free reflections       =     5.0984
Overall R factor                     =     0.1870
Free R factor                        =     0.2310
Average Fourier shell correlation    =     0.9392
AverageFree Fourier shell correlation=     0.9255
Overall weighted R factor            =     0.1649
Free weighted R factor               =     0.2045
Overall weighted R2 factor           =     0.1964
Free weighted R2 factor              =     0.2405
Average correlation coefficient      =     0.9212
Overall correlation coefficient      =     0.9578
Free correlation coefficient         =     0.9336
Cruickshanks DPI for coordinate error=     0.1013
DPI based on free R factor           =     0.1049
Overall figure of merit              =     0.8118
ML based su of positional parameters =     0.0725
ML based su of thermal parameters    =     2.1913
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    126395.06       13562.923       847717.75      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.37571996    
 Actual weight    6.5995836      is applied to the X-ray term


 function value    836117.38    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0436, B  =   -0.0545
Partial structure    1: scale =     0.3869, B  =   42.1476
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.43 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1871
Free R factor                        =     0.2301
Average Fourier shell correlation    =     0.9483
AverageFree Fourier shell correlation=     0.9362
Average correlation coefficient      =     0.9204
Overall figure of merit              =     0.8460
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    125391.53       8585.5059       836117.38       847717.75    


     CGMAT cycle number =      3

 Weight matrix   0.38382614    
 Actual weight    6.5995836      is applied to the X-ray term


 function value    835635.44    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0436, B  =   -0.0140
Partial structure    1: scale =     0.3868, B  =   42.1960
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.43 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1867
Free R factor                        =     0.2298
Average Fourier shell correlation    =     0.9492
AverageFree Fourier shell correlation=     0.9369
Average correlation coefficient      =     0.9215
Overall figure of merit              =     0.8490
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    125260.70       8966.9404       835635.44       836117.38    


     CGMAT cycle number =      4

 Weight matrix   0.38493538    
 Actual weight    6.5995836      is applied to the X-ray term


 function value    835575.38    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0436, B  =   -0.0036
Partial structure    1: scale =     0.3869, B  =   42.2636
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.43 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1867
Free R factor                        =     0.2297
Average Fourier shell correlation    =     0.9493
AverageFree Fourier shell correlation=     0.9370
Average correlation coefficient      =     0.9218
Overall figure of merit              =     0.8494
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    125233.94       9083.5605       835575.38       835635.44    


     CGMAT cycle number =      5

 Weight matrix   0.38507140    
 Actual weight    6.5995836      is applied to the X-ray term


 function value    835565.06    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0436, B  =   -0.0151
Partial structure    1: scale =     0.3870, B  =   42.3271
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.43 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1867
Free R factor                        =     0.2297
Average Fourier shell correlation    =     0.9494
AverageFree Fourier shell correlation=     0.9370
Average correlation coefficient      =     0.9219
Overall figure of merit              =     0.8496
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    125227.05       9118.7139       835565.06       835575.38    


     CGMAT cycle number =      6

 Weight matrix   0.38498798    
 Actual weight    6.5995836      is applied to the X-ray term


 function value    835575.44    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0436, B  =   -0.0127
Partial structure    1: scale =     0.3871, B  =   42.3102
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.43 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1867
Free R factor                        =     0.2298
Average Fourier shell correlation    =     0.9494
AverageFree Fourier shell correlation=     0.9370
Average correlation coefficient      =     0.9220
Overall figure of merit              =     0.8496
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    125226.70       9137.0273       835586.25       835565.06    

 fvalues    125226.70       9137.0273       835571.50       835581.13    
 fvalues    125226.70       9137.0273       835571.50       835581.13    


     CGMAT cycle number =      7

 Weight matrix   0.38490188    
 Actual weight    6.5995836      is applied to the X-ray term


 function value    835576.50    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0436, B  =   -0.0110
Partial structure    1: scale =     0.3871, B  =   42.3065
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.43 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1867
Free R factor                        =     0.2298
Average Fourier shell correlation    =     0.9494
AverageFree Fourier shell correlation=     0.9370
Average correlation coefficient      =     0.9220
Overall figure of merit              =     0.8496
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    125225.91       9137.7070       835576.50       835581.13    


     CGMAT cycle number =      8

 Weight matrix   0.38465047    
 Actual weight    6.5995836      is applied to the X-ray term


 function value    835580.38    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0436, B  =   -0.0101
Partial structure    1: scale =     0.3871, B  =   42.2507
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.43 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1867
Free R factor                        =     0.2298
Average Fourier shell correlation    =     0.9494
AverageFree Fourier shell correlation=     0.9370
Average correlation coefficient      =     0.9221
Overall figure of merit              =     0.8495
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02

 fvalues    125225.95       9135.6670       835574.81       835576.50    


     CGMAT cycle number =      9

 Weight matrix   0.38468668    
 Actual weight    6.5995836      is applied to the X-ray term


 function value    835571.00    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0436, B  =   -0.0101
Partial structure    1: scale =     0.3871, B  =   42.1574
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.43 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1868
Free R factor                        =     0.2297
Average Fourier shell correlation    =     0.9494
AverageFree Fourier shell correlation=     0.9370
Average correlation coefficient      =     0.9221
Overall figure of merit              =     0.8495
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    125225.57       9134.3545       835571.00       835574.81    


     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.= 0.915 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        :   128  128  264
 Maximuum H,K,L                 :    36   36   75
 Minimum acceptable grid spacing:    81   81  172
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    36   36   75
 Minimum acceptable grid spacing:    81   81  172
 Weight matrix   0.38448977    
 Actual weight    6.5995836      is applied to the X-ray term
Norm of X_ray positional gradient                44.1
Norm of Geom. positional gradient                44.1
Norm of X_ray B-factor gradient                  123.
Norm of Geom. B-factor gradient                  123.
Product of X_ray and Geom posit. gradients     -0.188E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.489E+08
 Cosine of angle between them                      -0.999


Residuals: XRAY=     0.8264E+06 GEOM=      9136.     TOTAL=     0.8356E+06
 function value    835578.38    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.861     1.644
Bond angles  : others                          3238     1.525     1.580
Torsion angles, period  1. refined              185     6.812     5.000
Torsion angles, period  2. refined               90    34.976    22.778
Torsion angles, period  3. refined              268    13.146    15.000
Torsion angles, period  4. refined                9    12.544    15.000
Chiral centres: refined atoms                   196     0.092     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   301     0.246     0.200
VDW repulsions.others                          1358     0.193     0.200
VDW; torsion: refined_atoms                     730     0.174     0.200
VDW; torsion.others                             779     0.085     0.200
HBOND: refined_atoms                            208     0.208     0.200
HBOND.others                                      1     0.054     0.200
VDW repulsions: symmetry: refined_atoms           8     0.209     0.200
VDW repulsions: symmetry: others                 24     0.185     0.200
HBOND: symmetry: refined_atoms                   21     0.169     0.200
M. chain bond B values: refined atoms           746     1.742     1.461
M. chain bond B values: others                  746     1.737     1.461
M. chain angle B values: refined atoms          929     2.707     2.181
M. chain angle B values: others                 930     2.705     2.181
S. chain bond B values: refined atoms           811     3.113     1.861
S. chain bond B values: others                  810     3.108     1.860
S. chain angle B values: refined atoms         1177     4.739     2.624
S. chain angle B values: others                1178     4.737     2.623
Long range B values: refined atoms             1842     7.147    20.219
Long range B values: others                    1753     6.849    18.826
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0436, B  =   -0.0086
Partial structure    1: scale =     0.3871, B  =   42.1407
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.43 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.047    3375 100.00   442.1   451.0  0.16  0.17     153   441.4   451.3  0.20  0.21
 0.140    5673  99.98   272.4   258.7  0.17  0.15     333   279.8   258.9  0.22  0.20
 0.233    7233  99.99   183.2   165.7  0.18  0.16     385   186.2   169.1  0.21  0.18
 0.325    8489 100.00    82.4    96.3  0.29  0.23     460    77.9    93.1  0.34  0.27
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0470   2446   0.925    929   0.831   3375   0.899  0.952  0.9658  0.9726  0.9072  0.9373
  0.1398   4745   0.869    928   0.760   5673   0.851  1.008  0.9426  0.9561  0.8819  0.9388
  0.2326   6296   0.887    937   0.779   7233   0.873  1.057  0.9558  0.9624  0.9098  0.9411
  0.3254   7567   0.816    927   0.746   8494   0.809  0.798  0.9077  0.9248  0.8401  0.8886
 $$
Resolution limits                    =     41.964     1.640
Number of used reflections           =      24775
Percentage observed                  =    99.9885
Percentage of free reflections       =     5.0984
Overall R factor                     =     0.1868
Free R factor                        =     0.2297
Average Fourier shell correlation    =     0.9494
AverageFree Fourier shell correlation=     0.9370
Overall weighted R factor            =     0.1649
Free weighted R factor               =     0.2036
Overall weighted R2 factor           =     0.1963
Free weighted R2 factor              =     0.2400
Average correlation coefficient      =     0.9221
Overall correlation coefficient      =     0.9579
Free correlation coefficient         =     0.9341
Cruickshanks DPI for coordinate error=     0.1012
DPI based on free R factor           =     0.1044
Overall figure of merit              =     0.8495
ML based su of positional parameters =     0.0634
ML based su of thermal parameters    =     1.8606
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    125227.04       9135.7256       835594.56       835571.00    

 fvalues    125227.04       9135.7256       835579.88       835582.06    
 fvalues    125227.04       9135.7256       835579.88       835582.06    

    ****                              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.= 0.915 id.= 3.000 dev= -2.08 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_1-64A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.861     1.644
Bond angles  : others                          3238     1.525     1.580
Torsion angles, period  1. refined              185     6.812     5.000
Torsion angles, period  2. refined               90    34.976    22.778
Torsion angles, period  3. refined              268    13.147    15.000
Torsion angles, period  4. refined                9    12.541    15.000
Chiral centres: refined atoms                   196     0.092     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   301     0.246     0.200
VDW repulsions.others                          1360     0.193     0.200
VDW; torsion: refined_atoms                     730     0.174     0.200
VDW; torsion.others                             780     0.085     0.200
HBOND: refined_atoms                            208     0.208     0.200
HBOND.others                                      1     0.055     0.200
VDW repulsions: symmetry: refined_atoms           8     0.209     0.200
VDW repulsions: symmetry: others                 24     0.185     0.200
HBOND: symmetry: refined_atoms                   21     0.169     0.200
M. chain bond B values: refined atoms           746     1.741     1.460
M. chain bond B values: others                  746     1.737     1.461
M. chain angle B values: refined atoms          929     2.706     2.181
M. chain angle B values: others                 930     2.705     2.181
S. chain bond B values: refined atoms           811     3.113     1.861
S. chain bond B values: others                  810     3.108     1.860
S. chain angle B values: refined atoms         1177     4.739     2.624
S. chain angle B values: others                1178     4.737     2.623
Long range B values: refined atoms             1842     7.149    20.219
Long range B values: others                    1753     6.851    18.826
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0436, B  =   -0.0004
Partial structure    1: scale =     0.3871, B  =   42.1346
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.43 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.047    3375 100.00   442.1   451.0  0.16  0.17     153   441.4   451.3  0.20  0.21
 0.140    5673  99.98   272.4   258.6  0.17  0.15     333   279.8   258.8  0.22  0.20
 0.233    7233  99.99   183.2   165.6  0.18  0.16     385   186.2   169.0  0.21  0.18
 0.325    8489 100.00    82.4    96.3  0.29  0.22     460    77.9    93.1  0.34  0.27
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0470   2446   0.925    929   0.831   3375   0.899  0.952  0.9658  0.9726  0.9071  0.9373
  0.1398   4745   0.869    928   0.760   5673   0.851  1.008  0.9426  0.9561  0.8819  0.9388
  0.2326   6296   0.887    937   0.779   7233   0.873  1.057  0.9557  0.9623  0.9098  0.9411
  0.3254   7567   0.816    927   0.746   8494   0.808  0.798  0.9077  0.9247  0.8401  0.8886
 $$
Resolution limits                    =     41.964     1.640
Number of used reflections           =      24775
Percentage observed                  =    99.9885
Percentage of free reflections       =     5.0984
Overall R factor                     =     0.1868
Free R factor                        =     0.2297
Average Fourier shell correlation    =     0.9494
AverageFree Fourier shell correlation=     0.9370
Overall weighted R factor            =     0.1649
Free weighted R factor               =     0.2037
Overall weighted R2 factor           =     0.1964
Free weighted R2 factor              =     0.2400
Average correlation coefficient      =     0.9221
Overall correlation coefficient      =     0.9579
Free correlation coefficient         =     0.9341
Cruickshanks DPI for coordinate error=     0.1012
DPI based on free R factor           =     0.1043
Overall figure of merit              =     0.8494
ML based su of positional parameters =     0.0634
ML based su of thermal parameters    =     1.8606
-----------------------------------------------------------------------------
  Time in seconds: CPU =        20.13
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1870   0.2310   0.812      126395.    6953.0   0.0131  0.984   1.843  1.072   0.091
       1   0.1871   0.2301   0.846      125392.    6917.9   0.0121  0.907   1.783  1.036   0.087
       2   0.1867   0.2298   0.849      125261.    6914.1   0.0131  0.982   1.825  1.061   0.090
       3   0.1867   0.2297   0.849      125234.    6913.7   0.0132  0.993   1.842  1.072   0.091
       4   0.1867   0.2297   0.850      125227.    6913.9   0.0133  0.997   1.851  1.077   0.092
       5   0.1867   0.2298   0.850      125226.    6914.1   0.0133  0.998   1.856  1.080   0.092
       6   0.1867   0.2298   0.850      125226.    6914.0   0.0133  0.998   1.857  1.081   0.092
       7   0.1867   0.2298   0.850      125227.    6914.3   0.0133  0.998   1.859  1.082   0.092
       8   0.1868   0.2297   0.850      125226.    6914.1   0.0133  0.998   1.860  1.082   0.092
       9   0.1868   0.2297   0.850      125226.    6914.2   0.0133  0.998   1.861  1.083   0.092
      10   0.1868   0.2297   0.849      125229.    6914.2   0.0133  0.999   1.861  1.083   0.092
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1870   0.1868
             R free    0.2310   0.2297
     Rms BondLength    0.0131   0.0133
      Rms BondAngle    1.8429   1.8610
     Rms ChirVolume    0.0908   0.0917
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      52.3s System:    0.2s Elapsed:     0:53