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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: 21:11:26 


 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 1.61     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_1-62A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-61A.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_1-61A.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       0.0964
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.6100
  Estimated number of reflections :      34927
  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  1.6100

  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_1-62A.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=   2.051 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=   2.198 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=   1.830 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=   2.222 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=   2.419 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=   2.394 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=   2.144 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       1405
Number of   all  reflections      27550
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          27550

   Current auto weighting coefficient =    6.5246096    

 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.= 0.896 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   77
 Minimum acceptable grid spacing:    82   82  174
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    36   36   77
 Minimum acceptable grid spacing:    82   82  174
 Weight matrix   0.29315069    
 Actual weight    6.5246096      is applied to the X-ray term
Norm of X_ray positional gradient                37.1
Norm of Geom. positional gradient                82.8
Norm of X_ray B-factor gradient                  106.
Norm of Geom. B-factor gradient                  115.
Product of X_ray and Geom posit. gradients     -0.144E+08
 Cosine of angle between them                      -0.486
Product of X_ray and Geom B-fact gradients     -0.344E+08
 Cosine of angle between them                      -0.868


Residuals: XRAY=     0.8628E+06 GEOM=     0.1359E+05 TOTAL=     0.8764E+06
 function value    876360.69    

-------------------------------------------------------------------------------
             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     1.867     1.644
Bond angles  : others                          3238     2.371     1.580
Torsion angles, period  1. refined              185     6.791     5.000
Torsion angles, period  2. refined               90    35.032    22.778
Torsion angles, period  3. refined              268    13.224    15.000
Torsion angles, period  4. refined                9    12.394    15.000
Chiral centres: refined atoms                   196     0.091     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.018     0.020
VDW repulsions: refined_atoms                   299     0.247     0.200
VDW repulsions.others                          1345     0.219     0.200
VDW; torsion: refined_atoms                     728     0.174     0.200
VDW; torsion.others                             713     0.082     0.200
HBOND: refined_atoms                            212     0.204     0.200
HBOND.others                                      2     0.045     0.200
VDW repulsions: symmetry: refined_atoms           8     0.203     0.200
VDW repulsions: symmetry: others                 23     0.203     0.200
HBOND: symmetry: refined_atoms                   22     0.192     0.200
M. chain bond B values: refined atoms           746     1.752     1.484
M. chain bond B values: others                  746     1.746     1.484
M. chain angle B values: refined atoms          929     2.722     2.217
M. chain angle B values: others                 930     2.721     2.217
S. chain bond B values: refined atoms           811     3.130     1.883
S. chain bond B values: others                  810     3.126     1.883
S. chain angle B values: refined atoms         1177     4.766     2.658
S. chain angle B values: others                1178     4.764     2.657
Long range B values: refined atoms             1844     7.190    20.579
Long range B values: others                    1754     6.918    19.157
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0440, B  =    0.0975
Partial structure    1: scale =     0.3864, B  =   41.6162
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.42 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3541 100.00   434.2   443.8  0.17  0.17     165   434.4   442.6  0.20  0.21
 0.145    5999  99.97   261.9   247.4  0.17  0.15     343   267.5   246.0  0.23  0.20
 0.241    7631 100.00   171.6   155.0  0.18  0.16     408   175.5   159.8  0.21  0.19
 0.338    8966 100.00    73.9    87.9  0.31  0.24     488    71.0    86.4  0.37  0.30
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0487   2579   0.910    962   0.806   3541   0.882  0.948  0.9623  0.9692  0.9073  0.9372
  0.1450   5033   0.865    966   0.766   5999   0.849  1.016  0.9411  0.9554  0.8808  0.9383
  0.2413   6669   0.869    962   0.760   7631   0.856  1.055  0.9505  0.9573  0.9043  0.9393
  0.3376   7995   0.686    977   0.610   8972   0.678  0.728  0.8594  0.8812  0.8149  0.8756
 $$
Resolution limits                    =     41.964     1.610
Number of used reflections           =      26143
Percentage observed                  =    99.9891
Percentage of free reflections       =     5.1002
Overall R factor                     =     0.1908
Free R factor                        =     0.2341
Average Fourier shell correlation    =     0.9324
AverageFree Fourier shell correlation=     0.9179
Overall weighted R factor            =     0.1671
Free weighted R factor               =     0.2064
Overall weighted R2 factor           =     0.1985
Free weighted R2 factor              =     0.2417
Average correlation coefficient      =     0.9169
Overall correlation coefficient      =     0.9582
Free correlation coefficient         =     0.9347
Cruickshanks DPI for coordinate error=     0.0977
DPI based on free R factor           =     0.1016
Overall figure of merit              =     0.7967
ML based su of positional parameters =     0.0723
ML based su of thermal parameters    =     2.1687
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    132233.11       13591.252       876360.69      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.37062663    
 Actual weight    6.5246096      is applied to the X-ray term


 function value    863991.00    

-------------------------------------------------------------------------------
             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 =     0.0440, B  =   -0.0673
Partial structure    1: scale =     0.3869, B  =   41.7956
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.42 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1910
Free R factor                        =     0.2334
Average Fourier shell correlation    =     0.9437
AverageFree Fourier shell correlation=     0.9310
Average correlation coefficient      =     0.9157
Overall figure of merit              =     0.8344
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    131111.58       8539.1152       863991.00       876360.69    


     CGMAT cycle number =      3

 Weight matrix   0.38127068    
 Actual weight    6.5246096      is applied to the X-ray term


 function value    863269.44    

-------------------------------------------------------------------------------
             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 =     0.0440, B  =   -0.0264
Partial structure    1: scale =     0.3868, B  =   41.7834
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.42 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1906
Free R factor                        =     0.2335
Average Fourier shell correlation    =     0.9453
AverageFree Fourier shell correlation=     0.9325
Average correlation coefficient      =     0.9167
Overall figure of merit              =     0.8398
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    130950.46       8868.7939       863269.44       863991.00    


     CGMAT cycle number =      4

 Weight matrix   0.38058490    
 Actual weight    6.5246096      is applied to the X-ray term


 function value    863271.94    

-------------------------------------------------------------------------------
             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 =     0.0440, B  =   -0.0053
Partial structure    1: scale =     0.3867, B  =   41.7650
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.42 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1906
Free R factor                        =     0.2336
Average Fourier shell correlation    =     0.9454
AverageFree Fourier shell correlation=     0.9324
Average correlation coefficient      =     0.9171
Overall figure of merit              =     0.8400
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02


 fvalues    130936.95       8971.5830       863322.31       863269.44    

 fvalues    130936.95       8971.5830       863298.75       863284.06    
 fvalues    130936.95       8971.5830       863298.75       863284.06    


     CGMAT cycle number =      5

 Weight matrix   0.38082924    
 Actual weight    6.5246096      is applied to the X-ray term


 function value    863296.69    

-------------------------------------------------------------------------------
             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 =     0.0440, B  =   -0.0126
Partial structure    1: scale =     0.3867, B  =   41.7510
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.42 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1906
Free R factor                        =     0.2336
Average Fourier shell correlation    =     0.9454
AverageFree Fourier shell correlation=     0.9324
Average correlation coefficient      =     0.9171
Overall figure of merit              =     0.8400
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03


 fvalues    130937.76       8978.2666       863330.75       863284.06    

 fvalues    130937.76       8978.2666       863320.63       863296.00    
 fvalues    130937.76       8978.2666       863320.63       863296.00    


     CGMAT cycle number =      6

 Weight matrix   0.38081360    
 Actual weight    6.5246096      is applied to the X-ray term


 function value    863310.44    

-------------------------------------------------------------------------------
             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 =     0.0440, B  =   -0.0138
Partial structure    1: scale =     0.3867, B  =   41.7561
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.42 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1906
Free R factor                        =     0.2336
Average Fourier shell correlation    =     0.9454
AverageFree Fourier shell correlation=     0.9324
Average correlation coefficient      =     0.9171
Overall figure of merit              =     0.8400
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    130940.15       8980.4990       863331.38       863296.00    

 fvalues    130940.15       8980.4990       863314.56       863313.88    
 fvalues    130940.15       8980.4990       863314.56       863313.88    


     CGMAT cycle number =      7

 Weight matrix   0.38085967    
 Actual weight    6.5246096      is applied to the X-ray term


 function value    863310.38    

-------------------------------------------------------------------------------
             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 =     0.0440, B  =   -0.0145
Partial structure    1: scale =     0.3867, B  =   41.7559
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.42 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1906
Free R factor                        =     0.2336
Average Fourier shell correlation    =     0.9454
AverageFree Fourier shell correlation=     0.9324
Average correlation coefficient      =     0.9171
Overall figure of merit              =     0.8400
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    130939.52       8981.1025       863310.38       863313.88    


     CGMAT cycle number =      8

 Weight matrix   0.38064852    
 Actual weight    6.5246096      is applied to the X-ray term


 function value    863316.31    

-------------------------------------------------------------------------------
             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 =     0.0440, B  =   -0.0121
Partial structure    1: scale =     0.3868, B  =   41.7478
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.42 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1906
Free R factor                        =     0.2336
Average Fourier shell correlation    =     0.9454
AverageFree Fourier shell correlation=     0.9324
Average correlation coefficient      =     0.9171
Overall figure of merit              =     0.8400
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    130940.81       8980.7744       863301.75       863310.38    
 fvalues    130940.81       8980.7744       863301.75       863318.44    


     CGMAT cycle number =      9

 Weight matrix   0.38041842    
 Actual weight    6.5246096      is applied to the X-ray term


 function value    863328.81    

-------------------------------------------------------------------------------
             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 =     0.0440, B  =   -0.0099
Partial structure    1: scale =     0.3867, B  =   41.7404
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.42 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1906
Free R factor                        =     0.2337
Average Fourier shell correlation    =     0.9454
AverageFree Fourier shell correlation=     0.9324
Average correlation coefficient      =     0.9171
Overall figure of merit              =     0.8399
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    130942.32       8982.2324       863324.69       863318.44    
 fvalues    130942.32       8982.2324       863324.69       863329.75    


     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.= 0.912 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        :   128  128  264
 Maximuum H,K,L                 :    36   36   77
 Minimum acceptable grid spacing:    82   82  174
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    36   36   77
 Minimum acceptable grid spacing:    82   82  174
 Weight matrix   0.38038453    
 Actual weight    6.5246096      is applied to the X-ray term
Norm of X_ray positional gradient                43.4
Norm of Geom. positional gradient                43.2
Norm of X_ray B-factor gradient                  118.
Norm of Geom. B-factor gradient                  118.
Product of X_ray and Geom posit. gradients     -0.181E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.450E+08
 Cosine of angle between them                      -0.999


Residuals: XRAY=     0.8544E+06 GEOM=      8984.     TOTAL=     0.8633E+06
 function value    863334.06    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2106     1.853     1.644
Bond angles  : others                          3238     1.521     1.580
Torsion angles, period  1. refined              185     6.802     5.000
Torsion angles, period  2. refined               90    34.975    22.778
Torsion angles, period  3. refined              268    13.197    15.000
Torsion angles, period  4. refined                9    12.367    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   301     0.246     0.200
VDW repulsions.others                          1337     0.199     0.200
VDW; torsion: refined_atoms                     731     0.174     0.200
VDW; torsion.others                             731     0.087     0.200
HBOND: refined_atoms                            215     0.201     0.200
HBOND.others                                      1     0.040     0.200
VDW repulsions: symmetry: refined_atoms           8     0.203     0.200
VDW repulsions: symmetry: others                 21     0.202     0.200
HBOND: symmetry: refined_atoms                   22     0.205     0.200
M. chain bond B values: refined atoms           746     1.741     1.497
M. chain bond B values: others                  746     1.737     1.497
M. chain angle B values: refined atoms          929     2.707     2.235
M. chain angle B values: others                 930     2.705     2.235
S. chain bond B values: refined atoms           811     3.135     1.896
S. chain bond B values: others                  810     3.130     1.896
S. chain angle B values: refined atoms         1177     4.763     2.678
S. chain angle B values: others                1178     4.761     2.677
Long range B values: refined atoms             1851     7.314    20.733
Long range B values: others                    1762     7.069    19.343
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0440, B  =   -0.0101
Partial structure    1: scale =     0.3867, B  =   41.7616
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.42 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3541 100.00   434.8   444.2  0.17  0.17     165   435.0   443.1  0.20  0.21
 0.145    5999  99.97   262.3   247.6  0.17  0.15     343   267.9   246.1  0.23  0.20
 0.241    7631 100.00   171.9   155.3  0.18  0.16     408   175.7   160.2  0.21  0.19
 0.338    8966 100.00    74.1    88.0  0.31  0.24     488    71.1    86.6  0.37  0.30
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0487   2579   0.923    962   0.825   3541   0.897  0.950  0.9652  0.9722  0.9064  0.9373
  0.1450   5033   0.869    966   0.769   5999   0.853  1.016  0.9421  0.9560  0.8816  0.9381
  0.2413   6669   0.880    962   0.774   7631   0.867  1.055  0.9540  0.9611  0.9051  0.9403
  0.3376   7995   0.794    977   0.719   8972   0.786  0.770  0.8966  0.9144  0.8157  0.8755
 $$
Resolution limits                    =     41.964     1.610
Number of used reflections           =      26143
Percentage observed                  =    99.9891
Percentage of free reflections       =     5.1002
Overall R factor                     =     0.1906
Free R factor                        =     0.2337
Average Fourier shell correlation    =     0.9454
AverageFree Fourier shell correlation=     0.9324
Overall weighted R factor            =     0.1669
Free weighted R factor               =     0.2063
Overall weighted R2 factor           =     0.1983
Free weighted R2 factor              =     0.2425
Average correlation coefficient      =     0.9171
Overall correlation coefficient      =     0.9583
Free correlation coefficient         =     0.9347
Cruickshanks DPI for coordinate error=     0.0976
DPI based on free R factor           =     0.1015
Overall figure of merit              =     0.8399
ML based su of positional parameters =     0.0634
ML based su of thermal parameters    =     1.8505
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02

 fvalues    130939.78       8983.6416       863314.56       863329.75    

    ****                              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.= 0.912 id.= 3.000 dev= -2.09 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_1-61A.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     1.853     1.644
Bond angles  : others                          3238     1.521     1.580
Torsion angles, period  1. refined              185     6.802     5.000
Torsion angles, period  2. refined               90    34.974    22.778
Torsion angles, period  3. refined              268    13.197    15.000
Torsion angles, period  4. refined                9    12.367    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   301     0.246     0.200
VDW repulsions.others                          1338     0.198     0.200
VDW; torsion: refined_atoms                     731     0.174     0.200
VDW; torsion.others                             732     0.087     0.200
HBOND: refined_atoms                            215     0.201     0.200
HBOND.others                                      1     0.040     0.200
VDW repulsions: symmetry: refined_atoms           8     0.203     0.200
VDW repulsions: symmetry: others                 21     0.202     0.200
HBOND: symmetry: refined_atoms                   22     0.205     0.200
M. chain bond B values: refined atoms           746     1.741     1.497
M. chain bond B values: others                  746     1.737     1.497
M. chain angle B values: refined atoms          929     2.707     2.235
M. chain angle B values: others                 930     2.706     2.235
S. chain bond B values: refined atoms           811     3.135     1.896
S. chain bond B values: others                  810     3.130     1.896
S. chain angle B values: refined atoms         1177     4.763     2.678
S. chain angle B values: others                1178     4.761     2.677
Long range B values: refined atoms             1851     7.314    20.733
Long range B values: others                    1762     7.069    19.342
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0440, B  =   -0.0107
Partial structure    1: scale =     0.3867, B  =   41.8100
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.42 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3541 100.00   434.8   444.2  0.17  0.17     165   435.0   443.1  0.20  0.21
 0.145    5999  99.97   262.3   247.6  0.17  0.15     343   267.9   246.1  0.23  0.20
 0.241    7631 100.00   171.9   155.4  0.18  0.16     408   175.7   160.2  0.21  0.19
 0.338    8966 100.00    74.0    88.0  0.31  0.24     488    71.1    86.6  0.37  0.30
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0487   2579   0.923    962   0.825   3541   0.897  0.950  0.9652  0.9722  0.9064  0.9373
  0.1450   5033   0.869    966   0.769   5999   0.853  1.016  0.9421  0.9560  0.8816  0.9381
  0.2413   6669   0.880    962   0.774   7631   0.867  1.055  0.9540  0.9611  0.9051  0.9403
  0.3376   7995   0.794    977   0.719   8972   0.786  0.770  0.8966  0.9144  0.8157  0.8755
 $$
Resolution limits                    =     41.964     1.610
Number of used reflections           =      26143
Percentage observed                  =    99.9891
Percentage of free reflections       =     5.1002
Overall R factor                     =     0.1906
Free R factor                        =     0.2337
Average Fourier shell correlation    =     0.9454
AverageFree Fourier shell correlation=     0.9324
Overall weighted R factor            =     0.1669
Free weighted R factor               =     0.2063
Overall weighted R2 factor           =     0.1983
Free weighted R2 factor              =     0.2426
Average correlation coefficient      =     0.9171
Overall correlation coefficient      =     0.9583
Free correlation coefficient         =     0.9347
Cruickshanks DPI for coordinate error=     0.0976
DPI based on free R factor           =     0.1015
Overall figure of merit              =     0.8399
ML based su of positional parameters =     0.0634
ML based su of thermal parameters    =     1.8505
-----------------------------------------------------------------------------
  Time in seconds: CPU =        25.72
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1908   0.2341   0.797      132233.    7269.7   0.0133  0.994   1.867  1.087   0.091
       1   0.1910   0.2334   0.834      131112.    7229.5   0.0121  0.909   1.796  1.044   0.087
       2   0.1906   0.2335   0.840      130950.    7225.4   0.0130  0.976   1.832  1.065   0.089
       3   0.1906   0.2336   0.840      130935.    7226.0   0.0132  0.987   1.849  1.076   0.090
       4   0.1906   0.2336   0.840      130938.    7226.5   0.0132  0.987   1.850  1.077   0.090
       5   0.1906   0.2336   0.840      130940.    7226.7   0.0132  0.987   1.851  1.077   0.090
       6   0.1906   0.2336   0.840      130940.    7226.7   0.0132  0.987   1.851  1.077   0.090
       7   0.1906   0.2336   0.840      130940.    7226.8   0.0132  0.987   1.852  1.078   0.090
       8   0.1906   0.2337   0.840      130942.    7227.0   0.0132  0.987   1.852  1.078   0.090
       9   0.1906   0.2337   0.840      130943.    7227.0   0.0132  0.987   1.853  1.078   0.090
      10   0.1906   0.2337   0.840      130942.    7227.1   0.0132  0.987   1.853  1.078   0.090
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1908   0.1906
             R free    0.2341   0.2337
     Rms BondLength    0.0133   0.0132
      Rms BondAngle    1.8668   1.8531
     Rms ChirVolume    0.0911   0.0899
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      57.8s System:    0.1s Elapsed:     0:59