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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: 20:08:12 


 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 1.50     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 17
  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_complete_R17_1-60A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R17_1-50A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R17_1-50A.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       0.1111
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.5000
  Estimated number of reflections :      43652
  Free R exclusion - flag equals:    17
  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  1.5000

  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_complete_R17_1-60A.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=   2.040 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=   2.209 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=   1.814 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=   2.217 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=   2.376 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=   2.381 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=   2.124 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:26-MAY-20
  --------------------------------
  ATTENTION: atom:OXT  THR               171  AAA  is missing in the structure
  ATTENTION: atom:OXT  PRO               190  AAA  is missing in the structure
  Number of chains                  :       4
  Total number of monomers          :     502
  Number of atoms                   :    3948
  Number of missing atoms           :       0
  Number of rebuilt atoms           :    1482
  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:      2950         0      2950
               Angles:      5345         0      5345
              Chirals:       196         0       196
               Planes:       451         0       451
             Torsions:      1553         0      1553
            Intervals:         0         0         0
--------------------------------------------------------------------------------


  Number of harmonic restraints       =            0
  Number of atoms in special position =            0
 -----------------------------------------------------


    ****                           Info from mtz file                           ****

FreeR flag                           17
Number of "free" reflections       1720
Number of   all  reflections      33910
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          33910

   Current auto weighting coefficient =    6.2496691    

 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.= 0.883 id.= 3.000 dev= -2.12 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        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Weight matrix   0.25502935    
 Actual weight    6.2496691      is applied to the X-ray term
Norm of X_ray positional gradient                36.2
Norm of Geom. positional gradient                81.7
Norm of X_ray B-factor gradient                  101.
Norm of Geom. B-factor gradient                 0.224E+05
Product of X_ray and Geom posit. gradients     -0.137E+08
 Cosine of angle between them                      -0.478
Product of X_ray and Geom B-fact gradients     -0.335E+08
 Cosine of angle between them                      -0.005


Residuals: XRAY=     0.9806E+06 GEOM=     0.2685E+05 TOTAL=     0.1007E+07
 function value    1007436.1    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.837     1.644
Bond angles  : others                          3242     2.355     1.582
Torsion angles, period  1. refined              184     6.856     5.000
Torsion angles, period  2. refined               90    36.185    22.778
Torsion angles, period  3. refined              268    13.662    15.000
Torsion angles, period  4. refined                9    11.681    15.000
Chiral centres: refined atoms                   196     0.089     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.017     0.020
VDW repulsions: refined_atoms                   309     0.265     0.200
VDW repulsions.others                          1362     0.231     0.200
VDW; torsion: refined_atoms                     731     0.173     0.200
VDW; torsion.others                             727     0.082     0.200
HBOND: refined_atoms                            218     0.201     0.200
HBOND.others                                      2     0.044     0.200
VDW repulsions: symmetry: refined_atoms           8     0.220     0.200
VDW repulsions: symmetry: others                 24     0.174     0.200
HBOND: symmetry: refined_atoms                   18     0.224     0.200
M. chain bond B values: refined atoms           745     1.749     1.508
M. chain bond B values: others                  745     1.747     1.508
M. chain angle B values: refined atoms          926     2.727     2.250
M. chain angle B values: others                 927     2.726     2.250
S. chain bond B values: refined atoms           811     3.161     1.911
S. chain bond B values: others                  810     3.155     1.911
S. chain angle B values: refined atoms         1177     4.829     2.700
S. chain angle B values: others                1178     4.827     2.699
Long range B values: refined atoms             1859     7.762    21.144
Long range B values: others                    1770     7.359    19.712
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    1.1639
Partial structure    1: scale =     0.3923, B  =   46.9912
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4328 100.00   405.5   415.3  0.17  0.18     219   423.8   424.9  0.19  0.20
 0.167    7418  99.97   227.8   207.5  0.18  0.16     380   239.3   215.6  0.21  0.19
 0.278    9399 100.00   124.3   114.2  0.21  0.19     511   120.4   112.7  0.26  0.23
 0.389   11031 100.00    50.2    62.5  0.41  0.36     610    50.8    64.9  0.43  0.38
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3214   0.905   1114   0.805   4328   0.879  0.947  0.9626  0.9683  0.9093  0.9357
  0.1670   6313   0.871   1105   0.772   7418   0.856  1.062  0.9514  0.9588  0.9021  0.9387
  0.2780   8287   0.823   1112   0.741   9399   0.813  1.013  0.9260  0.9418  0.8871  0.9257
  0.3890   9909   0.495   1134   0.430  11043   0.488  0.521  0.7435  0.7430  0.7419  0.7741
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32188
Percentage observed                  =    99.9912
Percentage of free reflections       =     5.0725
Overall R factor                     =     0.2079
Free R factor                        =     0.2392
Average Fourier shell correlation    =     0.8811
AverageFree Fourier shell correlation=     0.8715
Overall weighted R factor            =     0.1756
Free weighted R factor               =     0.2008
Overall weighted R2 factor           =     0.2034
Free weighted R2 factor              =     0.2289
Average correlation coefficient      =     0.8781
Overall correlation coefficient      =     0.9592
Free correlation coefficient         =     0.9453
Cruickshanks DPI for coordinate error=     0.0862
DPI based on free R factor           =     0.0872
Overall figure of merit              =     0.7204
ML based su of positional parameters =     0.0759
ML based su of thermal parameters    =     2.2425
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    156901.59       26853.020       1007436.1      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.30976903    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    983359.19    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0455, B  =   -0.0674
Partial structure    1: scale =     0.3927, B  =   46.3032
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2084
Free R factor                        =     0.2385
Average Fourier shell correlation    =     0.8977
AverageFree Fourier shell correlation=     0.8890
Average correlation coefficient      =     0.8780
Overall figure of merit              =     0.7520
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    155800.36       9658.5254       983359.19       1007436.1    


     CGMAT cycle number =      3

 Weight matrix   0.32053795    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    980672.94    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =   -0.0021
Partial structure    1: scale =     0.3929, B  =   42.0294
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2074
Free R factor                        =     0.2379
Average Fourier shell correlation    =     0.9025
AverageFree Fourier shell correlation=     0.8937
Average correlation coefficient      =     0.8798
Overall figure of merit              =     0.7610
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    155487.67       8926.4180       980672.94       983359.19    


     CGMAT cycle number =      4

 Weight matrix   0.32460758    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    979764.75    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    0.0049
Partial structure    1: scale =     0.3930, B  =   40.6262
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2072
Free R factor                        =     0.2376
Average Fourier shell correlation    =     0.9044
AverageFree Fourier shell correlation=     0.8955
Average correlation coefficient      =     0.8806
Overall figure of merit              =     0.7649
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    155382.91       8672.9941       979764.75       980672.94    


     CGMAT cycle number =      5

 Weight matrix   0.32667881    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    979460.75    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    0.0101
Partial structure    1: scale =     0.3931, B  =   40.5521
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2072
Free R factor                        =     0.2373
Average Fourier shell correlation    =     0.9053
AverageFree Fourier shell correlation=     0.8964
Average correlation coefficient      =     0.8810
Overall figure of merit              =     0.7668
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    155337.30       8654.0859       979460.75       979764.75    


     CGMAT cycle number =      6

 Weight matrix   0.32733750    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    979270.69    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    0.0133
Partial structure    1: scale =     0.3935, B  =   40.5041
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2071
Free R factor                        =     0.2371
Average Fourier shell correlation    =     0.9056
AverageFree Fourier shell correlation=     0.8966
Average correlation coefficient      =     0.8812
Overall figure of merit              =     0.7674
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    155304.53       8668.7471       979270.69       979460.75    


     CGMAT cycle number =      7

 Weight matrix   0.32834512    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    979205.06    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    0.0014
Partial structure    1: scale =     0.3935, B  =   40.5065
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2071
Free R factor                        =     0.2370
Average Fourier shell correlation    =     0.9058
AverageFree Fourier shell correlation=     0.8967
Average correlation coefficient      =     0.8812
Overall figure of merit              =     0.7677
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    155292.95       8675.5176       979205.06       979270.69    


     CGMAT cycle number =      8

 Weight matrix   0.32760698    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    979227.44    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    0.0167
Partial structure    1: scale =     0.3939, B  =   40.5456
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2071
Free R factor                        =     0.2368
Average Fourier shell correlation    =     0.9057
AverageFree Fourier shell correlation=     0.8966
Average correlation coefficient      =     0.8813
Overall figure of merit              =     0.7674
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    155296.16       8682.1465       979197.50       979205.06    
 fvalues    155296.16       8682.1465       979197.50       979231.69    


     CGMAT cycle number =      9

 Weight matrix   0.32780078    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    979193.88    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    0.0123
Partial structure    1: scale =     0.3940, B  =   40.5337
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2071
Free R factor                        =     0.2368
Average Fourier shell correlation    =     0.9057
AverageFree Fourier shell correlation=     0.8967
Average correlation coefficient      =     0.8813
Overall figure of merit              =     0.7675
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    155291.70       8672.1260       979193.88       979231.69    


     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.= 0.903 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        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Weight matrix   0.32738075    
 Actual weight    6.2496691      is applied to the X-ray term
Norm of X_ray positional gradient                41.0
Norm of Geom. positional gradient                41.0
Norm of X_ray B-factor gradient                  106.
Norm of Geom. B-factor gradient                  105.
Product of X_ray and Geom posit. gradients     -0.163E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.357E+08
 Cosine of angle between them                      -0.998


Residuals: XRAY=     0.9705E+06 GEOM=      8673.     TOTAL=     0.9792E+06
 function value    979217.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.813     1.644
Bond angles  : others                          3242     1.496     1.582
Torsion angles, period  1. refined              184     6.819     5.000
Torsion angles, period  2. refined               90    35.949    22.778
Torsion angles, period  3. refined              268    13.404    15.000
Torsion angles, period  4. refined                9    11.764    15.000
Chiral centres: refined atoms                   196     0.089     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   306     0.266     0.200
VDW repulsions.others                          1363     0.204     0.200
VDW; torsion: refined_atoms                     727     0.172     0.200
VDW; torsion.others                             799     0.084     0.200
HBOND: refined_atoms                            209     0.199     0.200
HBOND.others                                      1     0.063     0.200
VDW repulsions: symmetry: refined_atoms           8     0.213     0.200
VDW repulsions: symmetry: others                 24     0.160     0.200
HBOND: symmetry: refined_atoms                   18     0.251     0.200
M. chain bond B values: refined atoms           745     1.796     1.622
M. chain bond B values: others                  745     1.793     1.622
M. chain angle B values: refined atoms          926     2.766     2.421
M. chain angle B values: others                 927     2.765     2.421
S. chain bond B values: refined atoms           811     3.221     2.034
S. chain bond B values: others                  810     3.215     2.033
S. chain angle B values: refined atoms         1177     4.911     2.881
S. chain angle B values: others                1178     4.909     2.881
Long range B values: refined atoms             1842     7.750    22.448
Long range B values: others                    1754     7.415    20.957
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    0.0148
Partial structure    1: scale =     0.3932, B  =   40.4119
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4328 100.00   405.4   415.5  0.17  0.18     219   423.7   425.8  0.19  0.19
 0.167    7418  99.97   227.8   207.6  0.18  0.16     380   239.2   216.3  0.20  0.18
 0.278    9399 100.00   124.2   114.4  0.21  0.19     511   120.4   112.6  0.25  0.22
 0.389   11031 100.00    50.2    62.4  0.41  0.36     610    50.8    64.9  0.43  0.38
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3214   0.919   1114   0.828   4328   0.896  0.949  0.9663  0.9714  0.9094  0.9349
  0.1670   6313   0.886   1105   0.787   7418   0.871  1.062  0.9558  0.9626  0.9048  0.9389
  0.2780   8287   0.833   1112   0.750   9399   0.823  1.013  0.9308  0.9469  0.8888  0.9283
  0.3890   9909   0.607   1134   0.539  11043   0.600  0.581  0.8062  0.8065  0.7394  0.7816
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32188
Percentage observed                  =    99.9912
Percentage of free reflections       =     5.0725
Overall R factor                     =     0.2071
Free R factor                        =     0.2368
Average Fourier shell correlation    =     0.9057
AverageFree Fourier shell correlation=     0.8966
Overall weighted R factor            =     0.1754
Free weighted R factor               =     0.1986
Overall weighted R2 factor           =     0.2042
Free weighted R2 factor              =     0.2282
Average correlation coefficient      =     0.8813
Overall correlation coefficient      =     0.9592
Free correlation coefficient         =     0.9457
Cruickshanks DPI for coordinate error=     0.0859
DPI based on free R factor           =     0.0863
Overall figure of merit              =     0.7674
ML based su of positional parameters =     0.0669
ML based su of thermal parameters    =     1.9520
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    155291.77       8672.6250       979236.81       979193.88    

 fvalues    155291.77       8672.6250       979167.69       979194.75    
 fvalues    155291.77       8672.6250       979167.69       979194.75    

    ****                              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.= 0.904 id.= 3.000 dev= -2.10 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_complete_R17_1-50A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.813     1.644
Bond angles  : others                          3242     1.496     1.582
Torsion angles, period  1. refined              184     6.817     5.000
Torsion angles, period  2. refined               90    35.939    22.778
Torsion angles, period  3. refined              268    13.368    15.000
Torsion angles, period  4. refined                9    11.758    15.000
Chiral centres: refined atoms                   196     0.089     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   306     0.266     0.200
VDW repulsions.others                          1363     0.204     0.200
VDW; torsion: refined_atoms                     727     0.172     0.200
VDW; torsion.others                             801     0.084     0.200
HBOND: refined_atoms                            209     0.199     0.200
HBOND.others                                      1     0.063     0.200
VDW repulsions: symmetry: refined_atoms           8     0.213     0.200
VDW repulsions: symmetry: others                 24     0.160     0.200
HBOND: symmetry: refined_atoms                   18     0.254     0.200
M. chain bond B values: refined atoms           745     1.796     1.622
M. chain bond B values: others                  745     1.793     1.622
M. chain angle B values: refined atoms          926     2.766     2.421
M. chain angle B values: others                 927     2.764     2.421
S. chain bond B values: refined atoms           811     3.220     2.034
S. chain bond B values: others                  810     3.215     2.033
S. chain angle B values: refined atoms         1177     4.911     2.881
S. chain angle B values: others                1178     4.909     2.880
Long range B values: refined atoms             1842     7.747    22.446
Long range B values: others                    1754     7.411    20.956
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    0.0144
Partial structure    1: scale =     0.3931, B  =   40.3928
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4328 100.00   405.4   415.5  0.17  0.18     219   423.7   425.9  0.19  0.19
 0.167    7418  99.97   227.8   207.6  0.18  0.16     380   239.2   216.3  0.20  0.18
 0.278    9399 100.00   124.2   114.4  0.21  0.19     511   120.4   112.6  0.25  0.22
 0.389   11031 100.00    50.2    62.4  0.41  0.36     610    50.8    64.9  0.43  0.38
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3214   0.919   1114   0.828   4328   0.896  0.949  0.9662  0.9713  0.9093  0.9350
  0.1670   6313   0.886   1105   0.787   7418   0.871  1.062  0.9558  0.9626  0.9048  0.9389
  0.2780   8287   0.833   1112   0.750   9399   0.823  1.013  0.9308  0.9469  0.8888  0.9283
  0.3890   9909   0.607   1134   0.539  11043   0.600  0.581  0.8062  0.8066  0.7394  0.7816
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32188
Percentage observed                  =    99.9912
Percentage of free reflections       =     5.0725
Overall R factor                     =     0.2071
Free R factor                        =     0.2368
Average Fourier shell correlation    =     0.9057
AverageFree Fourier shell correlation=     0.8966
Overall weighted R factor            =     0.1754
Free weighted R factor               =     0.1986
Overall weighted R2 factor           =     0.2042
Free weighted R2 factor              =     0.2282
Average correlation coefficient      =     0.8813
Overall correlation coefficient      =     0.9592
Free correlation coefficient         =     0.9457
Cruickshanks DPI for coordinate error=     0.0859
DPI based on free R factor           =     0.0863
Overall figure of merit              =     0.7674
ML based su of positional parameters =     0.0669
ML based su of thermal parameters    =     1.9520
-----------------------------------------------------------------------------
  Time in seconds: CPU =        24.43
             Elapsed =         128.00

    ****           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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2079   0.2392   0.720      156902.    8551.5   0.0132  0.985   1.837  1.063   0.089
       1   0.2084   0.2385   0.752      155800.    8513.8   0.0120  0.897   1.762  1.021   0.087
       2   0.2074   0.2379   0.761      155488.    8503.2   0.0127  0.956   1.788  1.036   0.088
       3   0.2072   0.2376   0.765      155383.    8499.4   0.0128  0.962   1.799  1.043   0.088
       4   0.2072   0.2373   0.767      155337.    8497.4   0.0129  0.965   1.804  1.046   0.088
       5   0.2071   0.2371   0.767      155305.    8496.2   0.0129  0.967   1.807  1.048   0.089
       6   0.2071   0.2370   0.768      155293.    8496.1   0.0129  0.968   1.810  1.050   0.089
       7   0.2071   0.2368   0.767      155295.    8495.9   0.0129  0.969   1.812  1.051   0.089
       8   0.2071   0.2368   0.767      155292.    8496.0   0.0129  0.968   1.812  1.051   0.089
       9   0.2071   0.2368   0.767      155295.    8496.4   0.0129  0.968   1.813  1.051   0.089
      10   0.2071   0.2368   0.767      155294.    8496.6   0.0129  0.968   1.813  1.052   0.089
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2079   0.2071
             R free    0.2392   0.2368
     Rms BondLength    0.0132   0.0129
      Rms BondAngle    1.8374   1.8129
     Rms ChirVolume    0.0893   0.0890
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      56.5s System:    0.2s Elapsed:     0:57