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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
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 User: maly  Run date: 26/ 5/2020 Run time: 19:09:35 


 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 5
  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_R05_1-60A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R05_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_R05_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:     5
  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_R05_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=   2.057 ideal_dist=   2.090
            ch:AAA  res:  86  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.196 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=   2.220 ideal_dist=   2.090
            ch:AAA  res: 140  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.381 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=   2.397 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=   2.093 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                            5
Number of "free" reflections       1655
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.= 0.896 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        :   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   0.28011268    
 Actual weight    6.2496691      is applied to the X-ray term
Norm of X_ray positional gradient                38.9
Norm of Geom. positional gradient                79.8
Norm of X_ray B-factor gradient                  108.
Norm of Geom. B-factor gradient                 0.224E+05
Product of X_ray and Geom posit. gradients     -0.138E+08
 Cosine of angle between them                      -0.458
Product of X_ray and Geom B-fact gradients     -0.344E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.9795E+06 GEOM=     0.2624E+05 TOTAL=     0.1006E+07
 function value    1005735.1    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.766     1.644
Bond angles  : others                          3242     2.343     1.582
Torsion angles, period  1. refined              184     6.960     5.000
Torsion angles, period  2. refined               90    35.870    22.778
Torsion angles, period  3. refined              268    13.485    15.000
Torsion angles, period  4. refined                9    13.119    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.014     0.020
VDW repulsions: refined_atoms                   311     0.263     0.200
VDW repulsions.others                          1361     0.228     0.200
VDW; torsion: refined_atoms                     722     0.173     0.200
VDW; torsion.others                             718     0.081     0.200
HBOND: refined_atoms                            218     0.196     0.200
HBOND.others                                      2     0.082     0.200
VDW repulsions: symmetry: refined_atoms           9     0.183     0.200
VDW repulsions: symmetry: others                 26     0.175     0.200
HBOND: symmetry: refined_atoms                   21     0.195     0.200
M. chain bond B values: refined atoms           745     1.675     1.510
M. chain bond B values: others                  745     1.670     1.510
M. chain angle B values: refined atoms          926     2.659     2.252
M. chain angle B values: others                 927     2.658     2.252
S. chain bond B values: refined atoms           811     3.004     1.902
S. chain bond B values: others                  810     3.001     1.902
S. chain angle B values: refined atoms         1177     4.647     2.689
S. chain angle B values: others                1178     4.645     2.689
Long range B values: refined atoms             1854     7.309    21.127
Long range B values: others                    1763     7.038    19.724
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0455, B  =    1.1397
Partial structure    1: scale =     0.3928, B  =   46.6210
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4318 100.00   408.4   417.7  0.17  0.18     229   375.2   387.2  0.21  0.21
 0.167    7413  99.97   228.8   208.5  0.18  0.16     385   223.4   206.7  0.22  0.19
 0.278    9435 100.00   124.4   114.4  0.21  0.19     475   118.8   110.7  0.25  0.22
 0.389   11076 100.00    50.2    62.5  0.41  0.36     565    51.1    64.3  0.41  0.36
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3214   0.916   1104   0.814   4318   0.890  0.948  0.9621  0.9709  0.9240  0.9344
  0.1670   6285   0.871   1128   0.770   7413   0.855  1.058  0.9431  0.9572  0.8800  0.9339
  0.2780   8309   0.835   1126   0.751   9435   0.825  1.019  0.9320  0.9447  0.8897  0.9291
  0.3890   9946   0.566   1142   0.493  11088   0.558  0.570  0.7707  0.7692  0.7717  0.7728
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32254
Percentage observed                  =    99.9912
Percentage of free reflections       =     4.8779
Overall R factor                     =     0.2084
Free R factor                        =     0.2453
Average Fourier shell correlation    =     0.8908
AverageFree Fourier shell correlation=     0.8836
Overall weighted R factor            =     0.1769
Free weighted R factor               =     0.2087
Overall weighted R2 factor           =     0.2059
Free weighted R2 factor              =     0.2366
Average correlation coefficient      =     0.8772
Overall correlation coefficient      =     0.9586
Free correlation coefficient         =     0.9428
Cruickshanks DPI for coordinate error=     0.0863
DPI based on free R factor           =     0.0893
Overall figure of merit              =     0.7489
ML based su of positional parameters =     0.0724
ML based su of thermal parameters    =     2.1250
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    156727.56       26239.711       1005735.1      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.35698384    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    982197.06    

-------------------------------------------------------------------------------
             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  =   -0.0431
Partial structure    1: scale =     0.3924, B  =   45.8285
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                     =     0.2078
Free R factor                        =     0.2452
Average Fourier shell correlation    =     0.9053
AverageFree Fourier shell correlation=     0.8976
Average correlation coefficient      =     0.8772
Overall figure of merit              =     0.7745
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    155603.67       9725.6436       982197.06       1005735.1    


     CGMAT cycle number =      3

 Weight matrix   0.36433095    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    980204.44    

-------------------------------------------------------------------------------
             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 =     0.0455, B  =   -0.0158
Partial structure    1: scale =     0.3920, B  =   41.6288
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                     =     0.2069
Free R factor                        =     0.2449
Average Fourier shell correlation    =     0.9076
AverageFree Fourier shell correlation=     0.8995
Average correlation coefficient      =     0.8794
Overall figure of merit              =     0.7767
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    155373.69       9170.2988       980204.44       982197.06    


     CGMAT cycle number =      4

 Weight matrix   0.33191502    
 Actual weight    5.6815171      is applied to the X-ray term


 function value    891496.31    

-------------------------------------------------------------------------------
             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 =     0.0455, B  =   -0.0003
Partial structure    1: scale =     0.3920, B  =   40.2613
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                     =     0.2067
Free R factor                        =     0.2447
Average Fourier shell correlation    =     0.9080
AverageFree Fourier shell correlation=     0.8997
Average correlation coefficient      =     0.8803
Overall figure of merit              =     0.7767
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    155327.95       8997.9043       891496.31       980204.44    


     CGMAT cycle number =      5

 Weight matrix   0.30157804    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    811190.69    

-------------------------------------------------------------------------------
             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 =     0.0455, B  =   -0.0002
Partial structure    1: scale =     0.3920, B  =   40.1079
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                     =     0.2069
Free R factor                        =     0.2445
Average Fourier shell correlation    =     0.9079
AverageFree Fourier shell correlation=     0.8997
Average correlation coefficient      =     0.8802
Overall figure of merit              =     0.7767
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    155366.05       8722.7080       811190.69       891496.31    


     CGMAT cycle number =      6

 Weight matrix   0.30105186    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    811186.81    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0455, B  =   -0.0001
Partial structure    1: scale =     0.3920, B  =   40.0956
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                     =     0.2073
Free R factor                        =     0.2445
Average Fourier shell correlation    =     0.9078
AverageFree Fourier shell correlation=     0.8995
Average correlation coefficient      =     0.8798
Overall figure of merit              =     0.7766
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    155425.59       8411.2305       811186.81       811190.69    


     CGMAT cycle number =      7

 Weight matrix   0.30044773    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    811251.31    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0455, B  =   -0.0004
Partial structure    1: scale =     0.3918, B  =   39.9453
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                        =     0.2445
Average Fourier shell correlation    =     0.9077
AverageFree Fourier shell correlation=     0.8995
Average correlation coefficient      =     0.8798
Overall figure of merit              =     0.7765
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    155453.92       8334.6895       811291.50       811186.81    

 fvalues    155453.92       8334.6895       811276.75       811256.56    
 fvalues    155453.92       8334.6895       811276.75       811256.56    


     CGMAT cycle number =      8

 Weight matrix   0.30032945    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    811257.94    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0455, B  =    0.0000
Partial structure    1: scale =     0.3918, B  =   39.9413
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                        =     0.2446
Average Fourier shell correlation    =     0.9077
AverageFree Fourier shell correlation=     0.8994
Average correlation coefficient      =     0.8798
Overall figure of merit              =     0.7765
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    155456.69       8322.5537       811258.63       811256.56    
 fvalues    155456.69       8322.5537       811258.63       811258.75    


     CGMAT cycle number =      9

 Weight matrix   0.30030465    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    811258.56    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0455, B  =    0.0006
Partial structure    1: scale =     0.3918, B  =   39.9279
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                        =     0.2446
Average Fourier shell correlation    =     0.9077
AverageFree Fourier shell correlation=     0.8994
Average correlation coefficient      =     0.8798
Overall figure of merit              =     0.7765
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    155458.97       8310.6113       811258.56       811258.75    


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

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   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   0.30031076    
 Actual weight    5.1650152      is applied to the X-ray term
Norm of X_ray positional gradient                38.2
Norm of Geom. positional gradient                38.3
Norm of X_ray B-factor gradient                  99.3
Norm of Geom. B-factor gradient                  99.7
Product of X_ray and Geom posit. gradients     -0.142E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.320E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.8030E+06 GEOM=      8299.     TOTAL=     0.8113E+06
 function value    811258.56    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.758     1.644
Bond angles  : others                          3242     1.493     1.582
Torsion angles, period  1. refined              184     6.945     5.000
Torsion angles, period  2. refined               90    35.510    22.778
Torsion angles, period  3. refined              268    13.128    15.000
Torsion angles, period  4. refined                9    13.242    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   303     0.266     0.200
VDW repulsions.others                          1367     0.202     0.200
VDW; torsion: refined_atoms                     718     0.174     0.200
VDW; torsion.others                             764     0.084     0.200
HBOND: refined_atoms                            215     0.197     0.200
HBOND.others                                      2     0.095     0.200
VDW repulsions: symmetry: refined_atoms           8     0.195     0.200
VDW repulsions: symmetry: others                 25     0.179     0.200
HBOND: symmetry: refined_atoms                   20     0.201     0.200
M. chain bond B values: refined atoms           745     1.719     1.620
M. chain bond B values: others                  745     1.715     1.620
M. chain angle B values: refined atoms          926     2.703     2.417
M. chain angle B values: others                 927     2.702     2.417
S. chain bond B values: refined atoms           811     3.085     2.022
S. chain bond B values: others                  810     3.082     2.022
S. chain angle B values: refined atoms         1177     4.768     2.866
S. chain angle B values: others                1178     4.766     2.865
Long range B values: refined atoms             1840     7.078    22.292
Long range B values: others                    1747     6.793    20.807
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0455, B  =    0.0000
Partial structure    1: scale =     0.3918, B  =   39.9279
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4318 100.00   408.8   418.2  0.17  0.18     229   375.5   388.5  0.21  0.21
 0.167    7413  99.97   229.0   208.7  0.18  0.16     385   223.6   207.1  0.22  0.19
 0.278    9435 100.00   124.5   114.7  0.21  0.18     475   118.9   111.0  0.25  0.22
 0.389   11076 100.00    50.3    62.5  0.41  0.36     565    51.1    64.3  0.41  0.37
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3214   0.927   1104   0.835   4318   0.904  0.949  0.9655  0.9737  0.9244  0.9350
  0.1670   6285   0.883   1128   0.783   7413   0.868  1.060  0.9465  0.9600  0.8810  0.9341
  0.2780   8309   0.858   1126   0.776   9435   0.848  1.024  0.9396  0.9522  0.8906  0.9298
  0.3890   9946   0.612   1142   0.545  11088   0.605  0.589  0.8068  0.8091  0.7719  0.7792
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32254
Percentage observed                  =    99.9912
Percentage of free reflections       =     4.8779
Overall R factor                     =     0.2074
Free R factor                        =     0.2446
Average Fourier shell correlation    =     0.9077
AverageFree Fourier shell correlation=     0.8994
Overall weighted R factor            =     0.1762
Free weighted R factor               =     0.2079
Overall weighted R2 factor           =     0.2051
Free weighted R2 factor              =     0.2364
Average correlation coefficient      =     0.8798
Overall correlation coefficient      =     0.9589
Free correlation coefficient         =     0.9432
Cruickshanks DPI for coordinate error=     0.0859
DPI based on free R factor           =     0.0890
Overall figure of merit              =     0.7765
ML based su of positional parameters =     0.0635
ML based su of thermal parameters    =     1.8353
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    155461.31       8298.5137       811258.56       811258.56    

    ****                              VDW outliers                              ****

VDW deviations from the ideal >10.000Sigma or dist <  1.000 will be monitored

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.913 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 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_R05_1-50A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.757     1.644
Bond angles  : others                          3242     1.492     1.582
Torsion angles, period  1. refined              184     6.945     5.000
Torsion angles, period  2. refined               90    35.482    22.778
Torsion angles, period  3. refined              268    13.110    15.000
Torsion angles, period  4. refined                9    13.234    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   303     0.266     0.200
VDW repulsions.others                          1370     0.201     0.200
VDW; torsion: refined_atoms                     719     0.173     0.200
VDW; torsion.others                             766     0.084     0.200
HBOND: refined_atoms                            215     0.197     0.200
HBOND.others                                      2     0.096     0.200
VDW repulsions: symmetry: refined_atoms           8     0.195     0.200
VDW repulsions: symmetry: others                 25     0.179     0.200
HBOND: symmetry: refined_atoms                   20     0.201     0.200
M. chain bond B values: refined atoms           745     1.718     1.620
M. chain bond B values: others                  745     1.713     1.620
M. chain angle B values: refined atoms          926     2.701     2.417
M. chain angle B values: others                 927     2.700     2.417
S. chain bond B values: refined atoms           811     3.083     2.022
S. chain bond B values: others                  810     3.080     2.022
S. chain angle B values: refined atoms         1177     4.766     2.866
S. chain angle B values: others                1178     4.763     2.865
Long range B values: refined atoms             1841     7.077    22.303
Long range B values: others                    1748     6.793    20.819
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0455, B  =    0.0032
Partial structure    1: scale =     0.3917, B  =   39.8929
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4318 100.00   408.8   418.2  0.17  0.18     229   375.5   388.6  0.21  0.21
 0.167    7413  99.97   229.0   208.7  0.18  0.16     385   223.6   207.1  0.22  0.19
 0.278    9435 100.00   124.5   114.7  0.21  0.18     475   118.9   111.0  0.25  0.22
 0.389   11076 100.00    50.3    62.4  0.41  0.36     565    51.1    64.3  0.41  0.36
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3214   0.927   1104   0.835   4318   0.903  0.949  0.9655  0.9737  0.9242  0.9350
  0.1670   6285   0.883   1128   0.783   7413   0.868  1.060  0.9464  0.9600  0.8810  0.9341
  0.2780   8309   0.858   1126   0.776   9435   0.848  1.024  0.9395  0.9521  0.8906  0.9298
  0.3890   9946   0.612   1142   0.545  11088   0.605  0.589  0.8068  0.8091  0.7719  0.7792
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32254
Percentage observed                  =    99.9912
Percentage of free reflections       =     4.8779
Overall R factor                     =     0.2074
Free R factor                        =     0.2447
Average Fourier shell correlation    =     0.9077
AverageFree Fourier shell correlation=     0.8994
Overall weighted R factor            =     0.1762
Free weighted R factor               =     0.2080
Overall weighted R2 factor           =     0.2052
Free weighted R2 factor              =     0.2368
Average correlation coefficient      =     0.8798
Overall correlation coefficient      =     0.9589
Free correlation coefficient         =     0.9431
Cruickshanks DPI for coordinate error=     0.0859
DPI based on free R factor           =     0.0890
Overall figure of merit              =     0.7764
ML based su of positional parameters =     0.0635
ML based su of thermal parameters    =     1.8353
-----------------------------------------------------------------------------
  Time in seconds: CPU =        23.37
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2084   0.2453   0.749      156728.    8187.1   0.0122  0.919   1.766  1.029   0.087
       1   0.2078   0.2452   0.774      155604.    8155.9   0.0121  0.912   1.745  1.016   0.087
       2   0.2069   0.2449   0.777      155374.    8151.5   0.0133  1.001   1.801  1.050   0.091
       3   0.2067   0.2447   0.777      155328.    8151.2   0.0134  1.011   1.824  1.064   0.092
       4   0.2069   0.2445   0.777      155366.    8151.7   0.0128  0.969   1.805  1.052   0.091
       5   0.2073   0.2445   0.777      155426.    8152.5   0.0122  0.925   1.772  1.032   0.089
       6   0.2074   0.2445   0.777      155453.    8153.7   0.0122  0.920   1.762  1.026   0.088
       7   0.2074   0.2446   0.776      155457.    8154.0   0.0122  0.920   1.761  1.026   0.088
       8   0.2074   0.2446   0.776      155459.    8154.1   0.0122  0.919   1.759  1.025   0.088
       9   0.2074   0.2446   0.777      155461.    8154.3   0.0122  0.918   1.758  1.024   0.088
      10   0.2074   0.2447   0.776      155465.    8154.6   0.0121  0.917   1.757  1.024   0.088
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2084   0.2074
             R free    0.2453   0.2447
     Rms BondLength    0.0122   0.0121
      Rms BondAngle    1.7660   1.7570
     Rms ChirVolume    0.0871   0.0882
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      55.4s System:    0.2s Elapsed:     0:55