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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: 20:22:53 


 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 1.42     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- bins 4
  Data line--- ncyc 10
  Data line--- monitor MEDIum
  Data line--- free 0
  Data line--- END

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN   Filename: CDO_R.mtz 

 LABIN FP=FP SIGFP=SIGFP FREE=FreeR_flag

    ****                     Input and Default parameters#                      ****


Input coordinate file.  Logical name - XYZIN actual file name  - CDO_complete_R00_1-50A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R00_1-42A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R00_1-42A.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       0.1240
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.4200
  Estimated number of reflections :      51186
  Free R exclusion - flag equals:     0
  Auto weighting. An attempt
  Refinement cycles       :    10
  Scaling type                           :
          Wilson scaling type with Guassians

  Estimation of D/Sigma in resolution bins
  using  free set of reflns with experimental sigmas
  using  free set of reflns with experimental sigmas

  Scaling and SigmaA resln:    41.9635  1.4200

  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_R00_1-50A.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=   2.197 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=   1.825 ideal_dist=   1.720
            ch:AAA  res:  93  CYS              at:SG  .->ch:AAA  res: 157  TYR              at:CE1 .
  INFO:     link is found (not be used) dist=   2.222 ideal_dist=   2.090
            ch:AAA  res: 140  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.413 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=   2.389 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=   2.104 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                            0
Number of "free" reflections       2004
Number of   all  reflections      39817
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          39817

   Current auto weighting coefficient =    6.0498405    

 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.= 0.890 id.= 3.000 dev= -2.11 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  288
 Maximuum H,K,L                 :    41   41   87
 Minimum acceptable grid spacing:    91   91  192
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  288
 Maximuum H,K,L                 :    41   41   87
 Minimum acceptable grid spacing:    91   91  192
 Weight matrix   0.24843861    
 Actual weight    6.0498405      is applied to the X-ray term
Norm of X_ray positional gradient                35.5
Norm of Geom. positional gradient                82.7
Norm of X_ray B-factor gradient                  91.0
Norm of Geom. B-factor gradient                 0.238E+05
Product of X_ray and Geom posit. gradients     -0.143E+08
 Cosine of angle between them                      -0.504
Product of X_ray and Geom B-fact gradients     -0.292E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.1067E+07 GEOM=     0.2757E+05 TOTAL=     0.1095E+07
 function value    1094679.4    

-------------------------------------------------------------------------------
             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     1.862     1.644
Bond angles  : others                          3242     2.365     1.582
Torsion angles, period  1. refined              184     6.802     5.000
Torsion angles, period  2. refined               90    35.339    22.778
Torsion angles, period  3. refined              268    13.169    15.000
Torsion angles, period  4. refined                9    12.245    15.000
Chiral centres: refined atoms                   196     0.092     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.018     0.020
VDW repulsions: refined_atoms                   301     0.268     0.200
VDW repulsions.others                          1343     0.228     0.200
VDW; torsion: refined_atoms                     723     0.174     0.200
VDW; torsion.others                             722     0.082     0.200
HBOND: refined_atoms                            202     0.196     0.200
HBOND.others                                      1     0.007     0.200
VDW repulsions: symmetry: refined_atoms           8     0.199     0.200
VDW repulsions: symmetry: others                 21     0.210     0.200
HBOND: symmetry: refined_atoms                   21     0.169     0.200
M. chain bond B values: refined atoms           745     1.804     1.614
M. chain bond B values: others                  745     1.799     1.614
M. chain angle B values: refined atoms          926     2.783     2.408
M. chain angle B values: others                 927     2.782     2.408
S. chain bond B values: refined atoms           811     3.227     2.029
S. chain bond B values: others                  810     3.222     2.029
S. chain angle B values: refined atoms         1177     4.904     2.872
S. chain angle B values: others                1178     4.902     2.872
Long range B values: refined atoms             1830     7.017    21.937
Long range B values: others                    1745     6.792    20.526
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =    0.8026
Partial structure    1: scale =     0.3927, B  =   44.4436
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5089 100.00   380.6   390.2  0.18  0.18     240   375.6   378.3  0.22  0.22
 0.186    8652  99.98   205.7   181.7  0.19  0.17     491   214.3   189.6  0.23  0.20
 0.310   11047 100.00    92.0    88.6  0.23  0.20     600    92.2    89.1  0.27  0.24
 0.434   12831  98.63    38.7    48.0  0.47  0.46     664    39.1    49.0  0.47  0.46
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3846   0.894   1243   0.781   5089   0.866  0.946  0.9551  0.9650  0.9003  0.9352
  0.1863   7407   0.860   1245   0.759   8652   0.846  1.094  0.9463  0.9547  0.9004  0.9357
  0.3102   9814   0.800   1233   0.720  11047   0.791  0.950  0.9242  0.9316  0.8859  0.9141
  0.4340  11579   0.427   1252   0.378  12831   0.423  0.404  0.6571  0.6350  0.6784  0.6433
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37619
Percentage observed                  =    99.4927
Percentage of free reflections       =     5.0361
Overall R factor                     =     0.2190
Free R factor                        =     0.2547
Average Fourier shell correlation    =     0.8403
AverageFree Fourier shell correlation=     0.8444
Overall weighted R factor            =     0.1834
Free weighted R factor               =     0.2182
Overall weighted R2 factor           =     0.2123
Free weighted R2 factor              =     0.2520
Average correlation coefficient      =     0.8296
Overall correlation coefficient      =     0.9598
Free correlation coefficient         =     0.9413
Cruickshanks DPI for coordinate error=     0.0780
DPI based on free R factor           =     0.0814
Overall figure of merit              =     0.6880
ML based su of positional parameters =     0.0757
ML based su of thermal parameters    =     2.1585
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    176385.72       27573.814       1094679.4      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.31481078    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1070420.0    

-------------------------------------------------------------------------------
             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 =     0.0465, B  =   -0.0592
Partial structure    1: scale =     0.3927, B  =   43.6336
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2197
Free R factor                        =     0.2537
Average Fourier shell correlation    =     0.8526
AverageFree Fourier shell correlation=     0.8564
Average correlation coefficient      =     0.8282
Overall figure of merit              =     0.7095
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    175283.97       9979.9805       1070420.0       1094679.4    


     CGMAT cycle number =      3

 Weight matrix   0.32123801    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1068247.9    

-------------------------------------------------------------------------------
             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 =     0.0465, B  =   -0.0078
Partial structure    1: scale =     0.3928, B  =   39.9732
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2188
Free R factor                        =     0.2538
Average Fourier shell correlation    =     0.8560
AverageFree Fourier shell correlation=     0.8592
Average correlation coefficient      =     0.8293
Overall figure of merit              =     0.7131
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    175075.05       9071.7705       1068247.9       1070420.0    


     CGMAT cycle number =      4

 Weight matrix   0.32238758    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1067577.4    

-------------------------------------------------------------------------------
             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 =     0.0465, B  =    0.0020
Partial structure    1: scale =     0.3931, B  =   37.1123
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2187
Free R factor                        =     0.2538
Average Fourier shell correlation    =     0.8568
AverageFree Fourier shell correlation=     0.8598
Average correlation coefficient      =     0.8298
Overall figure of merit              =     0.7141
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    175025.91       8698.6289       1067577.4       1068247.9    


     CGMAT cycle number =      5

 Weight matrix   0.32234290    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1067414.1    

-------------------------------------------------------------------------------
             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 =     0.0466, B  =    0.0086
Partial structure    1: scale =     0.3933, B  =   37.0715
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2186
Free R factor                        =     0.2537
Average Fourier shell correlation    =     0.8569
AverageFree Fourier shell correlation=     0.8599
Average correlation coefficient      =     0.8300
Overall figure of merit              =     0.7142
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    175008.94       8637.9746       1067414.1       1067577.4    


     CGMAT cycle number =      6

 Weight matrix   0.32246503    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1067388.0    

-------------------------------------------------------------------------------
             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 =     0.0466, B  =    0.0064
Partial structure    1: scale =     0.3934, B  =   37.0141
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2185
Free R factor                        =     0.2537
Average Fourier shell correlation    =     0.8569
AverageFree Fourier shell correlation=     0.8599
Average correlation coefficient      =     0.8300
Overall figure of merit              =     0.7143
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    175004.02       8641.5996       1067388.0       1067414.1    


     CGMAT cycle number =      7

 Weight matrix   0.32260427    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1067393.5    

-------------------------------------------------------------------------------
             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 =     0.0466, B  =    0.0067
Partial structure    1: scale =     0.3934, B  =   36.9434
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2185
Free R factor                        =     0.2537
Average Fourier shell correlation    =     0.8569
AverageFree Fourier shell correlation=     0.8599
Average correlation coefficient      =     0.8300
Overall figure of merit              =     0.7142
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    175004.31       8641.0127       1067425.6       1067388.0    

 fvalues    175004.31       8641.0127       1067425.3       1067389.1    
 fvalues    175004.31       8641.0127       1067425.3       1067389.1    


     CGMAT cycle number =      8

 Weight matrix   0.32228771    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1067424.4    

-------------------------------------------------------------------------------
             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 =     0.0466, B  =    0.0075
Partial structure    1: scale =     0.3935, B  =   37.0118
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2185
Free R factor                        =     0.2538
Average Fourier shell correlation    =     0.8569
AverageFree Fourier shell correlation=     0.8598
Average correlation coefficient      =     0.8300
Overall figure of merit              =     0.7142
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    175011.97       8638.4844       1067412.0       1067389.1    
 fvalues    175011.97       8638.4844       1067412.0       1067433.0    


     CGMAT cycle number =      9

 Weight matrix   0.32220343    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1067442.0    

-------------------------------------------------------------------------------
             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 =     0.0465, B  =    0.0081
Partial structure    1: scale =     0.3936, B  =   36.9675
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2185
Free R factor                        =     0.2537
Average Fourier shell correlation    =     0.8569
AverageFree Fourier shell correlation=     0.8598
Average correlation coefficient      =     0.8300
Overall figure of merit              =     0.7141
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02

 fvalues    175011.55       8637.5625       1067429.5       1067433.0    


     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.= 0.911 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  288
 Maximuum H,K,L                 :    41   41   87
 Minimum acceptable grid spacing:    91   91  192
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  288
 Maximuum H,K,L                 :    41   41   87
 Minimum acceptable grid spacing:    91   91  192
 Weight matrix   0.32246411    
 Actual weight    6.0498405      is applied to the X-ray term
Norm of X_ray positional gradient                42.9
Norm of Geom. positional gradient                42.9
Norm of X_ray B-factor gradient                  102.
Norm of Geom. B-factor gradient                  102.
Product of X_ray and Geom posit. gradients     -0.178E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.336E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.1059E+07 GEOM=      8637.     TOTAL=     0.1067E+07
 function value    1067423.9    

-------------------------------------------------------------------------------
             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     1.848     1.644
Bond angles  : others                          3242     1.509     1.582
Torsion angles, period  1. refined              184     6.790     5.000
Torsion angles, period  2. refined               90    35.238    22.778
Torsion angles, period  3. refined              268    13.159    15.000
Torsion angles, period  4. refined                9    12.222    15.000
Chiral centres: refined atoms                   196     0.092     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   302     0.267     0.200
VDW repulsions.others                          1362     0.202     0.200
VDW; torsion: refined_atoms                     720     0.174     0.200
VDW; torsion.others                             765     0.085     0.200
HBOND: refined_atoms                            201     0.195     0.200
HBOND.others                                      1     0.008     0.200
VDW repulsions: symmetry: refined_atoms           8     0.195     0.200
VDW repulsions: symmetry: others                 21     0.193     0.200
HBOND: symmetry: refined_atoms                   19     0.168     0.200
M. chain bond B values: refined atoms           745     1.840     1.692
M. chain bond B values: others                  745     1.835     1.692
M. chain angle B values: refined atoms          926     2.820     2.526
M. chain angle B values: others                 927     2.818     2.525
S. chain bond B values: refined atoms           811     3.272     2.112
S. chain bond B values: others                  810     3.267     2.112
S. chain angle B values: refined atoms         1177     4.968     2.995
S. chain angle B values: others                1178     4.966     2.994
Long range B values: refined atoms             1827     7.154    22.879
Long range B values: others                    1743     6.909    21.455
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =    0.0069
Partial structure    1: scale =     0.3936, B  =   36.9351
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5089 100.00   380.9   390.4  0.18  0.18     240   376.0   379.1  0.22  0.22
 0.186    8652  99.98   205.9   182.0  0.19  0.17     491   214.5   189.9  0.23  0.20
 0.310   11047 100.00    92.1    88.8  0.23  0.20     600    92.3    89.4  0.27  0.24
 0.434   12831  98.63    38.8    48.0  0.47  0.46     664    39.2    49.0  0.47  0.46
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3846   0.910   1243   0.806   5089   0.885  0.949  0.9602  0.9695  0.9006  0.9352
  0.1863   7407   0.881   1245   0.781   8652   0.867  1.096  0.9512  0.9599  0.9014  0.9361
  0.3102   9814   0.829   1233   0.752  11047   0.820  0.959  0.9337  0.9411  0.8873  0.9149
  0.4340  11579   0.457   1252   0.410  12831   0.452  0.418  0.6893  0.6704  0.6790  0.6438
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37619
Percentage observed                  =    99.4927
Percentage of free reflections       =     5.0361
Overall R factor                     =     0.2185
Free R factor                        =     0.2536
Average Fourier shell correlation    =     0.8569
AverageFree Fourier shell correlation=     0.8599
Overall weighted R factor            =     0.1831
Free weighted R factor               =     0.2174
Overall weighted R2 factor           =     0.2119
Free weighted R2 factor              =     0.2516
Average correlation coefficient      =     0.8300
Overall correlation coefficient      =     0.9599
Free correlation coefficient         =     0.9418
Cruickshanks DPI for coordinate error=     0.0779
DPI based on free R factor           =     0.0811
Overall figure of merit              =     0.7142
ML based su of positional parameters =     0.0663
ML based su of thermal parameters    =     1.8889
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    175010.78       8636.5732       1067423.9       1067429.5    

    ****                              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.= 0.911 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
          28          24          36  0.70425701      2.37302221E-02  0.70425248    
          36           8          36  0.70425701      2.37302221E-02  0.70425248    

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R00_1-42A.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     1.848     1.644
Bond angles  : others                          3242     1.509     1.582
Torsion angles, period  1. refined              184     6.789     5.000
Torsion angles, period  2. refined               90    35.229    22.778
Torsion angles, period  3. refined              268    13.160    15.000
Torsion angles, period  4. refined                9    12.222    15.000
Chiral centres: refined atoms                   196     0.092     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   302     0.267     0.200
VDW repulsions.others                          1365     0.202     0.200
VDW; torsion: refined_atoms                     720     0.174     0.200
VDW; torsion.others                             768     0.085     0.200
HBOND: refined_atoms                            201     0.195     0.200
HBOND.others                                      1     0.008     0.200
VDW repulsions: symmetry: refined_atoms           8     0.195     0.200
VDW repulsions: symmetry: others                 21     0.193     0.200
HBOND: symmetry: refined_atoms                   19     0.168     0.200
M. chain bond B values: refined atoms           745     1.840     1.692
M. chain bond B values: others                  745     1.835     1.692
M. chain angle B values: refined atoms          926     2.820     2.526
M. chain angle B values: others                 927     2.819     2.525
S. chain bond B values: refined atoms           811     3.273     2.112
S. chain bond B values: others                  810     3.268     2.112
S. chain angle B values: refined atoms         1177     4.970     2.995
S. chain angle B values: others                1178     4.968     2.995
Long range B values: refined atoms             1827     7.157    22.880
Long range B values: others                    1743     6.912    21.456
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =    0.0001
Partial structure    1: scale =     0.3936, B  =   36.9349
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5089 100.00   380.9   390.4  0.18  0.18     240   376.0   379.2  0.22  0.22
 0.186    8652  99.98   205.9   182.1  0.19  0.17     491   214.5   190.0  0.23  0.20
 0.310   11047 100.00    92.1    88.8  0.23  0.20     600    92.3    89.5  0.27  0.24
 0.434   12831  98.63    38.8    48.1  0.47  0.46     664    39.2    49.0  0.47  0.46
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3846   0.910   1243   0.806   5089   0.885  0.949  0.9602  0.9695  0.9006  0.9352
  0.1863   7407   0.882   1245   0.781   8652   0.867  1.096  0.9513  0.9600  0.9014  0.9361
  0.3102   9814   0.829   1233   0.752  11047   0.820  0.959  0.9338  0.9411  0.8873  0.9148
  0.4340  11579   0.457   1252   0.410  12831   0.453  0.418  0.6895  0.6705  0.6789  0.6438
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37619
Percentage observed                  =    99.4927
Percentage of free reflections       =     5.0361
Overall R factor                     =     0.2185
Free R factor                        =     0.2537
Average Fourier shell correlation    =     0.8570
AverageFree Fourier shell correlation=     0.8599
Overall weighted R factor            =     0.1831
Free weighted R factor               =     0.2174
Overall weighted R2 factor           =     0.2118
Free weighted R2 factor              =     0.2516
Average correlation coefficient      =     0.8300
Overall correlation coefficient      =     0.9599
Free correlation coefficient         =     0.9418
Cruickshanks DPI for coordinate error=     0.0779
DPI based on free R factor           =     0.0811
Overall figure of merit              =     0.7143
ML based su of positional parameters =     0.0663
ML based su of thermal parameters    =     1.8889
-----------------------------------------------------------------------------
  Time in seconds: CPU =        27.62
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2190   0.2547   0.688      176386.    9519.2   0.0131  0.986   1.862  1.080   0.092
       1   0.2197   0.2537   0.710      175284.    9487.5   0.0117  0.884   1.780  1.032   0.088
       2   0.2188   0.2538   0.713      175075.    9483.9   0.0128  0.970   1.825  1.059   0.091
       3   0.2187   0.2538   0.714      175026.    9482.4   0.0129  0.974   1.838  1.067   0.091
       4   0.2186   0.2537   0.714      175009.    9482.0   0.0129  0.977   1.843  1.070   0.091
       5   0.2185   0.2537   0.714      175004.    9482.1   0.0129  0.977   1.846  1.072   0.092
       6   0.2185   0.2537   0.714      175005.    9482.3   0.0129  0.977   1.847  1.072   0.092
       7   0.2185   0.2538   0.714      175011.    9482.8   0.0129  0.977   1.848  1.072   0.092
       8   0.2185   0.2537   0.714      175014.    9482.9   0.0129  0.977   1.848  1.073   0.092
       9   0.2185   0.2536   0.714      175011.    9482.7   0.0129  0.977   1.848  1.073   0.092
      10   0.2185   0.2537   0.714      175008.    9482.7   0.0129  0.977   1.848  1.073   0.092
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2190   0.2185
             R free    0.2547   0.2537
     Rms BondLength    0.0131   0.0129
      Rms BondAngle    1.8621   1.8481
     Rms ChirVolume    0.0919   0.0917
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      59.8s System:    0.2s Elapsed:     1:00