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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 26/ 5/2020 Run time: 20:55:57 


 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 6
  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_R06_1-50A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R06_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_R06_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:     6
  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_R06_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=   2.055 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=   2.188 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=   1.823 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=   2.201 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=   2.363 ideal_dist=   1.945
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:N   .
  INFO:     link is found (not be used) dist=   2.394 ideal_dist=   2.235
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:SG  .
  INFO:     link is found (not be used) dist=   2.094 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                            6
Number of "free" reflections       2017
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.= 0.888 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   0.23983599    
 Actual weight    6.0498405      is applied to the X-ray term
Norm of X_ray positional gradient                37.3
Norm of Geom. positional gradient                80.2
Norm of X_ray B-factor gradient                  99.3
Norm of Geom. B-factor gradient                 0.234E+05
Product of X_ray and Geom posit. gradients     -0.134E+08
 Cosine of angle between them                      -0.464
Product of X_ray and Geom B-fact gradients     -0.305E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.1067E+07 GEOM=     0.2660E+05 TOTAL=     0.1094E+07
 function value    1093503.8    

-------------------------------------------------------------------------------
             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     1.764     1.644
Bond angles  : others                          3242     2.346     1.582
Torsion angles, period  1. refined              184     6.870     5.000
Torsion angles, period  2. refined               90    35.073    22.778
Torsion angles, period  3. refined              268    12.730    15.000
Torsion angles, period  4. refined                9    11.299    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.015     0.020
VDW repulsions: refined_atoms                   301     0.264     0.200
VDW repulsions.others                          1344     0.231     0.200
VDW; torsion: refined_atoms                     722     0.173     0.200
VDW; torsion.others                             713     0.081     0.200
HBOND: refined_atoms                            234     0.181     0.200
HBOND.others                                      2     0.060     0.200
VDW repulsions: symmetry: refined_atoms           8     0.192     0.200
VDW repulsions: symmetry: others                 26     0.178     0.200
HBOND: symmetry: refined_atoms                   19     0.172     0.200
M. chain bond B values: refined atoms           745     1.714     1.613
M. chain bond B values: others                  745     1.711     1.613
M. chain angle B values: refined atoms          926     2.640     2.407
M. chain angle B values: others                 927     2.639     2.407
S. chain bond B values: refined atoms           811     2.950     2.001
S. chain bond B values: others                  810     2.945     2.000
S. chain angle B values: refined atoms         1177     4.517     2.844
S. chain angle B values: others                1178     4.515     2.843
Long range B values: refined atoms             1860     7.034    22.333
Long range B values: others                    1763     6.719    20.736
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =    0.7950
Partial structure    1: scale =     0.3951, B  =   45.6139
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5045 100.00   379.1   388.9  0.18  0.19     284   390.0   408.8  0.22  0.23
 0.186    8678  99.98   205.8   182.2  0.19  0.17     465   205.3   178.2  0.22  0.20
 0.310   11070 100.00    92.1    88.8  0.23  0.20     577    87.5    84.7  0.27  0.24
 0.434   12817  98.63    38.7    47.9  0.47  0.46     678    38.5    48.4  0.48  0.47
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3812   0.883   1233   0.771   5045   0.856  0.938  0.9537  0.9596  0.8980  0.9303
  0.1863   7439   0.865   1239   0.764   8678   0.851  1.095  0.9501  0.9572  0.9091  0.9380
  0.3102   9817   0.805   1253   0.723  11070   0.796  0.949  0.9129  0.9334  0.8547  0.9147
  0.4340  11574   0.332   1243   0.292  12817   0.328  0.322  0.5895  0.5955  0.6030  0.6493
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37610
Percentage observed                  =    99.4927
Percentage of free reflections       =     5.0588
Overall R factor                     =     0.2201
Free R factor                        =     0.2529
Average Fourier shell correlation    =     0.8272
AverageFree Fourier shell correlation=     0.8179
Overall weighted R factor            =     0.1856
Free weighted R factor               =     0.2263
Overall weighted R2 factor           =     0.2169
Free weighted R2 factor              =     0.2743
Average correlation coefficient      =     0.8317
Overall correlation coefficient      =     0.9585
Free correlation coefficient         =     0.9434
Cruickshanks DPI for coordinate error=     0.0785
DPI based on free R factor           =     0.0809
Overall figure of merit              =     0.6570
ML based su of positional parameters =     0.0770
ML based su of thermal parameters    =     2.2166
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    176351.88       26602.947       1093503.8      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.31622535    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1069144.1    

-------------------------------------------------------------------------------
             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 =     0.0467, B  =   -0.0251
Partial structure    1: scale =     0.3950, B  =   45.3984
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                     =     0.2203
Free R factor                        =     0.2529
Average Fourier shell correlation    =     0.8457
AverageFree Fourier shell correlation=     0.8386
Average correlation coefficient      =     0.8304
Overall figure of merit              =     0.6861
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    175097.30       9833.4053       1069144.1       1093503.8    


     CGMAT cycle number =      3

 Weight matrix   0.32230878    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1067061.1    

-------------------------------------------------------------------------------
             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 =     0.0467, B  =   -0.0195
Partial structure    1: scale =     0.3952, B  =   42.0565
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                     =     0.2193
Free R factor                        =     0.2529
Average Fourier shell correlation    =     0.8470
AverageFree Fourier shell correlation=     0.8394
Average correlation coefficient      =     0.8320
Overall figure of merit              =     0.6871
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    174887.14       9021.9004       1067061.1       1069144.1    


     CGMAT cycle number =      4

 Weight matrix   0.32579622    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1066157.5    

-------------------------------------------------------------------------------
             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 =     0.0467, B  =   -0.0127
Partial structure    1: scale =     0.3947, B  =   38.7499
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                     =     0.2191
Free R factor                        =     0.2529
Average Fourier shell correlation    =     0.8503
AverageFree Fourier shell correlation=     0.8428
Average correlation coefficient      =     0.8326
Overall figure of merit              =     0.6915
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    174789.92       8706.4375       1066157.5       1067061.1    


     CGMAT cycle number =      5

 Weight matrix   0.32370433    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1066295.8    

-------------------------------------------------------------------------------
             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 =     0.0467, B  =   -0.0068
Partial structure    1: scale =     0.3949, B  =   38.7088
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                     =     0.2190
Free R factor                        =     0.2529
Average Fourier shell correlation    =     0.8482
AverageFree Fourier shell correlation=     0.8404
Average correlation coefficient      =     0.8328
Overall figure of merit              =     0.6886
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03

 fvalues    174790.69       8666.4160       1066122.1       1066157.5    


     CGMAT cycle number =      6

 Weight matrix   0.32322869    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1066320.4    

-------------------------------------------------------------------------------
             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 =     0.0467, B  =   -0.0001
Partial structure    1: scale =     0.3949, B  =   38.7083
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                     =     0.2190
Free R factor                        =     0.2529
Average Fourier shell correlation    =     0.8480
AverageFree Fourier shell correlation=     0.8401
Average correlation coefficient      =     0.8329
Overall figure of merit              =     0.6882
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03

 fvalues    174768.64       8678.7520       1066001.1       1066122.1    


     CGMAT cycle number =      7

 Weight matrix   0.32452050    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1066232.9    

-------------------------------------------------------------------------------
             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 =     0.0467, B  =   -0.0048
Partial structure    1: scale =     0.3949, B  =   38.7186
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                     =     0.2190
Free R factor                        =     0.2528
Average Fourier shell correlation    =     0.8489
AverageFree Fourier shell correlation=     0.8412
Average correlation coefficient      =     0.8329
Overall figure of merit              =     0.6896
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    174843.67       8683.3682       1066086.0       1066001.1    
 fvalues    174843.67       8683.3682       1066086.0       1066459.8    


     CGMAT cycle number =      8

 Weight matrix   0.32618684    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1066122.6    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =   -0.0063
Partial structure    1: scale =     0.3950, B  =   38.7624
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                     =     0.2190
Free R factor                        =     0.2528
Average Fourier shell correlation    =     0.8503
AverageFree Fourier shell correlation=     0.8428
Average correlation coefficient      =     0.8328
Overall figure of merit              =     0.6914
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    174786.58       8691.7607       1066122.6       1066459.8    


     CGMAT cycle number =      9

 Weight matrix   0.32400629    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1066374.1    

-------------------------------------------------------------------------------
             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  =   -0.0002
Partial structure    1: scale =     0.3950, B  =   38.7628
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                     =     0.2190
Free R factor                        =     0.2527
Average Fourier shell correlation    =     0.8482
AverageFree Fourier shell correlation=     0.8405
Average correlation coefficient      =     0.8329
Overall figure of merit              =     0.6886
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    174799.27       8688.5479       1066391.0       1066122.6    

 fvalues    174799.27       8688.5479       1066394.1       1066196.1    
 fvalues    174799.27       8688.5479       1066394.1       1066196.1    


     CGMAT cycle number =     10

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.903 id.= 3.000 dev= -2.10 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  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   0.32395735    
 Actual weight    6.0498405      is applied to the X-ray term
Norm of X_ray positional gradient                43.7
Norm of Geom. positional gradient                43.7
Norm of X_ray B-factor gradient                  105.
Norm of Geom. B-factor gradient                  105.
Product of X_ray and Geom posit. gradients     -0.185E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.354E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.1058E+07 GEOM=      8689.     TOTAL=     0.1066E+07
 function value    1066403.1    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2103     1.842     1.644
Bond angles  : others                          3242     1.515     1.582
Torsion angles, period  1. refined              184     6.894     5.000
Torsion angles, period  2. refined               90    35.108    22.778
Torsion angles, period  3. refined              268    12.683    15.000
Torsion angles, period  4. refined                9    11.215    15.000
Chiral centres: refined atoms                   196     0.093     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   310     0.264     0.200
VDW repulsions.others                          1366     0.205     0.200
VDW; torsion: refined_atoms                     722     0.174     0.200
VDW; torsion.others                             788     0.084     0.200
HBOND: refined_atoms                            223     0.188     0.200
HBOND.others                                      2     0.034     0.200
VDW repulsions: symmetry: refined_atoms           8     0.194     0.200
VDW repulsions: symmetry: others                 30     0.157     0.200
HBOND: symmetry: refined_atoms                   18     0.177     0.200
M. chain bond B values: refined atoms           745     1.848     1.686
M. chain bond B values: others                  745     1.844     1.686
M. chain angle B values: refined atoms          926     2.781     2.516
M. chain angle B values: others                 927     2.779     2.516
S. chain bond B values: refined atoms           811     3.194     2.094
S. chain bond B values: others                  810     3.189     2.094
S. chain angle B values: refined atoms         1177     4.847     2.976
S. chain angle B values: others                1178     4.845     2.975
Long range B values: refined atoms             1855     7.301    23.404
Long range B values: others                    1763     7.020    21.859
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =   -0.0020
Partial structure    1: scale =     0.3950, B  =   38.7599
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5045 100.00   379.4   389.1  0.18  0.19     284   390.2   408.6  0.22  0.23
 0.186    8678  99.98   205.9   182.4  0.19  0.17     465   205.4   178.6  0.22  0.20
 0.310   11070 100.00    92.1    89.0  0.23  0.20     577    87.5    84.9  0.27  0.24
 0.434   12817  98.63    38.7    48.0  0.47  0.46     678    38.6    48.3  0.48  0.47
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3812   0.904   1233   0.805   5045   0.879  0.943  0.9598  0.9664  0.8983  0.9312
  0.1863   7439   0.889   1239   0.787   8678   0.874  1.099  0.9558  0.9629  0.9082  0.9387
  0.3102   9817   0.831   1253   0.753  11070   0.822  0.958  0.9229  0.9421  0.8570  0.9165
  0.4340  11574   0.376   1243   0.339  12817   0.372  0.352  0.6410  0.6427  0.6031  0.6503
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37610
Percentage observed                  =    99.4927
Percentage of free reflections       =     5.0588
Overall R factor                     =     0.2190
Free R factor                        =     0.2527
Average Fourier shell correlation    =     0.8481
AverageFree Fourier shell correlation=     0.8404
Overall weighted R factor            =     0.1846
Free weighted R factor               =     0.2263
Overall weighted R2 factor           =     0.2158
Free weighted R2 factor              =     0.2744
Average correlation coefficient      =     0.8329
Overall correlation coefficient      =     0.9590
Free correlation coefficient         =     0.9435
Cruickshanks DPI for coordinate error=     0.0781
DPI based on free R factor           =     0.0808
Overall figure of merit              =     0.6885
ML based su of positional parameters =     0.0662
ML based su of thermal parameters    =     1.8900
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02

 fvalues    174787.16       8689.0166       1066123.4       1066196.1    

    ****                              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.= 0.903 id.= 3.000 dev= -2.10 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 LABOUT FreeR_flag=FreeR_flag FP=FP SIGFP=SIGFP FC=FC PHIC=PHIC FC_ALL=FC_ALL PHIC_ALL=PHIC_ALL FWT=FWT PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM FC_ALL_LS=FC_ALL_LS PHIC_ALL_LS=PHIC_ALL_LS
          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_R06_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     1.842     1.644
Bond angles  : others                          3242     1.515     1.582
Torsion angles, period  1. refined              184     6.894     5.000
Torsion angles, period  2. refined               90    35.105    22.778
Torsion angles, period  3. refined              268    12.682    15.000
Torsion angles, period  4. refined                9    11.211    15.000
Chiral centres: refined atoms                   196     0.093     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   310     0.264     0.200
VDW repulsions.others                          1367     0.205     0.200
VDW; torsion: refined_atoms                     721     0.174     0.200
VDW; torsion.others                             789     0.084     0.200
HBOND: refined_atoms                            223     0.188     0.200
HBOND.others                                      2     0.034     0.200
VDW repulsions: symmetry: refined_atoms           8     0.194     0.200
VDW repulsions: symmetry: others                 29     0.159     0.200
HBOND: symmetry: refined_atoms                   18     0.177     0.200
M. chain bond B values: refined atoms           745     1.848     1.686
M. chain bond B values: others                  745     1.844     1.686
M. chain angle B values: refined atoms          926     2.781     2.516
M. chain angle B values: others                 927     2.780     2.516
S. chain bond B values: refined atoms           811     3.195     2.094
S. chain bond B values: others                  810     3.189     2.094
S. chain angle B values: refined atoms         1177     4.847     2.976
S. chain angle B values: others                1178     4.845     2.975
Long range B values: refined atoms             1855     7.303    23.403
Long range B values: others                    1763     7.022    21.858
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =   -0.0019
Partial structure    1: scale =     0.3950, B  =   38.7512
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5045 100.00   379.4   389.1  0.18  0.19     284   390.3   408.6  0.22  0.23
 0.186    8678  99.98   205.9   182.4  0.19  0.17     465   205.5   178.6  0.22  0.20
 0.310   11070 100.00    92.2    89.0  0.23  0.20     577    87.5    85.0  0.27  0.24
 0.434   12817  98.63    38.7    48.0  0.47  0.46     678    38.6    48.3  0.48  0.47
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3812   0.904   1233   0.805   5045   0.880  0.943  0.9598  0.9664  0.8984  0.9313
  0.1863   7439   0.889   1239   0.787   8678   0.874  1.099  0.9558  0.9629  0.9082  0.9387
  0.3102   9817   0.831   1253   0.753  11070   0.822  0.958  0.9229  0.9421  0.8570  0.9165
  0.4340  11574   0.375   1243   0.339  12817   0.372  0.352  0.6409  0.6426  0.6031  0.6503
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37610
Percentage observed                  =    99.4927
Percentage of free reflections       =     5.0588
Overall R factor                     =     0.2190
Free R factor                        =     0.2527
Average Fourier shell correlation    =     0.8481
AverageFree Fourier shell correlation=     0.8404
Overall weighted R factor            =     0.1846
Free weighted R factor               =     0.2262
Overall weighted R2 factor           =     0.2157
Free weighted R2 factor              =     0.2742
Average correlation coefficient      =     0.8329
Overall correlation coefficient      =     0.9590
Free correlation coefficient         =     0.9435
Cruickshanks DPI for coordinate error=     0.0781
DPI based on free R factor           =     0.0808
Overall figure of merit              =     0.6884
ML based su of positional parameters =     0.0662
ML based su of thermal parameters    =     1.8900
-----------------------------------------------------------------------------
  Time in seconds: CPU =        29.48
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2201   0.2529   0.657      176352.    9551.9   0.0119  0.907   1.764  1.027   0.087
       1   0.2203   0.2529   0.686      175097.    9509.9   0.0115  0.875   1.738  1.012   0.088
       2   0.2193   0.2529   0.687      174887.    9506.1   0.0128  0.973   1.800  1.049   0.091
       3   0.2191   0.2529   0.691      174790.    9503.7   0.0128  0.980   1.821  1.062   0.092
       4   0.2190   0.2529   0.689      174819.    9505.2   0.0129  0.983   1.831  1.067   0.092
       5   0.2190   0.2529   0.688      174821.    9505.2   0.0129  0.983   1.835  1.070   0.092
       6   0.2190   0.2528   0.690      174806.    9504.4   0.0129  0.983   1.838  1.071   0.092
       7   0.2190   0.2528   0.691      174787.    9503.1   0.0129  0.984   1.840  1.072   0.093
       8   0.2190   0.2527   0.689      174829.    9504.7   0.0129  0.985   1.842  1.073   0.093
       9   0.2190   0.2527   0.688      174833.    9504.8   0.0129  0.985   1.842  1.073   0.093
      10   0.2190   0.2527   0.688      174837.    9504.9   0.0129  0.984   1.842  1.073   0.093
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2201   0.2190
             R free    0.2529   0.2527
     Rms BondLength    0.0119   0.0129
      Rms BondAngle    1.7644   1.8421
     Rms ChirVolume    0.0871   0.0928
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      61.6s System:    0.2s Elapsed:     1:02