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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: 19:33:55 


 Please reference: Collaborative Computational Project, Number 4. 2011.
 "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242.
 as well as any specific reference in the program write-up.


 $TEXT:Reference1: $$ Primary reference $$ 
   "Overview of refinement procedures within REFMAC5: utilizing data from different sources"
   O.Kovalevskiy, R.A.Nicholls, F.Long, G.N.Murshudov,(2018) 
   Acta Crystallogr. D74, 492-505

 $$
 $SUMMARY :Reference1:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference1: $$ Primary reference for EM $$ 
   "Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM
   R.A. Nicholls, M. Tykac, O.Kovalevskiy, G.N.Murshudov,(2018) 
   Acta Crystallogr. D74, 215-227

 $$
 $SUMMARY :Reference2:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference1: $$ Secondary reference $$ 
   "REFMAC5 for the refinement of macromolecular crystal structures:"
   G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011) 
   Acta Crystallogr. D67, 355-367

 $$
 $SUMMARY :Reference3:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference2: $$ Secondary reference $$ 
   "Refinement of Macromolecular Structures by the  Maximum-Likelihood Method:"
   G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
   Acta Crystallogr. D53, 240-255
   EU  Validation contract: BIO2CT-92-0524

 $$
 $SUMMARY :Reference4:  $$ Refmac: $$
 :TEXT:Reference2: $$

  Data line--- make     check NONE
  Data line--- refi     type REST reso 41.96 1.50     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- bins 4
  Data line--- ncyc 10
  Data line--- monitor MEDIum
  Data line--- free 10
  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_R10_1-60A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R10_1-50A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R10_1-50A.mtz

Cell from mtz :    57.632    57.632   122.391    90.000    90.000    90.000
Space group from mtz: number -   96; name - P 43 21 2

  Refinement type                        : Restrained

    ****                           Makecif parameters                           ****

Dictionary files for restraints : /protein2/ccp4/ccp4-7.0/ccp4-7.0/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /protein2/ccp4/ccp4-7.0/ccp4-7.0/lib/data/monomers/ener_lib.cif
    Program will rely on residue and atom names. No checking
    If this option is used then monomers should be checked carefully before using
    Hydrogens will be restored in their riding positions
    Links between monomers will be checked. Only those links present in the coordinate file will be used
    Standard sugar links will be analysed and used
    For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
    Symmetry related links will be analysed and used
    Cis peptides will be found and used automatically


  Residual                               : Rice Maximum Likelihood for Fs

    ****                    Least-square scaling parameters                     ****

Overall scale
Overall B value
Overall anisotropic B with tr(B) = 0.0
Constant bulk solvent in non protein region
Probe radii for non-ions     1.200
Probe radii for ions         0.800
Shrinkage of the mask  by    0.800


    ****                 Map sharpening parameters and methods                  ****

No map sharpening will be performed

  Method of minimisation                 : Sparse Matrix
  Experimental sigmas used for weighting
  Number of Bins and width:     4       0.1111
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.5000
  Estimated number of reflections :      43652
  Free R exclusion - flag equals:    10
  Auto weighting. An attempt
  Refinement cycles       :    10
  Scaling type                           :
          Wilson scaling type with Guassians

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

  Scaling and SigmaA resln:    41.9635  1.5000

  Damping factors:     1.0000  1.0000  1.0000


    ****                    Geometry restraints and weights                     ****


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

 Planar groups (all and main chain)
          WEIGHT= 1.00 1.00

 Chiral centers
          Weight= 1.00

 NON-BONDED CONTACTS
          Overall weight                          =  1.00
          Sigma for simple VDW                    =  0.20
          Sigma for VDW trhough torsion angle     =  0.20
          Sigma for HBOND                         =  0.20
          Sigma for metal-ion                     =  0.20
          Sigma for DUMMY and other atom          =  0.30
          Distance for donor-accepetor = vdw1+vdw2+(-0.30)
          Distance for acceptor - H    = vdw1+     ( 0.10)
          VDW distance through torsion = vdw1+vdw2+(-0.30)
          Distance for DUMMY-others    = vdw1+vdw2+(-0.70)

 TORSION ANGLES
          Weight= 1.00

 THERMAL FACTORS
          Weight= 1.00
     Main chain bond (1-2 neighbour)          1.5A**2
     Main chain angle (1-3 neighbour)         2.0A**2
     Side chain bond                          3.0A**2
     Side chain angle                         4.5A**2

 RESTRAINTS AGAINST EXCESSIVE SHIFTS
     Positional parameters                   0.00A
     Thermal parameters                      0.00A
     Occupancy parameters                    0.00

 RADIUS OF CONFIDENCE
     Positional parameters 0.00A
     Thermal parameters    0.00A**2
     Occupancy parameters  0.00

Monitoring style is "MEDIUM". Complete information will be printed out in the
first and last cycle. In all other cycles minimum information will be printed out
Sigma cutoffs for printing out outliers
If deviation of restraint parameter > alpha*sigma then information will be printed out
Distance outliers      10.000
Angle outliers         10.000
Torsion outliers       10.000
Chiral volume outliers 10.000
Plane outliers         10.000
Non-bonding outliers   10.000
B value  outliers      10.000
Rigid bond outliers    10.000
Sphericity outliers    10.000
---------------------------------------------------------------

 Input file :CDO_complete_R10_1-60A.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.51
 _lib_update       11/07/18
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 24624
                with complete description    : 24624
  NUMBER OF MODIFICATIONS                    :    70
  NUMBER OF LINKS                            :    77
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  Number of atoms    :    1836
  Number of residues :     502
  Number of chains   :       4
  I am reading library. Please wait.
                mon_lib.cif
  INFO:     link is found (not be used) dist=   2.058 ideal_dist=   2.090
            ch:AAA  res:  86  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.196 ideal_dist=   2.090
            ch:AAA  res:  88  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   1.826 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=   2.193 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=   2.425 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=   2.388 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=   2.082 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                           10
Number of "free" reflections       1719
Number of   all  reflections      33910
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          33910

   Current auto weighting coefficient =    6.2496691    

 mode : HKRF


######  TLS Group Definitions ######



     CGMAT cycle number =      1

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.895 id.= 3.000 dev= -2.10 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Weight matrix   0.29052338    
 Actual weight    6.2496691      is applied to the X-ray term
Norm of X_ray positional gradient                40.0
Norm of Geom. positional gradient                80.1
Norm of X_ray B-factor gradient                  111.
Norm of Geom. B-factor gradient                 0.230E+05
Product of X_ray and Geom posit. gradients     -0.144E+08
 Cosine of angle between them                      -0.466
Product of X_ray and Geom B-fact gradients     -0.357E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.9764E+06 GEOM=     0.2676E+05 TOTAL=     0.1003E+07
 function value    1003196.1    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.794     1.644
Bond angles  : others                          3242     2.345     1.582
Torsion angles, period  1. refined              184     6.761     5.000
Torsion angles, period  2. refined               90    35.268    22.778
Torsion angles, period  3. refined              268    12.803    15.000
Torsion angles, period  4. refined                9    11.350    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.016     0.020
VDW repulsions: refined_atoms                   311     0.265     0.200
VDW repulsions.others                          1325     0.234     0.200
VDW; torsion: refined_atoms                     725     0.172     0.200
VDW; torsion.others                             712     0.081     0.200
HBOND: refined_atoms                            233     0.190     0.200
HBOND.others                                      2     0.029     0.200
VDW repulsions: symmetry: refined_atoms          10     0.200     0.200
VDW repulsions: symmetry: others                 26     0.183     0.200
HBOND: symmetry: refined_atoms                   25     0.184     0.200
M. chain bond B values: refined atoms           745     1.685     1.507
M. chain bond B values: others                  745     1.681     1.507
M. chain angle B values: refined atoms          926     2.629     2.247
M. chain angle B values: others                 927     2.628     2.247
S. chain bond B values: refined atoms           811     2.953     1.894
S. chain bond B values: others                  810     2.946     1.894
S. chain angle B values: refined atoms         1177     4.541     2.681
S. chain angle B values: others                1178     4.539     2.680
Long range B values: refined atoms             1867     6.830    21.250
Long range B values: others                    1768     6.521    19.693
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0457, B  =    1.1672
Partial structure    1: scale =     0.3915, B  =   45.6585
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4316 100.00   405.6   416.3  0.18  0.18     231   402.7   406.4  0.21  0.22
 0.167    7416  99.97   228.0   208.2  0.17  0.15     382   225.4   209.2  0.21  0.18
 0.278    9368 100.00   123.7   114.3  0.21  0.18     542   124.4   112.5  0.24  0.22
 0.389   11077 100.00    50.2    62.5  0.41  0.36     564    49.7    63.4  0.45  0.40
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3205   0.901   1111   0.781   4316   0.870  0.943  0.9553  0.9656  0.8834  0.9322
  0.1670   6299   0.885   1117   0.788   7416   0.871  1.063  0.9520  0.9620  0.9116  0.9379
  0.2780   8247   0.831   1121   0.755   9368   0.822  1.017  0.9365  0.9466  0.9016  0.9308
  0.3890   9976   0.534   1113   0.469  11089   0.528  0.548  0.7421  0.7608  0.7190  0.7746
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32189
Percentage observed                  =    99.9912
Percentage of free reflections       =     5.0696
Overall R factor                     =     0.2077
Free R factor                        =     0.2431
Average Fourier shell correlation    =     0.8887
AverageFree Fourier shell correlation=     0.8787
Overall weighted R factor            =     0.1772
Free weighted R factor               =     0.2093
Overall weighted R2 factor           =     0.2095
Free weighted R2 factor              =     0.2561
Average correlation coefficient      =     0.8789
Overall correlation coefficient      =     0.9584
Free correlation coefficient         =     0.9397
Cruickshanks DPI for coordinate error=     0.0862
DPI based on free R factor           =     0.0886
Overall figure of merit              =     0.7383
ML based su of positional parameters =     0.0711
ML based su of thermal parameters    =     2.0996
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    156238.14       26759.451       1003196.1      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.35961795    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    979714.75    

-------------------------------------------------------------------------------
             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 =     0.0456, B  =   -0.0738
Partial structure    1: scale =     0.3914, B  =   44.8999
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2075
Free R factor                        =     0.2430
Average Fourier shell correlation    =     0.9027
AverageFree Fourier shell correlation=     0.8932
Average correlation coefficient      =     0.8788
Overall figure of merit              =     0.7632
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    155192.70       9811.6943       979714.75       1003196.1    


     CGMAT cycle number =      3

 Weight matrix   0.37722197    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    976636.06    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =   -0.0544
Partial structure    1: scale =     0.3908, B  =   40.7390
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2067
Free R factor                        =     0.2425
Average Fourier shell correlation    =     0.9095
AverageFree Fourier shell correlation=     0.9001
Average correlation coefficient      =     0.8807
Overall figure of merit              =     0.7787
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    154805.66       9151.9473       976636.06       979714.75    


     CGMAT cycle number =      4

 Weight matrix   0.37738398    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    976205.00    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =   -0.0351
Partial structure    1: scale =     0.3906, B  =   38.9473
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2065
Free R factor                        =     0.2424
Average Fourier shell correlation    =     0.9093
AverageFree Fourier shell correlation=     0.8997
Average correlation coefficient      =     0.8816
Overall figure of merit              =     0.7762
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    154770.45       8940.8730       976205.00       976636.06    


     CGMAT cycle number =      5

 Weight matrix   0.37610692    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    976287.63    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =   -0.0415
Partial structure    1: scale =     0.3907, B  =   38.7077
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2063
Free R factor                        =     0.2421
Average Fourier shell correlation    =     0.9088
AverageFree Fourier shell correlation=     0.8990
Average correlation coefficient      =     0.8820
Overall figure of merit              =     0.7735
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03


 fvalues    154820.53       8934.6299       976467.44       976205.00    
 fvalues    154820.53       8934.6299       976467.44       976511.69    


     CGMAT cycle number =      6

 Weight matrix   0.37649116    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    976429.38    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =   -0.0317
Partial structure    1: scale =     0.3910, B  =   38.6948
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2063
Free R factor                        =     0.2419
Average Fourier shell correlation    =     0.9086
AverageFree Fourier shell correlation=     0.8987
Average correlation coefficient      =     0.8822
Overall figure of merit              =     0.7728
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    154801.98       8968.2070       976429.38       976511.69    


     CGMAT cycle number =      7

 Weight matrix   0.37656406    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    976439.19    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =   -0.0317
Partial structure    1: scale =     0.3911, B  =   38.6951
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2063
Free R factor                        =     0.2418
Average Fourier shell correlation    =     0.9086
AverageFree Fourier shell correlation=     0.8987
Average correlation coefficient      =     0.8822
Overall figure of merit              =     0.7728
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    154803.09       8981.4248       976442.31       976429.38    
 fvalues    154803.09       8981.4248       976442.31       976449.56    


     CGMAT cycle number =      8

 Weight matrix   0.34288588    
 Actual weight    5.6815171      is applied to the X-ray term


 function value    888497.88    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =   -0.0302
Partial structure    1: scale =     0.3911, B  =   38.8401
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2063
Free R factor                        =     0.2416
Average Fourier shell correlation    =     0.9087
AverageFree Fourier shell correlation=     0.8988
Average correlation coefficient      =     0.8822
Overall figure of merit              =     0.7729
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    154801.02       8993.2334       888497.88       976449.56    


     CGMAT cycle number =      9

 Weight matrix   0.31126225    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    808553.44    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =   -0.0321
Partial structure    1: scale =     0.3910, B  =   38.7756
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2066
Free R factor                        =     0.2417
Average Fourier shell correlation    =     0.9085
AverageFree Fourier shell correlation=     0.8987
Average correlation coefficient      =     0.8819
Overall figure of merit              =     0.7728
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    154857.59       8711.6084       808553.44       888497.88    


     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  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Weight matrix   0.30994707    
 Actual weight    5.1650152      is applied to the X-ray term
Norm of X_ray positional gradient                38.5
Norm of Geom. positional gradient                38.9
Norm of X_ray B-factor gradient                  96.4
Norm of Geom. B-factor gradient                  101.
Product of X_ray and Geom posit. gradients     -0.145E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.313E+08
 Cosine of angle between them                      -0.998


Residuals: XRAY=     0.8003E+06 GEOM=      8385.     TOTAL=     0.8086E+06
 function value    808636.19    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.794     1.644
Bond angles  : others                          3242     1.489     1.582
Torsion angles, period  1. refined              184     6.764     5.000
Torsion angles, period  2. refined               90    35.206    22.778
Torsion angles, period  3. refined              268    12.724    15.000
Torsion angles, period  4. refined                9    11.521    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   303     0.269     0.200
VDW repulsions.others                          1356     0.206     0.200
VDW; torsion: refined_atoms                     725     0.171     0.200
VDW; torsion.others                             779     0.084     0.200
HBOND: refined_atoms                            228     0.188     0.200
HBOND.others                                      1     0.026     0.200
VDW repulsions: symmetry: refined_atoms          10     0.194     0.200
VDW repulsions: symmetry: others                 24     0.180     0.200
HBOND: symmetry: refined_atoms                   24     0.182     0.200
M. chain bond B values: refined atoms           745     1.740     1.621
M. chain bond B values: others                  745     1.736     1.621
M. chain angle B values: refined atoms          926     2.687     2.418
M. chain angle B values: others                 927     2.686     2.418
S. chain bond B values: refined atoms           811     3.032     2.018
S. chain bond B values: others                  810     3.026     2.018
S. chain angle B values: refined atoms         1177     4.663     2.864
S. chain angle B values: others                1178     4.661     2.863
Long range B values: refined atoms             1857     6.842    22.427
Long range B values: others                    1762     6.561    20.895
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =   -0.0256
Partial structure    1: scale =     0.3910, B  =   38.7349
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10.  v. resln :N:1,6,7,11,12:
:Cycle   10.  and  v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4316 100.00   406.4   416.8  0.18  0.18     231   403.4   406.8  0.21  0.22
 0.167    7416  99.97   228.4   208.6  0.18  0.15     382   225.8   209.3  0.21  0.18
 0.278    9368 100.00   124.0   114.5  0.21  0.18     542   124.6   113.0  0.24  0.21
 0.389   11077 100.00    50.2    62.4  0.41  0.36     564    49.8    63.6  0.45  0.40
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle   10. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3205   0.914   1111   0.803   4316   0.886  0.946  0.9596  0.9692  0.8847  0.9324
  0.1670   6299   0.894   1117   0.799   7416   0.880  1.063  0.9538  0.9639  0.9118  0.9377
  0.2780   8247   0.851   1121   0.777   9368   0.842  1.023  0.9458  0.9548  0.9033  0.9324
  0.3890   9976   0.605   1113   0.539  11089   0.598  0.583  0.7906  0.8080  0.7226  0.7805
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32189
Percentage observed                  =    99.9912
Percentage of free reflections       =     5.0696
Overall R factor                     =     0.2071
Free R factor                        =     0.2418
Average Fourier shell correlation    =     0.9082
AverageFree Fourier shell correlation=     0.8985
Overall weighted R factor            =     0.1771
Free weighted R factor               =     0.2086
Overall weighted R2 factor           =     0.2096
Free weighted R2 factor              =     0.2556
Average correlation coefficient      =     0.8813
Overall correlation coefficient      =     0.9586
Free correlation coefficient         =     0.9402
Cruickshanks DPI for coordinate error=     0.0859
DPI based on free R factor           =     0.0881
Overall figure of merit              =     0.7726
ML based su of positional parameters =     0.0625
ML based su of thermal parameters    =     1.8188
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    154940.41       8384.6689       808688.56       808553.44    

 fvalues    154940.41       8384.6689       808697.38       808654.25    
 fvalues    154940.41       8384.6689       808697.38       808654.25    

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.912 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 LABOUT FreeR_flag=FreeR_flag FP=FP SIGFP=SIGFP FC=FC PHIC=PHIC FC_ALL=FC_ALL PHIC_ALL=PHIC_ALL FWT=FWT PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM FC_ALL_LS=FC_ALL_LS PHIC_ALL_LS=PHIC_ALL_LS

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R10_1-50A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.791     1.644
Bond angles  : others                          3242     1.489     1.582
Torsion angles, period  1. refined              184     6.764     5.000
Torsion angles, period  2. refined               90    35.203    22.778
Torsion angles, period  3. refined              268    12.720    15.000
Torsion angles, period  4. refined                9    11.505    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   303     0.269     0.200
VDW repulsions.others                          1355     0.206     0.200
VDW; torsion: refined_atoms                     725     0.171     0.200
VDW; torsion.others                             779     0.084     0.200
HBOND: refined_atoms                            228     0.188     0.200
HBOND.others                                      1     0.025     0.200
VDW repulsions: symmetry: refined_atoms          10     0.193     0.200
VDW repulsions: symmetry: others                 24     0.180     0.200
HBOND: symmetry: refined_atoms                   24     0.182     0.200
M. chain bond B values: refined atoms           745     1.737     1.621
M. chain bond B values: others                  745     1.733     1.621
M. chain angle B values: refined atoms          926     2.684     2.419
M. chain angle B values: others                 927     2.683     2.418
S. chain bond B values: refined atoms           811     3.025     2.017
S. chain bond B values: others                  810     3.019     2.017
S. chain angle B values: refined atoms         1177     4.654     2.863
S. chain angle B values: others                1178     4.652     2.863
Long range B values: refined atoms             1857     6.837    22.426
Long range B values: others                    1762     6.555    20.894
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =   -0.0295
Partial structure    1: scale =     0.3909, B  =   38.7198
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4316 100.00   406.5   416.8  0.18  0.18     231   403.5   406.9  0.21  0.22
 0.167    7416  99.97   228.4   208.7  0.18  0.15     382   225.9   209.3  0.21  0.18
 0.278    9368 100.00   124.0   114.5  0.21  0.18     542   124.6   113.1  0.24  0.21
 0.389   11077 100.00    50.3    62.5  0.41  0.36     564    49.8    63.6  0.45  0.40
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3205   0.914   1111   0.803   4316   0.885  0.946  0.9596  0.9692  0.8846  0.9324
  0.1670   6299   0.894   1117   0.799   7416   0.880  1.063  0.9538  0.9639  0.9118  0.9377
  0.2780   8247   0.851   1121   0.777   9368   0.842  1.023  0.9458  0.9548  0.9033  0.9324
  0.3890   9976   0.605   1113   0.539  11089   0.598  0.583  0.7906  0.8080  0.7226  0.7804
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32189
Percentage observed                  =    99.9912
Percentage of free reflections       =     5.0696
Overall R factor                     =     0.2071
Free R factor                        =     0.2418
Average Fourier shell correlation    =     0.9082
AverageFree Fourier shell correlation=     0.8985
Overall weighted R factor            =     0.1771
Free weighted R factor               =     0.2086
Overall weighted R2 factor           =     0.2096
Free weighted R2 factor              =     0.2557
Average correlation coefficient      =     0.8813
Overall correlation coefficient      =     0.9586
Free correlation coefficient         =     0.9401
Cruickshanks DPI for coordinate error=     0.0859
DPI based on free R factor           =     0.0881
Overall figure of merit              =     0.7726
ML based su of positional parameters =     0.0625
ML based su of thermal parameters    =     1.8188
-----------------------------------------------------------------------------
  Time in seconds: CPU =        26.77
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2077   0.2431   0.738      156238.    8528.1   0.0120  0.911   1.794  1.044   0.087
       1   0.2075   0.2430   0.763      155193.    8495.4   0.0121  0.915   1.772  1.031   0.088
       2   0.2067   0.2425   0.779      154806.    8484.5   0.0130  0.987   1.817  1.059   0.090
       3   0.2065   0.2424   0.776      154770.    8484.5   0.0131  0.995   1.835  1.070   0.091
       4   0.2063   0.2421   0.774      154785.    8485.7   0.0131  0.998   1.845  1.076   0.092
       5   0.2063   0.2419   0.773      154802.    8486.6   0.0132  0.999   1.852  1.079   0.092
       6   0.2063   0.2418   0.773      154801.    8486.4   0.0132  1.000   1.856  1.082   0.092
       7   0.2063   0.2416   0.773      154801.    8485.8   0.0132  1.000   1.859  1.084   0.092
       8   0.2066   0.2417   0.773      154858.    8486.9   0.0126  0.956   1.831  1.067   0.090
       9   0.2071   0.2418   0.773      154937.    8488.5   0.0120  0.912   1.794  1.044   0.088
      10   0.2071   0.2418   0.773      154949.    8489.0   0.0120  0.910   1.791  1.043   0.088
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2077   0.2071
             R free    0.2431   0.2418
     Rms BondLength    0.0120   0.0120
      Rms BondAngle    1.7937   1.7905
     Rms ChirVolume    0.0866   0.0878
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      59.0s System:    0.2s Elapsed:     0:59