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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: 20:03:21 


 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 16
  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_R16_1-60A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R16_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_R16_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:    16
  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_R16_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=   2.047 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=   2.187 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=   1.829 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=   2.205 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=   2.399 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=   2.405 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=   2.073 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                           16
Number of "free" reflections       1682
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= -2.11 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  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   0.28703728    
 Actual weight    6.2496691      is applied to the X-ray term
Norm of X_ray positional gradient                39.7
Norm of Geom. positional gradient                79.4
Norm of X_ray B-factor gradient                  112.
Norm of Geom. B-factor gradient                 0.224E+05
Product of X_ray and Geom posit. gradients     -0.139E+08
 Cosine of angle between them                      -0.455
Product of X_ray and Geom B-fact gradients     -0.353E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.9770E+06 GEOM=     0.2631E+05 TOTAL=     0.1003E+07
 function value    1003293.4    

-------------------------------------------------------------------------------
             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     1.763     1.644
Bond angles  : others                          3242     2.341     1.582
Torsion angles, period  1. refined              184     6.872     5.000
Torsion angles, period  2. refined               90    35.917    22.778
Torsion angles, period  3. refined              268    13.322    15.000
Torsion angles, period  4. refined                9    11.818    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.014     0.020
VDW repulsions: refined_atoms                   299     0.269     0.200
VDW repulsions.others                          1334     0.232     0.200
VDW; torsion: refined_atoms                     716     0.173     0.200
VDW; torsion.others                             709     0.081     0.200
HBOND: refined_atoms                            217     0.199     0.200
HBOND.others                                      2     0.083     0.200
VDW repulsions: symmetry: refined_atoms           8     0.197     0.200
VDW repulsions: symmetry: others                 22     0.182     0.200
HBOND: symmetry: refined_atoms                   22     0.196     0.200
M. chain bond B values: refined atoms           745     1.702     1.513
M. chain bond B values: others                  745     1.698     1.513
M. chain angle B values: refined atoms          926     2.671     2.255
M. chain angle B values: others                 927     2.670     2.255
S. chain bond B values: refined atoms           811     3.002     1.910
S. chain bond B values: others                  810     2.995     1.910
S. chain angle B values: refined atoms         1177     4.655     2.699
S. chain angle B values: others                1178     4.653     2.699
Long range B values: refined atoms             1837     6.963    20.809
Long range B values: others                    1747     6.646    19.339
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0457, B  =    1.1655
Partial structure    1: scale =     0.3930, B  =   46.4425
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4310 100.00   405.9   416.3  0.17  0.18     237   392.7   403.2  0.20  0.21
 0.167    7383  99.97   228.1   208.2  0.18  0.16     415   221.5   203.9  0.22  0.19
 0.278    9451 100.00   123.9   114.0  0.21  0.19     459   120.2   113.2  0.24  0.21
 0.389   11070 100.00    50.0    62.3  0.41  0.36     571    51.8    63.6  0.40  0.35
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3209   0.915   1101   0.810   4310   0.888  0.944  0.9632  0.9704  0.9159  0.9339
  0.1670   6264   0.881   1119   0.781   7383   0.865  1.060  0.9488  0.9611  0.8926  0.9375
  0.2780   8321   0.834   1130   0.753   9451   0.824  1.019  0.9316  0.9473  0.8757  0.9302
  0.3890   9954   0.529   1128   0.461  11082   0.522  0.546  0.7622  0.7515  0.7907  0.7678
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32226
Percentage observed                  =    99.9912
Percentage of free reflections       =     4.9605
Overall R factor                     =     0.2079
Free R factor                        =     0.2374
Average Fourier shell correlation    =     0.8862
AverageFree Fourier shell correlation=     0.8828
Overall weighted R factor            =     0.1761
Free weighted R factor               =     0.2070
Overall weighted R2 factor           =     0.2072
Free weighted R2 factor              =     0.2350
Average correlation coefficient      =     0.8765
Overall correlation coefficient      =     0.9588
Free correlation coefficient         =     0.9452
Cruickshanks DPI for coordinate error=     0.0861
DPI based on free R factor           =     0.0864
Overall figure of merit              =     0.7384
ML based su of positional parameters =     0.0715
ML based su of thermal parameters    =     2.1294
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    156325.41       26311.389       1003293.4      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.34448096    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    980721.81    

-------------------------------------------------------------------------------
             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 =     0.0457, B  =   -0.0587
Partial structure    1: scale =     0.3933, B  =   45.7766
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2074
Free R factor                        =     0.2368
Average Fourier shell correlation    =     0.9008
AverageFree Fourier shell correlation=     0.8951
Average correlation coefficient      =     0.8767
Overall figure of merit              =     0.7601
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    155354.30       9808.8867       980721.81       1003293.4    


     CGMAT cycle number =      3

 Weight matrix   0.35423061    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    978305.94    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0457, B  =   -0.0103
Partial structure    1: scale =     0.3934, B  =   41.7675
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                        =     0.2363
Average Fourier shell correlation    =     0.9045
AverageFree Fourier shell correlation=     0.8983
Average correlation coefficient      =     0.8787
Overall figure of merit              =     0.7677
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    155072.72       9152.7734       978305.94       980721.81    


     CGMAT cycle number =      4

 Weight matrix   0.35621420    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    977813.44    

-------------------------------------------------------------------------------
             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 =     0.0457, B  =    0.0009
Partial structure    1: scale =     0.3938, B  =   40.2281
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                     =     0.2064
Free R factor                        =     0.2362
Average Fourier shell correlation    =     0.9052
AverageFree Fourier shell correlation=     0.8989
Average correlation coefficient      =     0.8795
Overall figure of merit              =     0.7692
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    155028.36       8937.4883       977813.44       978305.94    


     CGMAT cycle number =      5

 Weight matrix   0.35370412    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    978035.44    

-------------------------------------------------------------------------------
             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 =     0.0457, B  =    0.0008
Partial structure    1: scale =     0.3939, B  =   40.2145
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                        =     0.2361
Average Fourier shell correlation    =     0.9040
AverageFree Fourier shell correlation=     0.8972
Average correlation coefficient      =     0.8799
Overall figure of merit              =     0.7643
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03

 fvalues    155009.63       8932.0410       977690.94       977813.44    


     CGMAT cycle number =      6

 Weight matrix   0.35333118    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    978092.88    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0457, B  =    0.0008
Partial structure    1: scale =     0.3939, B  =   40.2206
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                        =     0.2361
Average Fourier shell correlation    =     0.9038
AverageFree Fourier shell correlation=     0.8968
Average correlation coefficient      =     0.8800
Overall figure of merit              =     0.7632
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03

 fvalues    155005.84       8954.0820       977689.31       977690.94    


     CGMAT cycle number =      7

 Weight matrix   0.32107827    
 Actual weight    5.6815171      is applied to the X-ray term


 function value    889952.44    

-------------------------------------------------------------------------------
             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 =     0.0457, B  =    0.0043
Partial structure    1: scale =     0.3939, B  =   40.2093
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                     =     0.2062
Free R factor                        =     0.2361
Average Fourier shell correlation    =     0.9039
AverageFree Fourier shell correlation=     0.8969
Average correlation coefficient      =     0.8801
Overall figure of merit              =     0.7636
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    155062.89       8959.9902       889952.44       977689.31    


     CGMAT cycle number =      8

 Weight matrix   0.29304054    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    809550.25    

-------------------------------------------------------------------------------
             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 =     0.0457, B  =    0.0003
Partial structure    1: scale =     0.3939, B  =   40.1844
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                        =     0.2364
Average Fourier shell correlation    =     0.9048
AverageFree Fourier shell correlation=     0.8983
Average correlation coefficient      =     0.8796
Overall figure of merit              =     0.7678
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    155060.02       8662.9678       809550.25       889952.44    


     CGMAT cycle number =      9

 Weight matrix   0.29262647    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    809642.00    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0457, B  =   -0.0019
Partial structure    1: scale =     0.3939, B  =   40.0338
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                     =     0.2070
Free R factor                        =     0.2367
Average Fourier shell correlation    =     0.9050
AverageFree Fourier shell correlation=     0.8987
Average correlation coefficient      =     0.8792
Overall figure of merit              =     0.7690
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    155195.06       8331.6006       809694.56       809550.25    
 fvalues    155195.06       8331.6006       809694.56       809916.50    


     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   0.29157537    
 Actual weight    5.1650152      is applied to the X-ray term
Norm of X_ray positional gradient                37.4
Norm of Geom. positional gradient                37.6
Norm of X_ray B-factor gradient                  97.3
Norm of Geom. B-factor gradient                  98.4
Product of X_ray and Geom posit. gradients     -0.136E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.309E+08
 Cosine of angle between them                      -0.999


Residuals: XRAY=     0.8015E+06 GEOM=      8249.     TOTAL=     0.8097E+06
 function value    809706.75    

-------------------------------------------------------------------------------
             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     1.751     1.644
Bond angles  : others                          3242     1.489     1.582
Torsion angles, period  1. refined              184     6.871     5.000
Torsion angles, period  2. refined               90    35.765    22.778
Torsion angles, period  3. refined              268    13.026    15.000
Torsion angles, period  4. refined                9    11.896    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   295     0.270     0.200
VDW repulsions.others                          1368     0.203     0.200
VDW; torsion: refined_atoms                     715     0.173     0.200
VDW; torsion.others                             788     0.083     0.200
HBOND: refined_atoms                            220     0.193     0.200
HBOND.others                                      1     0.135     0.200
VDW repulsions: symmetry: refined_atoms           8     0.197     0.200
VDW repulsions: symmetry: others                 22     0.169     0.200
HBOND: symmetry: refined_atoms                   22     0.191     0.200
M. chain bond B values: refined atoms           745     1.748     1.626
M. chain bond B values: others                  745     1.744     1.626
M. chain angle B values: refined atoms          926     2.716     2.425
M. chain angle B values: others                 927     2.715     2.425
S. chain bond B values: refined atoms           811     3.051     2.030
S. chain bond B values: others                  810     3.044     2.029
S. chain angle B values: refined atoms         1177     4.717     2.877
S. chain angle B values: others                1178     4.715     2.877
Long range B values: refined atoms             1835     6.961    22.255
Long range B values: others                    1742     6.654    20.679
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =   -0.0013
Partial structure    1: scale =     0.3939, B  =   40.0162
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4310 100.00   406.5   416.7  0.17  0.18     237   393.2   403.0  0.20  0.21
 0.167    7383  99.97   228.4   208.6  0.18  0.15     415   221.8   204.2  0.22  0.19
 0.278    9451 100.00   124.0   114.4  0.21  0.18     459   120.4   113.3  0.24  0.21
 0.389   11070 100.00    50.1    62.3  0.41  0.36     571    51.9    63.5  0.40  0.35
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3209   0.922   1101   0.824   4310   0.897  0.944  0.9649  0.9721  0.9156  0.9334
  0.1670   6264   0.892   1119   0.794   7383   0.877  1.062  0.9522  0.9639  0.8926  0.9382
  0.2780   8321   0.848   1130   0.768   9451   0.838  1.019  0.9374  0.9524  0.8772  0.9314
  0.3890   9954   0.591   1128   0.526  11082   0.584  0.573  0.7999  0.7981  0.7907  0.7739
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32226
Percentage observed                  =    99.9912
Percentage of free reflections       =     4.9605
Overall R factor                     =     0.2071
Free R factor                        =     0.2368
Average Fourier shell correlation    =     0.9046
AverageFree Fourier shell correlation=     0.8982
Overall weighted R factor            =     0.1758
Free weighted R factor               =     0.2059
Overall weighted R2 factor           =     0.2070
Free weighted R2 factor              =     0.2344
Average correlation coefficient      =     0.8791
Overall correlation coefficient      =     0.9589
Free correlation coefficient         =     0.9452
Cruickshanks DPI for coordinate error=     0.0858
DPI based on free R factor           =     0.0862
Overall figure of merit              =     0.7678
ML based su of positional parameters =     0.0645
ML based su of thermal parameters    =     1.8915
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    155170.50       8248.7617       809706.75       809916.50    

    ****                              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_R16_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     1.745     1.644
Bond angles  : others                          3242     1.487     1.582
Torsion angles, period  1. refined              184     6.872     5.000
Torsion angles, period  2. refined               90    35.758    22.778
Torsion angles, period  3. refined              268    13.006    15.000
Torsion angles, period  4. refined                9    11.870    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   296     0.269     0.200
VDW repulsions.others                          1371     0.202     0.200
VDW; torsion: refined_atoms                     714     0.173     0.200
VDW; torsion.others                             791     0.082     0.200
HBOND: refined_atoms                            219     0.193     0.200
HBOND.others                                      1     0.134     0.200
VDW repulsions: symmetry: refined_atoms           8     0.197     0.200
VDW repulsions: symmetry: others                 22     0.169     0.200
HBOND: symmetry: refined_atoms                   22     0.192     0.200
M. chain bond B values: refined atoms           745     1.743     1.625
M. chain bond B values: others                  745     1.740     1.626
M. chain angle B values: refined atoms          926     2.709     2.425
M. chain angle B values: others                 927     2.708     2.425
S. chain bond B values: refined atoms           811     3.038     2.028
S. chain bond B values: others                  810     3.031     2.027
S. chain angle B values: refined atoms         1177     4.698     2.875
S. chain angle B values: others                1178     4.696     2.875
Long range B values: refined atoms             1835     6.948    22.251
Long range B values: others                    1743     6.640    20.690
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    0.0003
Partial structure    1: scale =     0.3939, B  =   40.0160
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4310 100.00   406.5   416.8  0.17  0.18     237   393.2   403.0  0.20  0.21
 0.167    7383  99.97   228.4   208.6  0.18  0.15     415   221.8   204.3  0.22  0.19
 0.278    9451 100.00   124.0   114.4  0.21  0.18     459   120.4   113.3  0.24  0.21
 0.389   11070 100.00    50.1    62.3  0.41  0.36     571    51.9    63.5  0.40  0.35
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3209   0.922   1101   0.824   4310   0.897  0.944  0.9648  0.9721  0.9154  0.9334
  0.1670   6264   0.892   1119   0.794   7383   0.877  1.062  0.9522  0.9639  0.8925  0.9381
  0.2780   8321   0.848   1130   0.768   9451   0.838  1.019  0.9373  0.9524  0.8771  0.9313
  0.3890   9954   0.577   1128   0.513  11082   0.570  0.562  0.7949  0.7944  0.7907  0.7738
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32226
Percentage observed                  =    99.9912
Percentage of free reflections       =     4.9605
Overall R factor                     =     0.2072
Free R factor                        =     0.2370
Average Fourier shell correlation    =     0.9033
AverageFree Fourier shell correlation=     0.8965
Overall weighted R factor            =     0.1758
Free weighted R factor               =     0.2061
Overall weighted R2 factor           =     0.2071
Free weighted R2 factor              =     0.2345
Average correlation coefficient      =     0.8790
Overall correlation coefficient      =     0.9589
Free correlation coefficient         =     0.9451
Cruickshanks DPI for coordinate error=     0.0859
DPI based on free R factor           =     0.0863
Overall figure of merit              =     0.7628
ML based su of positional parameters =     0.0645
ML based su of thermal parameters    =     1.8915
-----------------------------------------------------------------------------
  Time in seconds: CPU =        23.83
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2079   0.2374   0.738      156325.    8367.5   0.0121  0.915   1.763  1.025   0.087
       1   0.2074   0.2368   0.760      155354.    8343.7   0.0123  0.924   1.752  1.017   0.089
       2   0.2066   0.2363   0.768      155073.    8336.3   0.0131  0.989   1.793  1.042   0.090
       3   0.2064   0.2362   0.769      155028.    8333.5   0.0132  0.996   1.810  1.052   0.091
       4   0.2063   0.2361   0.764      155065.    8335.6   0.0132  0.999   1.819  1.057   0.091
       5   0.2063   0.2361   0.763      155070.    8336.3   0.0132  1.000   1.824  1.060   0.092
       6   0.2062   0.2361   0.764      155063.    8336.0   0.0132  1.000   1.828  1.062   0.092
       7   0.2066   0.2364   0.768      155060.    8335.4   0.0126  0.955   1.797  1.044   0.090
       8   0.2070   0.2367   0.769      155142.    8336.6   0.0120  0.910   1.762  1.023   0.088
       9   0.2071   0.2368   0.768      155171.    8338.7   0.0119  0.905   1.751  1.016   0.087
      10   0.2072   0.2370   0.763      155250.    8342.1   0.0119  0.902   1.745  1.013   0.087
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2079   0.2072
             R free    0.2374   0.2370
     Rms BondLength    0.0121   0.0119
      Rms BondAngle    1.7628   1.7448
     Rms ChirVolume    0.0869   0.0869
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      55.9s System:    0.2s Elapsed:     0:56