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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: 17:58:45 


 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 1.60     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 9
  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_R09_1-70A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R09_1-60A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R09_1-60A.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       0.0977
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.6000
  Estimated number of reflections :      36894
  Free R exclusion - flag equals:     9
  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  1.6000

  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_R09_1-70A.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=   2.027 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=   2.214 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=   1.835 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=   2.216 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=   2.373 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=   2.391 ideal_dist=   2.235
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:SG  .
  INFO:     link is found (not be used) dist=   2.104 ideal_dist=   1.870
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:OD  .
  --------------------------------
  --- title of input coord file ---

  PDB_code:xxxx
  PDB_name:----
  PDB_date:26-MAY-20
  --------------------------------
  ATTENTION: atom:OXT  THR               171  AAA  is missing in the structure
  ATTENTION: atom:OXT  PRO               190  AAA  is missing in the structure
  Number of chains                  :       4
  Total number of monomers          :     502
  Number of atoms                   :    3948
  Number of missing atoms           :       0
  Number of rebuilt atoms           :    1482
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0

_ccp4_form_factor.scat_method    'Sum of Gaussians'
_ccp4_form_factor.scat_data_source  X-ray


 loop_
     _atom_type_symbol
     _atom_type_scat_Cromer_Mann_a1
     _atom_type_scat_Cromer_Mann_b1
     _atom_type_scat_Cromer_Mann_a2
     _atom_type_scat_Cromer_Mann_b2
     _atom_type_scat_Cromer_Mann_a3
     _atom_type_scat_Cromer_Mann_b3
     _atom_type_scat_Cromer_Mann_a4
     _atom_type_scat_Cromer_Mann_b4
     _atom_type_scat_Cromer_Mann_c


  N     12.2220   0.0057   3.1346   9.8933   2.0141  28.9975   1.1672   0.5826 -11.5379
  H      0.4930  10.5109   0.3229  26.1257   0.1402   3.1424   0.0408  57.7997   0.0030
  C      2.3103  20.8439   1.0201  10.2075   1.5888   0.5687   0.8651  51.6512   0.2156
  O      3.0487  13.2771   2.2870   5.7011   1.5464   0.3239   0.8671  32.9089   0.2508
  S      6.9054   1.4679   5.2035  22.2151   1.4379   0.2536   1.5863  56.1720   1.0490
  FE    11.7738   4.7611   7.3600   0.3072   3.5235  15.3535   2.3054  76.8805   1.2805


 Number of distances         :           0
 Number of angles            :           0
 Number of torsions          :           0
 Number of planes            :           0
 Number of chirals           :           0
 Number of intervals         :           0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
                        Standard  External       All
                Bonds:      2950         0      2950
               Angles:      5345         0      5345
              Chirals:       196         0       196
               Planes:       451         0       451
             Torsions:      1553         0      1553
            Intervals:         0         0         0
--------------------------------------------------------------------------------


  Number of harmonic restraints       =            0
  Number of atoms in special position =            0
 -----------------------------------------------------


    ****                           Info from mtz file                           ****

FreeR flag                            9
Number of "free" reflections       1427
Number of   all  reflections      28041
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          28041

   Current auto weighting coefficient =    6.4996524    

 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.= 0.902 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        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Weight matrix   0.33860070    
 Actual weight    6.4996524      is applied to the X-ray term
Norm of X_ray positional gradient                44.4
Norm of Geom. positional gradient                80.6
Norm of X_ray B-factor gradient                  128.
Norm of Geom. B-factor gradient                 0.223E+05
Product of X_ray and Geom posit. gradients     -0.157E+08
 Cosine of angle between them                      -0.452
Product of X_ray and Geom B-fact gradients     -0.426E+08
 Cosine of angle between them                      -0.005


Residuals: XRAY=     0.8697E+06 GEOM=     0.2676E+05 TOTAL=     0.8965E+06
 function value    896489.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.795     1.644
Bond angles  : others                          3242     2.344     1.582
Torsion angles, period  1. refined              184     6.902     5.000
Torsion angles, period  2. refined               90    36.427    22.778
Torsion angles, period  3. refined              268    14.083    15.000
Torsion angles, period  4. refined                9    10.665    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.016     0.020
VDW repulsions: refined_atoms                   303     0.267     0.200
VDW repulsions.others                          1318     0.232     0.200
VDW; torsion: refined_atoms                     716     0.172     0.200
VDW; torsion.others                             708     0.081     0.200
HBOND: refined_atoms                            219     0.200     0.200
HBOND.others                                      3     0.082     0.200
VDW repulsions: symmetry: refined_atoms           8     0.196     0.200
VDW repulsions: symmetry: others                 23     0.175     0.200
HBOND: symmetry: refined_atoms                   22     0.200     0.200
M. chain bond B values: refined atoms           745     1.673     1.387
M. chain bond B values: others                  745     1.671     1.387
M. chain angle B values: refined atoms          926     2.616     2.067
M. chain angle B values: others                 927     2.615     2.067
S. chain bond B values: refined atoms           811     3.001     1.787
S. chain bond B values: others                  810     2.995     1.786
S. chain angle B values: refined atoms         1177     4.652     2.513
S. chain angle B values: others                1178     4.650     2.512
Long range B values: refined atoms             1839     7.129    19.547
Long range B values: others                    1746     6.862    18.015
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0443, B  =    1.2412
Partial structure    1: scale =     0.3875, B  =   48.0503
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3590 100.00   432.9   443.2  0.17  0.18     192   404.7   423.3  0.21  0.22
 0.147    6108  99.97   259.0   244.0  0.16  0.14     336   244.1   229.2  0.20  0.18
 0.244    7796 100.00   166.9   151.2  0.19  0.17     422   168.0   152.7  0.22  0.19
 0.342    9114 100.00    71.1    85.6  0.33  0.26     476    73.2    87.0  0.34  0.27
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2620   0.908    970   0.811   3590   0.882  0.943  0.9589  0.9674  0.9165  0.9331
  0.1468   5123   0.902    985   0.808   6108   0.887  1.030  0.9544  0.9676  0.9082  0.9456
  0.2444   6809   0.871    987   0.767   7796   0.858  1.055  0.9474  0.9560  0.8942  0.9355
  0.3419   8124   0.679    995   0.602   9119   0.670  0.706  0.8735  0.8699  0.8365  0.8530
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26612
Percentage observed                  =    99.9893
Percentage of free reflections       =     5.0860
Overall R factor                     =     0.1931
Free R factor                        =     0.2233
Average Fourier shell correlation    =     0.9307
AverageFree Fourier shell correlation=     0.9259
Overall weighted R factor            =     0.1671
Free weighted R factor               =     0.2033
Overall weighted R2 factor           =     0.1985
Free weighted R2 factor              =     0.2449
Average correlation coefficient      =     0.9092
Overall correlation coefficient      =     0.9578
Free correlation coefficient         =     0.9391
Cruickshanks DPI for coordinate error=     0.0970
DPI based on free R factor           =     0.0955
Overall figure of merit              =     0.8035
ML based su of positional parameters =     0.0672
ML based su of thermal parameters    =     2.0407
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    133812.41       26755.141       896489.25      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.42247283    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    871979.75    

-------------------------------------------------------------------------------
             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 =     0.0442, B  =   -0.0591
Partial structure    1: scale =     0.3876, B  =   47.6708
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1928
Free R factor                        =     0.2229
Average Fourier shell correlation    =     0.9441
AverageFree Fourier shell correlation=     0.9378
Average correlation coefficient      =     0.9104
Overall figure of merit              =     0.8431
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    132588.83       10198.418       871979.75       896489.25    


     CGMAT cycle number =      3

 Weight matrix   0.43894872    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    869472.63    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.014     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =   -0.0306
Partial structure    1: scale =     0.3884, B  =   43.5291
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1915
Free R factor                        =     0.2219
Average Fourier shell correlation    =     0.9466
AverageFree Fourier shell correlation=     0.9399
Average correlation coefficient      =     0.9128
Overall figure of merit              =     0.8503
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    132278.50       9708.3750       869472.63       871979.75    


     CGMAT cycle number =      4

 Weight matrix   0.40183231    
 Actual weight    5.9087749      is applied to the X-ray term


 function value    790667.31    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.014     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =   -0.0069
Partial structure    1: scale =     0.3885, B  =   43.2706
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1912
Free R factor                        =     0.2218
Average Fourier shell correlation    =     0.9472
AverageFree Fourier shell correlation=     0.9403
Average correlation coefficient      =     0.9138
Overall figure of merit              =     0.8514
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    132181.69       9635.5000       790667.31       869472.63    


     CGMAT cycle number =      5

 Weight matrix   0.36675414    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    719506.69    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.014     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =   -0.0014
Partial structure    1: scale =     0.3889, B  =   43.2377
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1916
Free R factor                        =     0.2217
Average Fourier shell correlation    =     0.9473
AverageFree Fourier shell correlation=     0.9405
Average correlation coefficient      =     0.9138
Overall figure of merit              =     0.8518
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    132196.02       9400.7920       719506.69       790667.31    


     CGMAT cycle number =      6

 Weight matrix   0.36624867    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    719488.88    

-------------------------------------------------------------------------------
             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 =     0.0442, B  =   -0.0150
Partial structure    1: scale =     0.3892, B  =   43.3485
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1920
Free R factor                        =     0.2218
Average Fourier shell correlation    =     0.9472
AverageFree Fourier shell correlation=     0.9405
Average correlation coefficient      =     0.9136
Overall figure of merit              =     0.8518
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    132250.78       9088.7822       719488.88       719506.69    


     CGMAT cycle number =      7

 Weight matrix   0.36609811    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    719485.69    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =   -0.0064
Partial structure    1: scale =     0.3892, B  =   43.3238
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1921
Free R factor                        =     0.2217
Average Fourier shell correlation    =     0.9472
AverageFree Fourier shell correlation=     0.9405
Average correlation coefficient      =     0.9136
Overall figure of merit              =     0.8519
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    132263.72       9016.1191       719485.69       719488.88    


     CGMAT cycle number =      8

 Weight matrix   0.36583760    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    719503.13    

-------------------------------------------------------------------------------
             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 =     0.0442, B  =   -0.0064
Partial structure    1: scale =     0.3890, B  =   43.2246
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1922
Free R factor                        =     0.2218
Average Fourier shell correlation    =     0.9472
AverageFree Fourier shell correlation=     0.9406
Average correlation coefficient      =     0.9136
Overall figure of merit              =     0.8519
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    132273.98       8984.0068       719494.19       719485.69    
 fvalues    132273.98       8984.0068       719494.19       719508.75    


     CGMAT cycle number =      9

 Weight matrix   0.36551294    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    719498.44    

-------------------------------------------------------------------------------
             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 =     0.0442, B  =   -0.0000
Partial structure    1: scale =     0.3890, B  =   43.2107
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1922
Free R factor                        =     0.2218
Average Fourier shell correlation    =     0.9472
AverageFree Fourier shell correlation=     0.9406
Average correlation coefficient      =     0.9137
Overall figure of merit              =     0.8519
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    132276.25       8961.5898       719498.44       719508.75    


     CGMAT cycle number =     10

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.905 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        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Weight matrix   0.36555037    
 Actual weight    5.3716135      is applied to the X-ray term
Norm of X_ray positional gradient                41.7
Norm of Geom. positional gradient                41.7
Norm of X_ray B-factor gradient                  113.
Norm of Geom. B-factor gradient                  113.
Product of X_ray and Geom posit. gradients     -0.168E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.410E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.7105E+06 GEOM=      8954.     TOTAL=     0.7195E+06
 function value    719497.88    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2103     1.814     1.644
Bond angles  : others                          3242     1.509     1.582
Torsion angles, period  1. refined              184     6.879     5.000
Torsion angles, period  2. refined               90    36.303    22.778
Torsion angles, period  3. refined              268    13.811    15.000
Torsion angles, period  4. refined                9    10.707    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                   297     0.271     0.200
VDW repulsions.others                          1365     0.205     0.200
VDW; torsion: refined_atoms                     726     0.173     0.200
VDW; torsion.others                             787     0.085     0.200
HBOND: refined_atoms                            220     0.198     0.200
HBOND.others                                      3     0.103     0.200
VDW repulsions: symmetry: refined_atoms           8     0.202     0.200
VDW repulsions: symmetry: others                 22     0.177     0.200
HBOND: symmetry: refined_atoms                   20     0.198     0.200
M. chain bond B values: refined atoms           745     1.721     1.504
M. chain bond B values: others                  745     1.717     1.504
M. chain angle B values: refined atoms          926     2.681     2.244
M. chain angle B values: others                 927     2.680     2.244
S. chain bond B values: refined atoms           811     3.124     1.909
S. chain bond B values: others                  810     3.119     1.909
S. chain angle B values: refined atoms         1177     4.785     2.695
S. chain angle B values: others                1178     4.783     2.694
Long range B values: refined atoms             1845     7.147    20.856
Long range B values: others                    1753     6.874    19.372
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =   -0.0003
Partial structure    1: scale =     0.3890, B  =   43.2103
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3590 100.00   433.4   443.4  0.17  0.18     192   405.2   424.0  0.20  0.22
 0.147    6108  99.97   259.2   243.9  0.16  0.14     336   244.4   229.6  0.20  0.18
 0.244    7796 100.00   167.1   151.3  0.19  0.17     422   168.2   152.9  0.22  0.19
 0.342    9114 100.00    71.2    85.3  0.32  0.26     476    73.3    87.2  0.33  0.27
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2620   0.930    970   0.842   3590   0.906  0.947  0.9663  0.9729  0.9179  0.9333
  0.1468   5123   0.908    985   0.815   6108   0.893  1.030  0.9558  0.9685  0.9085  0.9450
  0.2444   6809   0.882    987   0.780   7796   0.869  1.056  0.9514  0.9597  0.8952  0.9350
  0.3419   8124   0.797    995   0.721   9119   0.789  0.759  0.9100  0.9123  0.8429  0.8668
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26612
Percentage observed                  =    99.9893
Percentage of free reflections       =     5.0860
Overall R factor                     =     0.1922
Free R factor                        =     0.2219
Average Fourier shell correlation    =     0.9473
AverageFree Fourier shell correlation=     0.9406
Overall weighted R factor            =     0.1672
Free weighted R factor               =     0.2023
Overall weighted R2 factor           =     0.1983
Free weighted R2 factor              =     0.2438
Average correlation coefficient      =     0.9137
Overall correlation coefficient      =     0.9581
Free correlation coefficient         =     0.9399
Cruickshanks DPI for coordinate error=     0.0966
DPI based on free R factor           =     0.0949
Overall figure of merit              =     0.8519
ML based su of positional parameters =     0.0587
ML based su of thermal parameters    =     1.7379
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    132277.47       8954.4531       719497.88       719498.44    

    ****                              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.= 0.905 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_R09_1-60A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.814     1.644
Bond angles  : others                          3242     1.509     1.582
Torsion angles, period  1. refined              184     6.881     5.000
Torsion angles, period  2. refined               90    36.281    22.778
Torsion angles, period  3. refined              268    13.788    15.000
Torsion angles, period  4. refined                9    10.698    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                   296     0.271     0.200
VDW repulsions.others                          1365     0.205     0.200
VDW; torsion: refined_atoms                     726     0.173     0.200
VDW; torsion.others                             796     0.084     0.200
HBOND: refined_atoms                            220     0.198     0.200
HBOND.others                                      2     0.128     0.200
VDW repulsions: symmetry: refined_atoms           8     0.203     0.200
VDW repulsions: symmetry: others                 22     0.176     0.200
HBOND: symmetry: refined_atoms                   20     0.198     0.200
M. chain bond B values: refined atoms           745     1.721     1.504
M. chain bond B values: others                  745     1.717     1.504
M. chain angle B values: refined atoms          926     2.681     2.245
M. chain angle B values: others                 927     2.680     2.244
S. chain bond B values: refined atoms           811     3.123     1.909
S. chain bond B values: others                  810     3.118     1.909
S. chain angle B values: refined atoms         1177     4.784     2.695
S. chain angle B values: others                1178     4.782     2.695
Long range B values: refined atoms             1844     7.166    20.848
Long range B values: others                    1752     6.875    19.368
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =   -0.0002
Partial structure    1: scale =     0.3890, B  =   43.2159
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3590 100.00   433.4   443.4  0.17  0.18     192   405.2   424.2  0.20  0.22
 0.147    6108  99.97   259.2   243.9  0.16  0.14     336   244.4   229.6  0.20  0.18
 0.244    7796 100.00   167.1   151.3  0.19  0.17     422   168.2   152.9  0.22  0.19
 0.342    9114 100.00    71.2    85.3  0.32  0.26     476    73.3    87.1  0.33  0.27
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2620   0.930    970   0.842   3590   0.906  0.947  0.9663  0.9729  0.9180  0.9333
  0.1468   5123   0.908    985   0.815   6108   0.893  1.030  0.9558  0.9685  0.9085  0.9450
  0.2444   6809   0.882    987   0.780   7796   0.869  1.056  0.9514  0.9597  0.8953  0.9350
  0.3419   8124   0.797    995   0.721   9119   0.789  0.759  0.9100  0.9123  0.8429  0.8669
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26612
Percentage observed                  =    99.9893
Percentage of free reflections       =     5.0860
Overall R factor                     =     0.1923
Free R factor                        =     0.2219
Average Fourier shell correlation    =     0.9473
AverageFree Fourier shell correlation=     0.9406
Overall weighted R factor            =     0.1673
Free weighted R factor               =     0.2024
Overall weighted R2 factor           =     0.1984
Free weighted R2 factor              =     0.2437
Average correlation coefficient      =     0.9137
Overall correlation coefficient      =     0.9581
Free correlation coefficient         =     0.9399
Cruickshanks DPI for coordinate error=     0.0966
DPI based on free R factor           =     0.0949
Overall figure of merit              =     0.8519
ML based su of positional parameters =     0.0587
ML based su of thermal parameters    =     1.7379
-----------------------------------------------------------------------------
  Time in seconds: CPU =        17.91
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1931   0.2233   0.804      133812.    7298.6   0.0128  0.955   1.795  1.039   0.088
       1   0.1928   0.2229   0.843      132589.    7257.4   0.0131  0.977   1.796  1.041   0.088
       2   0.1915   0.2219   0.850      132279.    7246.0   0.0142  1.058   1.846  1.070   0.091
       3   0.1912   0.2218   0.851      132182.    7242.5   0.0144  1.076   1.876  1.087   0.092
       4   0.1916   0.2217   0.852      132196.    7241.5   0.0139  1.034   1.861  1.078   0.090
       5   0.1920   0.2218   0.852      132251.    7242.4   0.0132  0.989   1.831  1.059   0.088
       6   0.1921   0.2217   0.852      132264.    7242.1   0.0132  0.985   1.820  1.053   0.088
       7   0.1922   0.2218   0.852      132273.    7242.2   0.0132  0.983   1.816  1.051   0.088
       8   0.1922   0.2218   0.852      132276.    7241.8   0.0132  0.983   1.815  1.050   0.088
       9   0.1922   0.2219   0.852      132277.    7242.1   0.0132  0.983   1.814  1.050   0.088
      10   0.1923   0.2219   0.852      132277.    7241.9   0.0131  0.982   1.814  1.050   0.088
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1931   0.1923
             R free    0.2233   0.2219
     Rms BondLength    0.0128   0.0131
      Rms BondAngle    1.7945   1.8138
     Rms ChirVolume    0.0879   0.0884
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      49.9s System:    0.1s Elapsed:     0:51