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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: 17:54:32 


 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 8
  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_R08_1-70A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R08_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_R08_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:     8
  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_R08_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=   2.052 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=   2.193 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=   1.832 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=   2.210 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=   2.397 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=   2.387 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=   2.033 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  PRO               190  AAA  is missing in the structure
  Number of chains                  :       4
  Total number of monomers          :     502
  Number of atoms                   :    3945
  Number of missing atoms           :       1
  Number of rebuilt atoms           :    1480
  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:      2949         0      2949
               Angles:      5344         0      5344
              Chirals:       196         0       196
               Planes:       453         0       453
             Torsions:      1556         0      1556
            Intervals:         0         0         0
--------------------------------------------------------------------------------


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


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

FreeR flag                            8
Number of "free" reflections       1404
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.= 0.899 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   0.31968910    
 Actual weight    6.4996524      is applied to the X-ray term
Norm of X_ray positional gradient                41.9
Norm of Geom. positional gradient                79.5
Norm of X_ray B-factor gradient                  126.
Norm of Geom. B-factor gradient                  115.
Product of X_ray and Geom posit. gradients     -0.136E+08
 Cosine of angle between them                      -0.421
Product of X_ray and Geom B-fact gradients     -0.388E+08
 Cosine of angle between them                      -0.831


Residuals: XRAY=     0.8711E+06 GEOM=     0.1314E+05 TOTAL=     0.8843E+06
 function value    884279.88    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.035     0.017
Bond angles  : refined atoms                   2106     1.764     1.644
Bond angles  : others                          3238     2.352     1.580
Torsion angles, period  1. refined              185     6.910     5.000
Torsion angles, period  2. refined               90    36.162    22.778
Torsion angles, period  3. refined              268    13.630    15.000
Torsion angles, period  4. refined                9    11.516    15.000
Chiral centres: refined atoms                   196     0.089     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.014     0.020
VDW repulsions: refined_atoms                   293     0.247     0.200
VDW repulsions.others                          1317     0.221     0.200
VDW; torsion: refined_atoms                     728     0.171     0.200
VDW; torsion.others                             716     0.081     0.200
HBOND: refined_atoms                            215     0.194     0.200
HBOND.others                                      1     0.026     0.200
VDW repulsions: symmetry: refined_atoms          10     0.187     0.200
VDW repulsions: symmetry: others                 22     0.196     0.200
HBOND: symmetry: refined_atoms                   20     0.195     0.200
M. chain bond B values: refined atoms           746     1.646     1.394
M. chain bond B values: others                  746     1.643     1.394
M. chain angle B values: refined atoms          929     2.619     2.081
M. chain angle B values: others                 930     2.618     2.081
S. chain bond B values: refined atoms           811     2.959     1.785
S. chain bond B values: others                  810     2.950     1.784
S. chain angle B values: refined atoms         1177     4.570     2.511
S. chain angle B values: others                1178     4.568     2.511
Long range B values: refined atoms             1839     6.984    19.368
Long range B values: others                    1748     6.678    17.959
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =    1.1987
Partial structure    1: scale =     0.3835, B  =   42.1540
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.42 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3592 100.00   433.0   443.2  0.17  0.17     190   430.0   438.5  0.21  0.21
 0.147    6118  99.97   258.9   243.5  0.17  0.15     326   259.8   244.5  0.21  0.19
 0.244    7809 100.00   167.6   151.7  0.19  0.17     409   165.0   149.5  0.22  0.20
 0.342    9111 100.00    71.5    85.9  0.33  0.26     479    70.2    83.3  0.34  0.27
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2621   0.917    971   0.815   3592   0.890  0.947  0.9630  0.9703  0.9103  0.9370
  0.1468   5128   0.881    990   0.784   6118   0.865  1.023  0.9498  0.9608  0.9012  0.9395
  0.2444   6815   0.869    994   0.760   7809   0.855  1.056  0.9411  0.9552  0.8827  0.9366
  0.3419   8126   0.708    990   0.626   9116   0.699  0.721  0.8680  0.8797  0.8422  0.8545
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26634
Percentage observed                  =    99.9893
Percentage of free reflections       =     5.0075
Overall R factor                     =     0.1935
Free R factor                        =     0.2290
Average Fourier shell correlation    =     0.9327
AverageFree Fourier shell correlation=     0.9211
Overall weighted R factor            =     0.1680
Free weighted R factor               =     0.2034
Overall weighted R2 factor           =     0.1996
Free weighted R2 factor              =     0.2355
Average correlation coefficient      =     0.9092
Overall correlation coefficient      =     0.9579
Free correlation coefficient         =     0.9396
Cruickshanks DPI for coordinate error=     0.0972
DPI based on free R factor           =     0.0979
Overall figure of merit              =     0.8085
ML based su of positional parameters =     0.0691
ML based su of thermal parameters    =     2.0676
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    134028.22       13143.033       884279.88      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.39509422    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    872848.94    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0595
Partial structure    1: scale =     0.3837, B  =   42.4573
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1929
Free R factor                        =     0.2277
Average Fourier shell correlation    =     0.9427
AverageFree Fourier shell correlation=     0.9315
Average correlation coefficient      =     0.9106
Overall figure of merit              =     0.8376
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    133021.97       8252.3535       872848.94       884279.88    


     CGMAT cycle number =      3

 Weight matrix   0.40698814    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    871687.75    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0198
Partial structure    1: scale =     0.3841, B  =   42.6549
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1919
Free R factor                        =     0.2271
Average Fourier shell correlation    =     0.9446
AverageFree Fourier shell correlation=     0.9332
Average correlation coefficient      =     0.9128
Overall figure of merit              =     0.8425
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    132748.20       8870.5889       871687.75       872848.94    


     CGMAT cycle number =      4

 Weight matrix   0.40895835    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    871419.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.014     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0003
Partial structure    1: scale =     0.3841, B  =   42.6604
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1917
Free R factor                        =     0.2271
Average Fourier shell correlation    =     0.9450
AverageFree Fourier shell correlation=     0.9335
Average correlation coefficient      =     0.9136
Overall figure of merit              =     0.8433
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    132671.75       9099.0127       871419.25       871687.75    


     CGMAT cycle number =      5

 Weight matrix   0.37357894    
 Actual weight    5.9087749      is applied to the X-ray term


 function value    792865.75    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.014     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0085
Partial structure    1: scale =     0.3840, B  =   42.7692
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1916
Free R factor                        =     0.2270
Average Fourier shell correlation    =     0.9453
AverageFree Fourier shell correlation=     0.9338
Average correlation coefficient      =     0.9141
Overall figure of merit              =     0.8438
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    132628.59       9193.2529       792865.75       871419.25    


     CGMAT cycle number =      6

 Weight matrix   0.33976874    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    721537.38    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0114
Partial structure    1: scale =     0.3838, B  =   42.7514
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1920
Free R factor                        =     0.2270
Average Fourier shell correlation    =     0.9452
AverageFree Fourier shell correlation=     0.9338
Average correlation coefficient      =     0.9139
Overall figure of merit              =     0.8439
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    132657.77       8951.1387       721537.38       792865.75    


     CGMAT cycle number =      7

 Weight matrix   0.33891553    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    721539.50    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0097
Partial structure    1: scale =     0.3837, B  =   42.7163
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1925
Free R factor                        =     0.2270
Average Fourier shell correlation    =     0.9451
AverageFree Fourier shell correlation=     0.9338
Average correlation coefficient      =     0.9135
Overall figure of merit              =     0.8437
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    132721.44       8617.3857       721535.06       721537.38    
 fvalues    132721.44       8617.3857       721535.06       721545.63    


     CGMAT cycle number =      8

 Weight matrix   0.33912337    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    721528.44    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0069
Partial structure    1: scale =     0.3837, B  =   42.6379
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1927
Free R factor                        =     0.2271
Average Fourier shell correlation    =     0.9450
AverageFree Fourier shell correlation=     0.9338
Average correlation coefficient      =     0.9134
Overall figure of merit              =     0.8437
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    132734.77       8528.5869       721528.44       721545.63    


     CGMAT cycle number =      9

 Weight matrix   0.33868045    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    721531.38    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0045
Partial structure    1: scale =     0.3837, B  =   42.5632
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1927
Free R factor                        =     0.2271
Average Fourier shell correlation    =     0.9450
AverageFree Fourier shell correlation=     0.9337
Average correlation coefficient      =     0.9134
Overall figure of merit              =     0.8436
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    132743.30       8486.6846       721543.75       721528.44    

 fvalues    132743.30       8486.6846       721525.81       721532.38    
 fvalues    132743.30       8486.6846       721525.81       721532.38    


     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.= 0.909 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   0.33843315    
 Actual weight    5.3716135      is applied to the X-ray term
Norm of X_ray positional gradient                39.2
Norm of Geom. positional gradient                39.3
Norm of X_ray B-factor gradient                  110.
Norm of Geom. B-factor gradient                  111.
Product of X_ray and Geom posit. gradients     -0.149E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.392E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.7131E+06 GEOM=      8477.     TOTAL=     0.7215E+06
 function value    721542.56    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.770     1.644
Bond angles  : others                          3238     1.503     1.580
Torsion angles, period  1. refined              185     6.881     5.000
Torsion angles, period  2. refined               90    35.888    22.778
Torsion angles, period  3. refined              268    13.116    15.000
Torsion angles, period  4. refined                9    11.332    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   293     0.247     0.200
VDW repulsions.others                          1352     0.194     0.200
VDW; torsion: refined_atoms                     720     0.173     0.200
VDW; torsion.others                             785     0.083     0.200
HBOND: refined_atoms                            215     0.199     0.200
HBOND.others                                      1     0.071     0.200
VDW repulsions: symmetry: refined_atoms           9     0.190     0.200
VDW repulsions: symmetry: others                 23     0.187     0.200
HBOND: symmetry: refined_atoms                   23     0.173     0.200
M. chain bond B values: refined atoms           746     1.713     1.511
M. chain bond B values: others                  746     1.709     1.511
M. chain angle B values: refined atoms          929     2.689     2.259
M. chain angle B values: others                 930     2.688     2.258
S. chain bond B values: refined atoms           811     3.054     1.902
S. chain bond B values: others                  810     3.047     1.902
S. chain angle B values: refined atoms         1177     4.668     2.688
S. chain angle B values: others                1178     4.666     2.688
Long range B values: refined atoms             1833     7.019    20.807
Long range B values: others                    1738     6.710    19.282
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0021
Partial structure    1: scale =     0.3836, B  =   42.5336
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3592 100.00   433.0   443.5  0.17  0.18     190   430.0   438.8  0.21  0.22
 0.147    6118  99.97   258.9   243.4  0.17  0.15     326   259.8   244.2  0.21  0.18
 0.244    7809 100.00   167.6   151.6  0.19  0.17     409   165.0   149.7  0.22  0.19
 0.342    9111 100.00    71.5    85.5  0.32  0.26     479    70.2    82.9  0.34  0.27
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2621   0.930    971   0.837   3592   0.905  0.948  0.9662  0.9736  0.9091  0.9369
  0.1468   5128   0.886    990   0.789   6118   0.871  1.023  0.9516  0.9618  0.9036  0.9393
  0.2444   6815   0.883    994   0.776   7809   0.869  1.057  0.9480  0.9600  0.8897  0.9368
  0.3419   8126   0.788    990   0.707   9116   0.779  0.756  0.8964  0.9096  0.8426  0.8666
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26634
Percentage observed                  =    99.9893
Percentage of free reflections       =     5.0075
Overall R factor                     =     0.1927
Free R factor                        =     0.2271
Average Fourier shell correlation    =     0.9450
AverageFree Fourier shell correlation=     0.9337
Overall weighted R factor            =     0.1683
Free weighted R factor               =     0.2026
Overall weighted R2 factor           =     0.2005
Free weighted R2 factor              =     0.2365
Average correlation coefficient      =     0.9134
Overall correlation coefficient      =     0.9582
Free correlation coefficient         =     0.9402
Cruickshanks DPI for coordinate error=     0.0968
DPI based on free R factor           =     0.0971
Overall figure of merit              =     0.8436
ML based su of positional parameters =     0.0610
ML based su of thermal parameters    =     1.7866
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    132746.92       8476.6328       721531.81       721532.38    
 fvalues    132746.92       8476.6328       721531.81       721541.81    

    ****                              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.= 0.910 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_R08_1-60A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.769     1.644
Bond angles  : others                          3238     1.503     1.580
Torsion angles, period  1. refined              185     6.881     5.000
Torsion angles, period  2. refined               90    35.872    22.778
Torsion angles, period  3. refined              268    13.097    15.000
Torsion angles, period  4. refined                9    11.330    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   293     0.247     0.200
VDW repulsions.others                          1352     0.193     0.200
VDW; torsion: refined_atoms                     721     0.173     0.200
VDW; torsion.others                             788     0.083     0.200
HBOND: refined_atoms                            215     0.199     0.200
HBOND.others                                      1     0.072     0.200
VDW repulsions: symmetry: refined_atoms           9     0.190     0.200
VDW repulsions: symmetry: others                 23     0.187     0.200
HBOND: symmetry: refined_atoms                   23     0.173     0.200
M. chain bond B values: refined atoms           746     1.712     1.511
M. chain bond B values: others                  746     1.708     1.512
M. chain angle B values: refined atoms          929     2.687     2.259
M. chain angle B values: others                 930     2.686     2.259
S. chain bond B values: refined atoms           811     3.052     1.902
S. chain bond B values: others                  810     3.044     1.901
S. chain angle B values: refined atoms         1177     4.664     2.688
S. chain angle B values: others                1178     4.662     2.687
Long range B values: refined atoms             1833     7.013    20.806
Long range B values: others                    1738     6.704    19.283
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0024
Partial structure    1: scale =     0.3836, B  =   42.5489
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3592 100.00   433.0   443.5  0.17  0.18     190   430.0   438.8  0.21  0.22
 0.147    6118  99.97   258.9   243.4  0.17  0.15     326   259.8   244.2  0.21  0.18
 0.244    7809 100.00   167.6   151.6  0.19  0.17     409   165.0   149.6  0.22  0.19
 0.342    9111 100.00    71.5    85.5  0.32  0.26     479    70.2    82.9  0.34  0.27
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2621   0.929    971   0.837   3592   0.904  0.948  0.9661  0.9735  0.9089  0.9369
  0.1468   5128   0.886    990   0.789   6118   0.871  1.023  0.9516  0.9618  0.9036  0.9392
  0.2444   6815   0.883    994   0.776   7809   0.869  1.057  0.9480  0.9600  0.8898  0.9368
  0.3419   8126   0.788    990   0.707   9116   0.779  0.756  0.8964  0.9096  0.8425  0.8666
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26634
Percentage observed                  =    99.9893
Percentage of free reflections       =     5.0075
Overall R factor                     =     0.1927
Free R factor                        =     0.2272
Average Fourier shell correlation    =     0.9450
AverageFree Fourier shell correlation=     0.9337
Overall weighted R factor            =     0.1684
Free weighted R factor               =     0.2027
Overall weighted R2 factor           =     0.2006
Free weighted R2 factor              =     0.2366
Average correlation coefficient      =     0.9134
Overall correlation coefficient      =     0.9582
Free correlation coefficient         =     0.9402
Cruickshanks DPI for coordinate error=     0.0968
DPI based on free R factor           =     0.0971
Overall figure of merit              =     0.8435
ML based su of positional parameters =     0.0610
ML based su of thermal parameters    =     1.7866
-----------------------------------------------------------------------------
  Time in seconds: CPU =        21.80
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1935   0.2290   0.809      134028.    7216.3   0.0122  0.913   1.764  1.027   0.089
       1   0.1929   0.2277   0.838      133022.    7178.8   0.0124  0.922   1.756  1.024   0.088
       2   0.1919   0.2271   0.842      132748.    7170.4   0.0133  0.997   1.807  1.055   0.090
       3   0.1917   0.2271   0.843      132672.    7167.7   0.0135  1.012   1.832  1.069   0.091
       4   0.1916   0.2270   0.844      132629.    7166.1   0.0136  1.016   1.845  1.077   0.092
       5   0.1920   0.2270   0.844      132658.    7165.9   0.0130  0.975   1.822  1.063   0.090
       6   0.1925   0.2270   0.844      132720.    7166.2   0.0124  0.930   1.786  1.042   0.088
       7   0.1927   0.2271   0.844      132735.    7166.3   0.0123  0.924   1.775  1.035   0.087
       8   0.1927   0.2271   0.844      132743.    7166.9   0.0123  0.922   1.771  1.033   0.087
       9   0.1927   0.2271   0.844      132747.    7167.0   0.0123  0.922   1.770  1.033   0.087
      10   0.1927   0.2272   0.844      132751.    7167.5   0.0123  0.921   1.769  1.032   0.087
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1935   0.1927
             R free    0.2290   0.2272
     Rms BondLength    0.0122   0.0123
      Rms BondAngle    1.7638   1.7690
     Rms ChirVolume    0.0889   0.0868
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      53.8s System:    0.1s Elapsed:     0:54