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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: 10:53:46 


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


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

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

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

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

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

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

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

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

  Data line--- make     check NONE
  Data line--- refi     type REST reso 41.96 1.42     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- bins 4
  Data line--- ncyc 10
  Data line--- monitor MEDIum
  Data line--- free 0
  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_step0-10A_R00_1-50A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-10A_R00_1-42A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_step0-10A_R00_1-42A.mtz

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

  Refinement type                        : Restrained

    ****                           Makecif parameters                           ****

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


  Residual                               : Rice Maximum Likelihood for Fs

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

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


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

No map sharpening will be performed

  Method of minimisation                 : Sparse Matrix
  Experimental sigmas used for weighting
  Number of Bins and width:     4       0.1240
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.4200
  Estimated number of reflections :      51186
  Free R exclusion - flag equals:     0
  Auto weighting. An attempt
  Refinement cycles       :    10
  Scaling type                           :
          Wilson scaling type with Guassians

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

  Scaling and SigmaA resln:    41.9635  1.4200

  Damping factors:     1.0000  1.0000  1.0000


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


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

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

 Chiral centers
          Weight= 1.00

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

 TORSION ANGLES
          Weight= 1.00

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

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

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

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

 Input file :CDO_step0-10A_R00_1-50A.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.51
 _lib_update       11/07/18
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 24624
                with complete description    : 24624
  NUMBER OF MODIFICATIONS                    :    70
  NUMBER OF LINKS                            :    77
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  Number of atoms    :    1836
  Number of residues :     502
  Number of chains   :       4
  I am reading library. Please wait.
                mon_lib.cif
  INFO:     link is found (not be used) dist=   2.055 ideal_dist=   2.090
            ch:AAA  res:  86  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.195 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=   1.822 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=   2.223 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=   2.413 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=   2.390 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=   2.101 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:22-OCT-19
  --------------------------------
  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                            0
Number of "free" reflections       2004
Number of   all  reflections      39817
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          39817

   Current auto weighting coefficient =    6.0498405    

 mode : HKRF


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



     CGMAT cycle number =      1

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.886 id.= 3.000 dev= -2.11 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  288
 Maximuum H,K,L                 :    41   41   87
 Minimum acceptable grid spacing:    91   91  192
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  288
 Maximuum H,K,L                 :    41   41   87
 Minimum acceptable grid spacing:    91   91  192
 Weight matrix   0.24972713    
 Actual weight    6.0498405      is applied to the X-ray term
Norm of X_ray positional gradient                35.6
Norm of Geom. positional gradient                82.9
Norm of X_ray B-factor gradient                  90.5
Norm of Geom. B-factor gradient                  104.
Product of X_ray and Geom posit. gradients     -0.144E+08
 Cosine of angle between them                      -0.503
Product of X_ray and Geom B-fact gradients     -0.275E+08
 Cosine of angle between them                      -0.908


Residuals: XRAY=     0.1067E+07 GEOM=     0.1333E+05 TOTAL=     0.1080E+07
 function value    1080132.5    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.035     0.017
Bond angles  : refined atoms                   2106     1.852     1.644
Bond angles  : others                          3238     2.370     1.580
Torsion angles, period  1. refined              185     6.835     5.000
Torsion angles, period  2. refined               90    35.385    22.778
Torsion angles, period  3. refined              268    13.700    15.000
Torsion angles, period  4. refined                9    12.292    15.000
Chiral centres: refined atoms                   196     0.091     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.018     0.020
VDW repulsions: refined_atoms                   296     0.249     0.200
VDW repulsions.others                          1334     0.220     0.200
VDW; torsion: refined_atoms                     722     0.174     0.200
VDW; torsion.others                             725     0.083     0.200
HBOND: refined_atoms                            202     0.194     0.200
VDW repulsions: symmetry: refined_atoms           8     0.201     0.200
VDW repulsions: symmetry: others                 21     0.212     0.200
HBOND: symmetry: refined_atoms                   19     0.174     0.200
M. chain bond B values: refined atoms           746     1.821     1.619
M. chain bond B values: others                  746     1.816     1.619
M. chain angle B values: refined atoms          929     2.815     2.419
M. chain angle B values: others                 930     2.814     2.419
S. chain bond B values: refined atoms           811     3.263     2.038
S. chain bond B values: others                  810     3.258     2.037
S. chain angle B values: refined atoms         1177     4.957     2.883
S. chain angle B values: others                1178     4.955     2.882
Long range B values: refined atoms             1825     7.094    21.923
Long range B values: others                    1742     6.867    20.547
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =    0.7661
Partial structure    1: scale =     0.3928, B  =   36.8854
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5089 100.00   380.5   390.1  0.17  0.18     240   375.6   378.6  0.22  0.22
 0.186    8652  99.98   205.6   181.7  0.19  0.17     491   214.3   189.7  0.23  0.20
 0.310   11047 100.00    92.0    88.6  0.23  0.20     600    92.2    89.1  0.27  0.24
 0.434   12831  98.63    38.7    48.0  0.47  0.46     664    39.1    48.9  0.47  0.46
$$

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

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3846   0.894   1243   0.782   5089   0.867  0.947  0.9554  0.9652  0.9006  0.9356
  0.1863   7407   0.862   1245   0.761   8652   0.847  1.094  0.9470  0.9552  0.9018  0.9358
  0.3102   9814   0.799   1233   0.720  11047   0.790  0.950  0.9238  0.9314  0.8847  0.9138
  0.4340  11579   0.427   1252   0.378  12831   0.422  0.403  0.6569  0.6348  0.6785  0.6427
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37619
Percentage observed                  =    99.4927
Percentage of free reflections       =     5.0361
Overall R factor                     =     0.2187
Free R factor                        =     0.2541
Average Fourier shell correlation    =     0.8403
AverageFree Fourier shell correlation=     0.8445
Overall weighted R factor            =     0.1831
Free weighted R factor               =     0.2175
Overall weighted R2 factor           =     0.2116
Free weighted R2 factor              =     0.2510
Average correlation coefficient      =     0.8294
Overall correlation coefficient      =     0.9599
Free correlation coefficient         =     0.9417
Cruickshanks DPI for coordinate error=     0.0780
DPI based on free R factor           =     0.0812
Overall figure of merit              =     0.6883
ML based su of positional parameters =     0.0754
ML based su of thermal parameters    =     2.1545
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    176336.16       13326.874       1080132.5      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.31726983    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1067886.8    

-------------------------------------------------------------------------------
             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 =     0.0466, B  =   -0.0614
Partial structure    1: scale =     0.3926, B  =   36.9122
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2193
Free R factor                        =     0.2533
Average Fourier shell correlation    =     0.8527
AverageFree Fourier shell correlation=     0.8565
Average correlation coefficient      =     0.8284
Overall figure of merit              =     0.7100
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    175204.25       7929.0146       1067886.8       1080132.5    


     CGMAT cycle number =      3

 Weight matrix   0.32333118    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1067225.4    

-------------------------------------------------------------------------------
             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 =     0.0466, B  =   -0.0059
Partial structure    1: scale =     0.3932, B  =   36.8859
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2184
Free R factor                        =     0.2534
Average Fourier shell correlation    =     0.8559
AverageFree Fourier shell correlation=     0.8592
Average correlation coefficient      =     0.8293
Overall figure of merit              =     0.7134
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    175009.58       8445.4180       1067225.4       1067886.8    


     CGMAT cycle number =      4

 Weight matrix   0.32380730    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1067088.3    

-------------------------------------------------------------------------------
             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 =     0.0466, B  =    0.0001
Partial structure    1: scale =     0.3932, B  =   36.8939
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2184
Free R factor                        =     0.2534
Average Fourier shell correlation    =     0.8567
AverageFree Fourier shell correlation=     0.8598
Average correlation coefficient      =     0.8297
Overall figure of merit              =     0.7142
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    174971.52       8538.4980       1067088.3       1067225.4    


     CGMAT cycle number =      5

 Weight matrix   0.32385269    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1067043.3    

-------------------------------------------------------------------------------
             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 =     0.0466, B  =    0.0074
Partial structure    1: scale =     0.3937, B  =   36.8732
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2183
Free R factor                        =     0.2534
Average Fourier shell correlation    =     0.8568
AverageFree Fourier shell correlation=     0.8598
Average correlation coefficient      =     0.8299
Overall figure of merit              =     0.7143
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    174958.47       8572.3281       1067043.3       1067088.3    


     CGMAT cycle number =      6

 Weight matrix   0.32366443    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1067069.1    

-------------------------------------------------------------------------------
             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 =     0.0466, B  =    0.0046
Partial structure    1: scale =     0.3939, B  =   36.9818
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2183
Free R factor                        =     0.2534
Average Fourier shell correlation    =     0.8568
AverageFree Fourier shell correlation=     0.8598
Average correlation coefficient      =     0.8300
Overall figure of merit              =     0.7142
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    174962.41       8580.4551       1067091.1       1067043.3    

 fvalues    174962.41       8580.4551       1067087.1       1067075.1    
 fvalues    174962.41       8580.4551       1067087.1       1067075.1    


     CGMAT cycle number =      7

 Weight matrix   0.32389352    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1067067.6    

-------------------------------------------------------------------------------
             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 =     0.0466, B  =    0.0000
Partial structure    1: scale =     0.3940, B  =   37.0067
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2183
Free R factor                        =     0.2534
Average Fourier shell correlation    =     0.8569
AverageFree Fourier shell correlation=     0.8598
Average correlation coefficient      =     0.8300
Overall figure of merit              =     0.7143
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    174961.34       8579.4170       1067067.6       1067075.1    


     CGMAT cycle number =      8

 Weight matrix   0.32356110    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1067083.0    

-------------------------------------------------------------------------------
             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 =     0.0466, B  =    0.0026
Partial structure    1: scale =     0.3940, B  =   37.0055
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2183
Free R factor                        =     0.2535
Average Fourier shell correlation    =     0.8568
AverageFree Fourier shell correlation=     0.8598
Average correlation coefficient      =     0.8300
Overall figure of merit              =     0.7142
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    174964.14       8574.8828       1067094.1       1067067.6    

 fvalues    174964.14       8574.8828       1067092.4       1067080.0    
 fvalues    174964.14       8574.8828       1067092.4       1067080.0    


     CGMAT cycle number =      9

 Weight matrix   0.32369068    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1067074.5    

-------------------------------------------------------------------------------
             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 =     0.0466, B  =    0.0009
Partial structure    1: scale =     0.3940, B  =   37.0053
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2183
Free R factor                        =     0.2535
Average Fourier shell correlation    =     0.8568
AverageFree Fourier shell correlation=     0.8598
Average correlation coefficient      =     0.8300
Overall figure of merit              =     0.7143
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    174963.30       8574.4902       1067074.5       1067080.0    


     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        :   144  144  288
 Maximuum H,K,L                 :    41   41   87
 Minimum acceptable grid spacing:    91   91  192
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  288
 Maximuum H,K,L                 :    41   41   87
 Minimum acceptable grid spacing:    91   91  192
 Weight matrix   0.32337743    
 Actual weight    6.0498405      is applied to the X-ray term
Norm of X_ray positional gradient                43.0
Norm of Geom. positional gradient                43.1
Norm of X_ray B-factor gradient                  102.
Norm of Geom. B-factor gradient                  102.
Product of X_ray and Geom posit. gradients     -0.179E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.336E+08
 Cosine of angle between them                      -0.999


Residuals: XRAY=     0.1059E+07 GEOM=      8574.     TOTAL=     0.1067E+07
 function value    1067087.3    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2106     1.840     1.644
Bond angles  : others                          3238     1.512     1.580
Torsion angles, period  1. refined              185     6.820     5.000
Torsion angles, period  2. refined               90    35.264    22.778
Torsion angles, period  3. refined              268    13.677    15.000
Torsion angles, period  4. refined                9    12.163    15.000
Chiral centres: refined atoms                   196     0.091     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   297     0.248     0.200
VDW repulsions.others                          1356     0.194     0.200
VDW; torsion: refined_atoms                     724     0.174     0.200
VDW; torsion.others                             757     0.086     0.200
HBOND: refined_atoms                            202     0.192     0.200
VDW repulsions: symmetry: refined_atoms           8     0.198     0.200
VDW repulsions: symmetry: others                 22     0.190     0.200
HBOND: symmetry: refined_atoms                   18     0.169     0.200
M. chain bond B values: refined atoms           746     1.851     1.695
M. chain bond B values: others                  746     1.846     1.695
M. chain angle B values: refined atoms          929     2.842     2.533
M. chain angle B values: others                 930     2.841     2.533
S. chain bond B values: refined atoms           811     3.295     2.117
S. chain bond B values: others                  810     3.290     2.116
S. chain angle B values: refined atoms         1177     5.001     3.000
S. chain angle B values: others                1178     4.999     2.999
Long range B values: refined atoms             1827     7.177    22.939
Long range B values: others                    1742     6.923    21.508
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =    0.0056
Partial structure    1: scale =     0.3941, B  =   36.9082
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10.  v. resln :N:1,6,7,11,12:
:Cycle   10.  and  v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5089 100.00   380.8   390.2  0.17  0.18     240   375.8   379.1  0.22  0.22
 0.186    8652  99.98   205.8   182.0  0.19  0.17     491   214.4   189.7  0.23  0.20
 0.310   11047 100.00    92.0    88.7  0.23  0.20     600    92.2    89.3  0.27  0.24
 0.434   12831  98.63    38.7    48.0  0.47  0.46     664    39.1    48.9  0.47  0.46
$$

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

 $TABLE: Cycle   10. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3846   0.910   1243   0.807   5089   0.885  0.949  0.9603  0.9696  0.9009  0.9354
  0.1863   7407   0.882   1245   0.781   8652   0.868  1.096  0.9516  0.9602  0.9023  0.9361
  0.3102   9814   0.829   1233   0.753  11047   0.820  0.960  0.9335  0.9410  0.8868  0.9147
  0.4340  11579   0.456   1252   0.409  12831   0.452  0.418  0.6887  0.6698  0.6789  0.6437
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37619
Percentage observed                  =    99.4927
Percentage of free reflections       =     5.0361
Overall R factor                     =     0.2183
Free R factor                        =     0.2535
Average Fourier shell correlation    =     0.8568
AverageFree Fourier shell correlation=     0.8597
Overall weighted R factor            =     0.1829
Free weighted R factor               =     0.2172
Overall weighted R2 factor           =     0.2114
Free weighted R2 factor              =     0.2506
Average correlation coefficient      =     0.8300
Overall correlation coefficient      =     0.9600
Free correlation coefficient         =     0.9420
Cruickshanks DPI for coordinate error=     0.0778
DPI based on free R factor           =     0.0810
Overall figure of merit              =     0.7142
ML based su of positional parameters =     0.0662
ML based su of thermal parameters    =     1.8874
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    174965.09       8574.1895       1067092.3       1067074.5    

 fvalues    174965.09       8574.1895       1067083.1       1067085.1    
 fvalues    174965.09       8574.1895       1067083.1       1067085.1    

    ****                              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.= 0.909 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
          28          24          36  0.70425701      2.37302221E-02  0.70425248    
          36           8          36  0.70425701      2.37302221E-02  0.70425248    

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_step0-10A_R00_1-42A.mtz 




-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2106     1.840     1.644
Bond angles  : others                          3238     1.512     1.580
Torsion angles, period  1. refined              185     6.820     5.000
Torsion angles, period  2. refined               90    35.261    22.778
Torsion angles, period  3. refined              268    13.678    15.000
Torsion angles, period  4. refined                9    12.163    15.000
Chiral centres: refined atoms                   196     0.091     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   297     0.248     0.200
VDW repulsions.others                          1356     0.194     0.200
VDW; torsion: refined_atoms                     724     0.174     0.200
VDW; torsion.others                             757     0.086     0.200
HBOND: refined_atoms                            203     0.192     0.200
VDW repulsions: symmetry: refined_atoms           8     0.198     0.200
VDW repulsions: symmetry: others                 22     0.190     0.200
HBOND: symmetry: refined_atoms                   18     0.169     0.200
M. chain bond B values: refined atoms           746     1.851     1.695
M. chain bond B values: others                  746     1.846     1.695
M. chain angle B values: refined atoms          929     2.842     2.533
M. chain angle B values: others                 930     2.841     2.533
S. chain bond B values: refined atoms           811     3.295     2.117
S. chain bond B values: others                  810     3.290     2.116
S. chain angle B values: refined atoms         1177     5.001     3.000
S. chain angle B values: others                1178     4.998     2.999
Long range B values: refined atoms             1828     7.188    22.969
Long range B values: others                    1742     6.923    21.508
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =    0.0058
Partial structure    1: scale =     0.3941, B  =   36.8987
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5089 100.00   380.8   390.2  0.17  0.18     240   375.8   379.1  0.22  0.22
 0.186    8652  99.98   205.8   182.0  0.19  0.17     491   214.4   189.7  0.23  0.20
 0.310   11047 100.00    92.0    88.7  0.23  0.20     600    92.2    89.3  0.27  0.24
 0.434   12831  98.63    38.7    48.0  0.47  0.46     664    39.1    48.9  0.47  0.46
$$

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

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3846   0.910   1243   0.807   5089   0.885  0.949  0.9603  0.9696  0.9009  0.9354
  0.1863   7407   0.882   1245   0.781   8652   0.868  1.096  0.9516  0.9602  0.9023  0.9362
  0.3102   9814   0.829   1233   0.753  11047   0.820  0.960  0.9336  0.9410  0.8868  0.9147
  0.4340  11579   0.456   1252   0.409  12831   0.452  0.418  0.6887  0.6698  0.6789  0.6437
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37619
Percentage observed                  =    99.4927
Percentage of free reflections       =     5.0361
Overall R factor                     =     0.2183
Free R factor                        =     0.2535
Average Fourier shell correlation    =     0.8568
AverageFree Fourier shell correlation=     0.8597
Overall weighted R factor            =     0.1829
Free weighted R factor               =     0.2172
Overall weighted R2 factor           =     0.2114
Free weighted R2 factor              =     0.2506
Average correlation coefficient      =     0.8300
Overall correlation coefficient      =     0.9600
Free correlation coefficient         =     0.9420
Cruickshanks DPI for coordinate error=     0.0778
DPI based on free R factor           =     0.0810
Overall figure of merit              =     0.7142
ML based su of positional parameters =     0.0662
ML based su of thermal parameters    =     1.8874
-----------------------------------------------------------------------------
  Time in seconds: CPU =        28.91
             Elapsed =         128.00

    ****           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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2187   0.2541   0.688      176336.    9515.7   0.0131  0.987   1.852  1.077   0.091
       1   0.2193   0.2533   0.710      175204.    9482.1   0.0117  0.884   1.771  1.030   0.087
       2   0.2184   0.2534   0.713      175010.    9478.6   0.0128  0.970   1.818  1.058   0.090
       3   0.2184   0.2534   0.714      174972.    9478.1   0.0129  0.975   1.831  1.066   0.090
       4   0.2183   0.2534   0.714      174958.    9477.7   0.0129  0.977   1.837  1.069   0.091
       5   0.2183   0.2534   0.714      174961.    9478.3   0.0129  0.978   1.839  1.070   0.091
       6   0.2183   0.2534   0.714      174961.    9478.4   0.0129  0.978   1.840  1.070   0.091
       7   0.2183   0.2535   0.714      174965.    9478.8   0.0129  0.978   1.840  1.071   0.091
       8   0.2183   0.2535   0.714      174963.    9478.8   0.0129  0.978   1.840  1.071   0.091
       9   0.2183   0.2535   0.714      174965.    9478.9   0.0129  0.978   1.840  1.071   0.091
      10   0.2183   0.2535   0.714      174964.    9478.8   0.0129  0.978   1.840  1.071   0.091
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2187   0.2183
             R free    0.2541   0.2535
     Rms BondLength    0.0131   0.0129
      Rms BondAngle    1.8524   1.8405
     Rms ChirVolume    0.0915   0.0906
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      61.1s System:    0.2s Elapsed:     1:02