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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: 22:50:16 


 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 1.57     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_step0-01A_R00_1-58A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-57A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_step0-01A_R00_1-57A.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       0.1014
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.5700
  Estimated number of reflections :      37373
  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  1.5700

  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_step0-01A_R00_1-58A.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=   2.056 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=   2.189 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=   1.823 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=   2.217 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=   2.408 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=   2.392 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=   2.137 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       1506
Number of   all  reflections      29658
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          29658

   Current auto weighting coefficient =    6.4246483    

 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.= 0.888 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        :   128  128  280
 Maximuum H,K,L                 :    37   37   79
 Minimum acceptable grid spacing:    84   84  178
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  280
 Maximuum H,K,L                 :    37   37   79
 Minimum acceptable grid spacing:    84   84  178
 Weight matrix   0.28795433    
 Actual weight    6.4246483      is applied to the X-ray term
Norm of X_ray positional gradient                36.9
Norm of Geom. positional gradient                82.8
Norm of X_ray B-factor gradient                  103.
Norm of Geom. B-factor gradient                  112.
Product of X_ray and Geom posit. gradients     -0.146E+08
 Cosine of angle between them                      -0.493
Product of X_ray and Geom B-fact gradients     -0.330E+08
 Cosine of angle between them                      -0.882


Residuals: XRAY=     0.9030E+06 GEOM=     0.1351E+05 TOTAL=     0.9165E+06
 function value    916478.50    

-------------------------------------------------------------------------------
             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     1.863     1.644
Bond angles  : others                          3238     2.367     1.580
Torsion angles, period  1. refined              185     6.792     5.000
Torsion angles, period  2. refined               90    34.890    22.778
Torsion angles, period  3. refined              268    13.259    15.000
Torsion angles, period  4. refined                9    12.370    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.017     0.020
VDW repulsions: refined_atoms                   303     0.246     0.200
VDW repulsions.others                          1342     0.220     0.200
VDW; torsion: refined_atoms                     730     0.174     0.200
VDW; torsion.others                             725     0.082     0.200
HBOND: refined_atoms                            208     0.202     0.200
HBOND.others                                      1     0.064     0.200
VDW repulsions: symmetry: refined_atoms           8     0.204     0.200
VDW repulsions: symmetry: others                 23     0.201     0.200
HBOND: symmetry: refined_atoms                   22     0.232     0.200
M. chain bond B values: refined atoms           746     1.770     1.528
M. chain bond B values: others                  746     1.765     1.528
M. chain angle B values: refined atoms          929     2.743     2.282
M. chain angle B values: others                 930     2.742     2.282
S. chain bond B values: refined atoms           811     3.173     1.931
S. chain bond B values: others                  810     3.168     1.931
S. chain angle B values: refined atoms         1177     4.822     2.729
S. chain angle B values: others                1178     4.820     2.728
Long range B values: refined atoms             1843     7.252    21.077
Long range B values: others                    1757     7.000    19.706
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0446, B  =    0.1246
Partial structure    1: scale =     0.3864, B  =   40.5689
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle    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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.051    3805 100.00   426.3   435.9  0.17  0.17     181   420.8   427.2  0.21  0.21
 0.152    6451  99.97   248.9   232.3  0.17  0.15     359   257.3   235.6  0.22  0.20
 0.254    8245 100.00   154.0   139.6  0.19  0.17     437   158.9   145.0  0.23  0.20
 0.355    9641 100.00    64.1    77.9  0.34  0.28     529    63.1    77.6  0.38  0.32
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0512   2791   0.908   1014   0.800   3805   0.879  0.947  0.9605  0.9688  0.9045  0.9366
  0.1525   5442   0.865   1009   0.771   6451   0.850  1.028  0.9433  0.9545  0.8845  0.9361
  0.2538   7220   0.857   1025   0.756   8245   0.844  1.049  0.9449  0.9538  0.8931  0.9361
  0.3551   8635   0.636   1014   0.562   9649   0.629  0.666  0.8336  0.8492  0.7926  0.8501
 $$
Resolution limits                    =     41.964     1.570
Number of used reflections           =      28150
Percentage observed                  =    99.9899
Percentage of free reflections       =     5.0782
Overall R factor                     =     0.1966
Free R factor                        =     0.2388
Average Fourier shell correlation    =     0.9201
AverageFree Fourier shell correlation=     0.9073
Overall weighted R factor            =     0.1704
Free weighted R factor               =     0.2093
Overall weighted R2 factor           =     0.2011
Free weighted R2 factor              =     0.2454
Average correlation coefficient      =     0.9067
Overall correlation coefficient      =     0.9586
Free correlation coefficient         =     0.9358
Cruickshanks DPI for coordinate error=     0.0933
DPI based on free R factor           =     0.0974
Overall figure of merit              =     0.7764
ML based su of positional parameters =     0.0724
ML based su of thermal parameters    =     2.1485
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    140547.09       13512.855       916478.50      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.37051380    
 Actual weight    6.4246483      is applied to the X-ray term


 function value    903617.75    

-------------------------------------------------------------------------------
             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 =     0.0446, B  =   -0.0516
Partial structure    1: scale =     0.3867, B  =   40.5683
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1969
Free R factor                        =     0.2379
Average Fourier shell correlation    =     0.9344
AverageFree Fourier shell correlation=     0.9230
Average correlation coefficient      =     0.9054
Overall figure of merit              =     0.8173
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    139331.00       8465.0840       903617.75       916478.50    


     CGMAT cycle number =      3

 Weight matrix   0.38509187    
 Actual weight    6.4246483      is applied to the X-ray term


 function value    902480.44    

-------------------------------------------------------------------------------
             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 =     0.0446, B  =   -0.0078
Partial structure    1: scale =     0.3870, B  =   40.4394
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1963
Free R factor                        =     0.2381
Average Fourier shell correlation    =     0.9375
AverageFree Fourier shell correlation=     0.9260
Average correlation coefficient      =     0.9064
Overall figure of merit              =     0.8269
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    139095.44       8841.1934       902480.44       903617.75    


     CGMAT cycle number =      4

 Weight matrix   0.38717428    
 Actual weight    6.4246483      is applied to the X-ray term


 function value    902258.63    

-------------------------------------------------------------------------------
             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 =     0.0446, B  =    0.0004
Partial structure    1: scale =     0.3870, B  =   40.4497
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1963
Free R factor                        =     0.2380
Average Fourier shell correlation    =     0.9381
AverageFree Fourier shell correlation=     0.9265
Average correlation coefficient      =     0.9069
Overall figure of merit              =     0.8287
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    139043.05       8955.9355       902258.63       902480.44    


     CGMAT cycle number =      5

 Weight matrix   0.38696131    
 Actual weight    6.4246483      is applied to the X-ray term


 function value    902274.56    

-------------------------------------------------------------------------------
             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 =     0.0446, B  =    0.0135
Partial structure    1: scale =     0.3871, B  =   40.3583
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1963
Free R factor                        =     0.2379
Average Fourier shell correlation    =     0.9381
AverageFree Fourier shell correlation=     0.9265
Average correlation coefficient      =     0.9071
Overall figure of merit              =     0.8286
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03

 fvalues    139034.61       9007.6377       902256.06       902258.63    


     CGMAT cycle number =      6

 Weight matrix   0.38686866    
 Actual weight    6.4246483      is applied to the X-ray term


 function value    902271.00    

-------------------------------------------------------------------------------
             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 =     0.0446, B  =    0.0146
Partial structure    1: scale =     0.3872, B  =   40.3516
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1963
Free R factor                        =     0.2380
Average Fourier shell correlation    =     0.9381
AverageFree Fourier shell correlation=     0.9264
Average correlation coefficient      =     0.9072
Overall figure of merit              =     0.8286
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    139035.05       9022.0508       902302.56       902256.06    

 fvalues    139035.05       9022.0508       902269.56       902273.31    
 fvalues    139035.05       9022.0508       902269.56       902273.31    


     CGMAT cycle number =      7

 Weight matrix   0.38671589    
 Actual weight    6.4246483      is applied to the X-ray term


 function value    902287.00    

-------------------------------------------------------------------------------
             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 =     0.0446, B  =    0.0146
Partial structure    1: scale =     0.3872, B  =   40.3115
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1963
Free R factor                        =     0.2379
Average Fourier shell correlation    =     0.9381
AverageFree Fourier shell correlation=     0.9264
Average correlation coefficient      =     0.9072
Overall figure of merit              =     0.8286
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    139036.95       9021.7080       902311.31       902273.31    

 fvalues    139036.95       9021.7080       902271.44       902285.19    
 fvalues    139036.95       9021.7080       902271.44       902285.19    


     CGMAT cycle number =      8

 Weight matrix   0.38654268    
 Actual weight    6.4246483      is applied to the X-ray term


 function value    902292.63    

-------------------------------------------------------------------------------
             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 =     0.0446, B  =    0.0149
Partial structure    1: scale =     0.3873, B  =   40.3094
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1963
Free R factor                        =     0.2379
Average Fourier shell correlation    =     0.9381
AverageFree Fourier shell correlation=     0.9264
Average correlation coefficient      =     0.9072
Overall figure of merit              =     0.8286
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    139038.41       9018.9111       902299.00       902285.19    

 fvalues    139038.41       9018.9111       902290.56       902291.81    
 fvalues    139038.41       9018.9111       902290.56       902291.81    


     CGMAT cycle number =      9

 Weight matrix   0.38652831    
 Actual weight    6.4246483      is applied to the X-ray term


 function value    902289.94    

-------------------------------------------------------------------------------
             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 =     0.0446, B  =    0.0150
Partial structure    1: scale =     0.3873, B  =   40.3238
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1963
Free R factor                        =     0.2379
Average Fourier shell correlation    =     0.9381
AverageFree Fourier shell correlation=     0.9264
Average correlation coefficient      =     0.9072
Overall figure of merit              =     0.8286
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    139038.06       9019.2842       902289.94       902291.81    


     CGMAT cycle number =     10

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.905 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  280
 Maximuum H,K,L                 :    37   37   79
 Minimum acceptable grid spacing:    84   84  178
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  280
 Maximuum H,K,L                 :    37   37   79
 Minimum acceptable grid spacing:    84   84  178
 Weight matrix   0.38654882    
 Actual weight    6.4246483      is applied to the X-ray term
Norm of X_ray positional gradient                44.0
Norm of Geom. positional gradient                43.9
Norm of X_ray B-factor gradient                  118.
Norm of Geom. B-factor gradient                  117.
Product of X_ray and Geom posit. gradients     -0.187E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.446E+08
 Cosine of angle between them                      -0.998


Residuals: XRAY=     0.8933E+06 GEOM=      9020.     TOTAL=     0.9023E+06
 function value    902295.75    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2106     1.867     1.644
Bond angles  : others                          3238     1.524     1.580
Torsion angles, period  1. refined              185     6.786     5.000
Torsion angles, period  2. refined               90    34.755    22.778
Torsion angles, period  3. refined              268    13.295    15.000
Torsion angles, period  4. refined                9    12.576    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   305     0.245     0.200
VDW repulsions.others                          1355     0.196     0.200
VDW; torsion: refined_atoms                     730     0.174     0.200
VDW; torsion.others                             763     0.086     0.200
HBOND: refined_atoms                            212     0.199     0.200
HBOND.others                                      1     0.008     0.200
VDW repulsions: symmetry: refined_atoms           7     0.218     0.200
VDW repulsions: symmetry: others                 23     0.188     0.200
HBOND: symmetry: refined_atoms                   22     0.229     0.200
M. chain bond B values: refined atoms           746     1.775     1.540
M. chain bond B values: others                  746     1.770     1.540
M. chain angle B values: refined atoms          929     2.751     2.300
M. chain angle B values: others                 930     2.750     2.300
S. chain bond B values: refined atoms           811     3.199     1.946
S. chain bond B values: others                  810     3.194     1.946
S. chain angle B values: refined atoms         1177     4.855     2.751
S. chain angle B values: others                1178     4.853     2.750
Long range B values: refined atoms             1850     7.307    21.327
Long range B values: others                    1762     7.059    19.923
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0446, B  =    0.0139
Partial structure    1: scale =     0.3873, B  =   40.3210
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10.  v. resln :N:1,6,7,11,12:
:Cycle   10.  and  v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.051    3805 100.00   426.8   436.2  0.17  0.17     181   421.3   428.3  0.20  0.21
 0.152    6451  99.97   249.2   232.6  0.17  0.15     359   257.6   236.1  0.22  0.20
 0.254    8245 100.00   154.2   140.0  0.19  0.17     437   159.1   145.0  0.23  0.20
 0.355    9641 100.00    64.2    78.0  0.34  0.28     529    63.2    77.8  0.38  0.32
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0512   2791   0.923   1014   0.823   3805   0.896  0.950  0.9643  0.9723  0.9049  0.9368
  0.1525   5442   0.871   1009   0.777   6451   0.856  1.028  0.9447  0.9557  0.8854  0.9356
  0.2538   7220   0.872   1025   0.773   8245   0.859  1.049  0.9496  0.9588  0.8940  0.9373
  0.3551   8635   0.765   1014   0.690   9649   0.757  0.724  0.8818  0.8952  0.7939  0.8506
 $$
Resolution limits                    =     41.964     1.570
Number of used reflections           =      28150
Percentage observed                  =    99.9899
Percentage of free reflections       =     5.0782
Overall R factor                     =     0.1963
Free R factor                        =     0.2379
Average Fourier shell correlation    =     0.9381
AverageFree Fourier shell correlation=     0.9264
Overall weighted R factor            =     0.1700
Free weighted R factor               =     0.2082
Overall weighted R2 factor           =     0.2006
Free weighted R2 factor              =     0.2446
Average correlation coefficient      =     0.9072
Overall correlation coefficient      =     0.9587
Free correlation coefficient         =     0.9362
Cruickshanks DPI for coordinate error=     0.0932
DPI based on free R factor           =     0.0971
Overall figure of merit              =     0.8286
ML based su of positional parameters =     0.0624
ML based su of thermal parameters    =     1.8063
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    139038.77       9019.5918       902288.50       902289.94    
 fvalues    139038.77       9019.5918       902288.50       902294.75    

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.905 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

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

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_step0-01A_R00_1-57A.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     1.868     1.644
Bond angles  : others                          3238     1.524     1.580
Torsion angles, period  1. refined              185     6.785     5.000
Torsion angles, period  2. refined               90    34.750    22.778
Torsion angles, period  3. refined              268    13.297    15.000
Torsion angles, period  4. refined                9    12.579    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                   305     0.245     0.200
VDW repulsions.others                          1358     0.195     0.200
VDW; torsion: refined_atoms                     730     0.174     0.200
VDW; torsion.others                             765     0.086     0.200
HBOND: refined_atoms                            211     0.200     0.200
HBOND.others                                      1     0.008     0.200
VDW repulsions: symmetry: refined_atoms           7     0.218     0.200
VDW repulsions: symmetry: others                 23     0.188     0.200
HBOND: symmetry: refined_atoms                   22     0.229     0.200
M. chain bond B values: refined atoms           746     1.775     1.540
M. chain bond B values: others                  746     1.770     1.540
M. chain angle B values: refined atoms          929     2.751     2.300
M. chain angle B values: others                 930     2.750     2.299
S. chain bond B values: refined atoms           811     3.199     1.946
S. chain bond B values: others                  810     3.195     1.946
S. chain angle B values: refined atoms         1177     4.855     2.751
S. chain angle B values: others                1178     4.853     2.750
Long range B values: refined atoms             1849     7.303    21.316
Long range B values: others                    1762     7.060    19.923
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0446, B  =    0.0152
Partial structure    1: scale =     0.3874, B  =   40.3278
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.051    3805 100.00   426.8   436.2  0.17  0.17     181   421.3   428.2  0.20  0.21
 0.152    6451  99.97   249.2   232.5  0.17  0.15     359   257.6   236.1  0.22  0.20
 0.254    8245 100.00   154.2   140.0  0.19  0.17     437   159.1   145.0  0.23  0.20
 0.355    9641 100.00    64.2    78.0  0.34  0.28     529    63.2    77.8  0.38  0.32
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0512   2791   0.923   1014   0.823   3805   0.896  0.950  0.9643  0.9723  0.9049  0.9368
  0.1525   5442   0.871   1009   0.777   6451   0.856  1.028  0.9447  0.9556  0.8853  0.9356
  0.2538   7220   0.872   1025   0.773   8245   0.859  1.049  0.9496  0.9588  0.8940  0.9373
  0.3551   8635   0.765   1014   0.690   9649   0.757  0.724  0.8818  0.8952  0.7939  0.8506
 $$
Resolution limits                    =     41.964     1.570
Number of used reflections           =      28150
Percentage observed                  =    99.9899
Percentage of free reflections       =     5.0782
Overall R factor                     =     0.1963
Free R factor                        =     0.2379
Average Fourier shell correlation    =     0.9381
AverageFree Fourier shell correlation=     0.9264
Overall weighted R factor            =     0.1700
Free weighted R factor               =     0.2082
Overall weighted R2 factor           =     0.2005
Free weighted R2 factor              =     0.2446
Average correlation coefficient      =     0.9072
Overall correlation coefficient      =     0.9587
Free correlation coefficient         =     0.9362
Cruickshanks DPI for coordinate error=     0.0932
DPI based on free R factor           =     0.0971
Overall figure of merit              =     0.8285
ML based su of positional parameters =     0.0624
ML based su of thermal parameters    =     1.8063
-----------------------------------------------------------------------------
  Time in seconds: CPU =        25.57
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1966   0.2388   0.776      140547.    7688.2   0.0133  0.998   1.863  1.085   0.090
       1   0.1969   0.2379   0.817      139331.    7645.0   0.0121  0.906   1.793  1.042   0.087
       2   0.1963   0.2381   0.827      139095.    7637.3   0.0130  0.980   1.832  1.066   0.089
       3   0.1963   0.2380   0.829      139043.    7635.7   0.0132  0.991   1.851  1.077   0.090
       4   0.1963   0.2379   0.829      139037.    7636.0   0.0132  0.995   1.860  1.082   0.090
       5   0.1963   0.2380   0.829      139035.    7636.4   0.0133  0.997   1.865  1.085   0.090
       6   0.1963   0.2379   0.829      139037.    7636.5   0.0133  0.997   1.866  1.086   0.090
       7   0.1963   0.2379   0.829      139039.    7636.7   0.0133  0.997   1.867  1.086   0.090
       8   0.1963   0.2379   0.829      139038.    7636.7   0.0133  0.997   1.867  1.086   0.090
       9   0.1963   0.2379   0.829      139039.    7636.8   0.0133  0.997   1.867  1.086   0.090
      10   0.1963   0.2379   0.829      139040.    7636.9   0.0133  0.997   1.868  1.087   0.091
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1966   0.1963
             R free    0.2388   0.2379
     Rms BondLength    0.0133   0.0133
      Rms BondAngle    1.8630   1.8678
     Rms ChirVolume    0.0899   0.0905
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      57.3s System:    0.2s Elapsed:     0:58