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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: 13:24:59 


 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 1.93     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_1-94A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-93A.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_1-93A.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       0.0671
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.9300
  Estimated number of reflections :      20160
  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  1.9300

  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_1-94A.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=   1.996 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=   2.209 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=   1.841 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=   2.202 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=   2.371 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=   2.428 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=   2.051 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        827
Number of   all  reflections      16226
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          16226

   Current auto weighting coefficient =    7.3245206    

 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.= 0.906 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        :   112  112  240
 Maximuum H,K,L                 :    30   30   64
 Minimum acceptable grid spacing:    72   72  152
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    30   30   64
 Minimum acceptable grid spacing:    72   72  152
 Weight matrix   0.20521833    
 Actual weight    7.3245206      is applied to the X-ray term
Norm of X_ray positional gradient                31.1
Norm of Geom. positional gradient                77.6
Norm of X_ray B-factor gradient                  106.
Norm of Geom. B-factor gradient                  104.
Product of X_ray and Geom posit. gradients     -0.846E+07
 Cosine of angle between them                      -0.363
Product of X_ray and Geom B-fact gradients     -0.327E+08
 Cosine of angle between them                      -0.925


Residuals: XRAY=     0.6186E+06 GEOM=     0.1252E+05 TOTAL=     0.6312E+06
 function value    631158.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.035     0.017
Bond angles  : refined atoms                   2106     1.694     1.644
Bond angles  : others                          3238     2.344     1.580
Torsion angles, period  1. refined              185     7.077     5.000
Torsion angles, period  2. refined               90    36.840    22.778
Torsion angles, period  3. refined              268    14.294    15.000
Torsion angles, period  4. refined                9    10.999    15.000
Chiral centres: refined atoms                   196     0.083     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.015     0.020
VDW repulsions: refined_atoms                   306     0.241     0.200
VDW repulsions.others                          1336     0.220     0.200
VDW; torsion: refined_atoms                     709     0.170     0.200
VDW; torsion.others                             705     0.079     0.200
HBOND: refined_atoms                            228     0.207     0.200
Metal-ion: refined_atoms                          1     0.004     0.200
VDW repulsions: symmetry: refined_atoms           9     0.225     0.200
VDW repulsions: symmetry: others                 24     0.202     0.200
HBOND: symmetry: refined_atoms                   19     0.225     0.200
M. chain bond B values: refined atoms           746     1.522     1.198
M. chain bond B values: others                  746     1.521     1.198
M. chain angle B values: refined atoms          929     2.460     1.783
M. chain angle B values: others                 930     2.458     1.783
S. chain bond B values: refined atoms           811     2.411     1.520
S. chain bond B values: others                  810     2.408     1.519
S. chain angle B values: refined atoms         1177     3.824     2.138
S. chain angle B values: others                1178     3.822     2.138
Long range B values: refined atoms             1853     6.652    16.745
Long range B values: others                    1753     6.326    15.348
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0400, B  =   -0.0985
Partial structure    1: scale =     0.3741, B  =   46.2854
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.034    2117 100.00   484.0   487.4  0.16  0.17      94   472.0   484.1  0.20  0.22
 0.101    3558 100.00   398.9   380.6  0.16  0.15     180   397.7   370.5  0.22  0.21
 0.168    4473  99.96   253.0   249.7  0.16  0.14     262   270.4   260.4  0.22  0.19
 0.235    5242 100.00   198.5   197.8  0.16  0.13     289   205.2   206.4  0.22  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0341   1453   0.906    664   0.806   2117   0.874  0.958  0.9602  0.9684  0.9164  0.9426
  0.1010   2885   0.882    673   0.764   3558   0.859  0.999  0.9454  0.9620  0.8790  0.9442
  0.1680   3801   0.861    672   0.770   4473   0.847  0.971  0.9445  0.9559  0.8867  0.9378
  0.2350   4569   0.866    680   0.743   5249   0.850  0.962  0.9438  0.9567  0.8739  0.9388
 $$
Resolution limits                    =     41.964     1.930
Number of used reflections           =      15397
Percentage observed                  =    99.9815
Percentage of free reflections       =     5.0974
Overall R factor                     =     0.1593
Free R factor                        =     0.2161
Average Fourier shell correlation    =     0.9593
AverageFree Fourier shell correlation=     0.9462
Overall weighted R factor            =     0.1495
Free weighted R factor               =     0.2013
Overall weighted R2 factor           =     0.1818
Free weighted R2 factor              =     0.2434
Average correlation coefficient      =     0.9403
Overall correlation coefficient      =     0.9547
Free correlation coefficient         =     0.9105
Cruickshanks DPI for coordinate error=     0.1494
DPI based on free R factor           =     0.1466
Overall figure of merit              =     0.8547
ML based su of positional parameters =     0.0916
ML based su of thermal parameters    =     3.0780
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    84460.945       12522.321       631158.25      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.21209963    
 Actual weight    7.3245206      is applied to the X-ray term


 function value    625339.13    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0400, B  =   -0.1273
Partial structure    1: scale =     0.3744, B  =   46.3664
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1591
Free R factor                        =     0.2156
Average Fourier shell correlation    =     0.9604
AverageFree Fourier shell correlation=     0.9473
Average correlation coefficient      =     0.9409
Overall figure of merit              =     0.8586
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    84276.391       8054.9248       625339.13       631158.25    


     CGMAT cycle number =      3

 Weight matrix   0.21246898    
 Actual weight    7.3245206      is applied to the X-ray term


 function value    625225.00    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0400, B  =   -0.1321
Partial structure    1: scale =     0.3746, B  =   46.3915
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1587
Free R factor                        =     0.2157
Average Fourier shell correlation    =     0.9605
AverageFree Fourier shell correlation=     0.9474
Average correlation coefficient      =     0.9411
Overall figure of merit              =     0.8588
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    84255.352       8094.9663       625225.00       625339.13    


     CGMAT cycle number =      4

 Weight matrix   0.21239193    
 Actual weight    7.3245206      is applied to the X-ray term


 function value    625218.00    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0400, B  =   -0.1359
Partial structure    1: scale =     0.3749, B  =   46.4650
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1586
Free R factor                        =     0.2158
Average Fourier shell correlation    =     0.9605
AverageFree Fourier shell correlation=     0.9474
Average correlation coefficient      =     0.9412
Overall figure of merit              =     0.8588
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    84252.383       8109.6621       625218.00       625225.00    


     CGMAT cycle number =      5

 Weight matrix   0.21238339    
 Actual weight    7.3245206      is applied to the X-ray term


 function value    625177.75    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0400, B  =   -0.1377
Partial structure    1: scale =     0.3751, B  =   46.5260
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1586
Free R factor                        =     0.2160
Average Fourier shell correlation    =     0.9605
AverageFree Fourier shell correlation=     0.9473
Average correlation coefficient      =     0.9412
Overall figure of merit              =     0.8587
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    84246.461       8112.7847       625177.75       625218.00    


     CGMAT cycle number =      6

 Weight matrix   0.21214545    
 Actual weight    7.3245206      is applied to the X-ray term


 function value    625196.50    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0400, B  =   -0.1457
Partial structure    1: scale =     0.3752, B  =   46.3907
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1586
Free R factor                        =     0.2160
Average Fourier shell correlation    =     0.9605
AverageFree Fourier shell correlation=     0.9473
Average correlation coefficient      =     0.9412
Overall figure of merit              =     0.8587
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    84250.016       8107.0610       625222.69       625177.75    

 fvalues    84250.016       8107.0610       625172.63       625198.06    
 fvalues    84250.016       8107.0610       625172.63       625198.06    


     CGMAT cycle number =      7

 Weight matrix   0.21211836    
 Actual weight    7.3245206      is applied to the X-ray term


 function value    625189.50    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0400, B  =   -0.1481
Partial structure    1: scale =     0.3752, B  =   46.3788
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1585
Free R factor                        =     0.2160
Average Fourier shell correlation    =     0.9605
AverageFree Fourier shell correlation=     0.9473
Average correlation coefficient      =     0.9413
Overall figure of merit              =     0.8586
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    84249.461       8102.5654       625189.50       625198.06    


     CGMAT cycle number =      8

 Weight matrix   0.21186477    
 Actual weight    7.3245206      is applied to the X-ray term


 function value    625195.81    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0400, B  =   -0.1539
Partial structure    1: scale =     0.3752, B  =   46.3741
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1586
Free R factor                        =     0.2161
Average Fourier shell correlation    =     0.9605
AverageFree Fourier shell correlation=     0.9473
Average correlation coefficient      =     0.9413
Overall figure of merit              =     0.8585
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    84251.492       8093.8779       625187.31       625189.50    
 fvalues    84251.492       8093.8779       625187.31       625195.69    


     CGMAT cycle number =      9

 Weight matrix   0.21188103    
 Actual weight    7.3245206      is applied to the X-ray term


 function value    625187.63    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0400, B  =   -0.1466
Partial structure    1: scale =     0.3752, B  =   46.3891
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1586
Free R factor                        =     0.2161
Average Fourier shell correlation    =     0.9605
AverageFree Fourier shell correlation=     0.9473
Average correlation coefficient      =     0.9413
Overall figure of merit              =     0.8585
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    84250.305       8094.5669       625187.63       625195.69    


     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.= 0.926 id.= 3.000 dev= -2.07 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        :   112  112  240
 Maximuum H,K,L                 :    30   30   64
 Minimum acceptable grid spacing:    72   72  152
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    30   30   64
 Minimum acceptable grid spacing:    72   72  152
 Weight matrix   0.21177803    
 Actual weight    7.3245206      is applied to the X-ray term
Norm of X_ray positional gradient                30.9
Norm of Geom. positional gradient                30.9
Norm of X_ray B-factor gradient                  103.
Norm of Geom. B-factor gradient                  109.
Product of X_ray and Geom posit. gradients     -0.925E+07
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.355E+08
 Cosine of angle between them                      -0.978


Residuals: XRAY=     0.6171E+06 GEOM=      8094.     TOTAL=     0.6252E+06
 function value    625211.31    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.696     1.644
Bond angles  : others                          3238     1.421     1.580
Torsion angles, period  1. refined              185     7.039     5.000
Torsion angles, period  2. refined               90    36.842    22.778
Torsion angles, period  3. refined              268    14.268    15.000
Torsion angles, period  4. refined                9    11.109    15.000
Chiral centres: refined atoms                   196     0.084     0.200
Planar groups: refined atoms                   1743     0.009     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   305     0.242     0.200
VDW repulsions.others                          1373     0.193     0.200
VDW; torsion: refined_atoms                     714     0.170     0.200
VDW; torsion.others                             778     0.083     0.200
HBOND: refined_atoms                            231     0.206     0.200
Metal-ion: refined_atoms                          1     0.009     0.200
VDW repulsions: symmetry: refined_atoms          10     0.205     0.200
VDW repulsions: symmetry: others                 25     0.184     0.200
HBOND: symmetry: refined_atoms                   21     0.211     0.200
M. chain bond B values: refined atoms           746     1.520     1.204
M. chain bond B values: others                  746     1.519     1.204
M. chain angle B values: refined atoms          929     2.455     1.792
M. chain angle B values: others                 930     2.454     1.792
S. chain bond B values: refined atoms           811     2.433     1.528
S. chain bond B values: others                  810     2.430     1.528
S. chain angle B values: refined atoms         1177     3.853     2.150
S. chain angle B values: others                1178     3.852     2.150
Long range B values: refined atoms             1859     6.597    16.817
Long range B values: others                    1757     6.288    15.424
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0400, B  =   -0.1475
Partial structure    1: scale =     0.3752, B  =   46.4112
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.034    2117 100.00   484.3   488.0  0.16  0.17      94   472.2   484.2  0.20  0.22
 0.101    3558 100.00   399.1   380.7  0.16  0.15     180   397.9   370.4  0.22  0.21
 0.168    4473  99.96   253.1   249.8  0.16  0.13     262   270.5   259.8  0.22  0.19
 0.235    5242 100.00   198.6   198.0  0.16  0.13     289   205.3   206.9  0.22  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0341   1453   0.919    664   0.821   2117   0.888  0.958  0.9631  0.9710  0.9163  0.9426
  0.1010   2885   0.884    673   0.768   3558   0.862  0.999  0.9466  0.9630  0.8798  0.9444
  0.1680   3801   0.861    672   0.771   4473   0.848  0.971  0.9446  0.9561  0.8879  0.9389
  0.2350   4569   0.869    680   0.745   5249   0.853  0.962  0.9450  0.9582  0.8743  0.9407
 $$
Resolution limits                    =     41.964     1.930
Number of used reflections           =      15397
Percentage observed                  =    99.9815
Percentage of free reflections       =     5.0974
Overall R factor                     =     0.1586
Free R factor                        =     0.2160
Average Fourier shell correlation    =     0.9605
AverageFree Fourier shell correlation=     0.9473
Overall weighted R factor            =     0.1490
Free weighted R factor               =     0.2010
Overall weighted R2 factor           =     0.1814
Free weighted R2 factor              =     0.2431
Average correlation coefficient      =     0.9413
Overall correlation coefficient      =     0.9550
Free correlation coefficient         =     0.9109
Cruickshanks DPI for coordinate error=     0.1487
DPI based on free R factor           =     0.1465
Overall figure of merit              =     0.8585
ML based su of positional parameters =     0.0901
ML based su of thermal parameters    =     3.0344
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    84254.891       8093.8828       625240.94       625187.63    

 fvalues    84254.891       8093.8828       625219.88       625220.56    
 fvalues    84254.891       8093.8828       625219.88       625220.56    

    ****                              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.= 0.926 id.= 3.000 dev= -2.07 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_1-93A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.697     1.644
Bond angles  : others                          3238     1.421     1.580
Torsion angles, period  1. refined              185     7.039     5.000
Torsion angles, period  2. refined               90    36.839    22.778
Torsion angles, period  3. refined              268    14.271    15.000
Torsion angles, period  4. refined                9    11.111    15.000
Chiral centres: refined atoms                   196     0.084     0.200
Planar groups: refined atoms                   1743     0.009     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   305     0.242     0.200
VDW repulsions.others                          1372     0.192     0.200
VDW; torsion: refined_atoms                     714     0.170     0.200
VDW; torsion.others                             780     0.083     0.200
HBOND: refined_atoms                            231     0.206     0.200
Metal-ion: refined_atoms                          1     0.009     0.200
VDW repulsions: symmetry: refined_atoms          10     0.205     0.200
VDW repulsions: symmetry: others                 25     0.184     0.200
HBOND: symmetry: refined_atoms                   21     0.211     0.200
M. chain bond B values: refined atoms           746     1.520     1.204
M. chain bond B values: others                  746     1.519     1.204
M. chain angle B values: refined atoms          929     2.455     1.792
M. chain angle B values: others                 930     2.454     1.792
S. chain bond B values: refined atoms           811     2.433     1.528
S. chain bond B values: others                  810     2.430     1.528
S. chain angle B values: refined atoms         1177     3.853     2.150
S. chain angle B values: others                1178     3.851     2.150
Long range B values: refined atoms             1859     6.596    16.817
Long range B values: others                    1757     6.288    15.425
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0400, B  =   -0.1481
Partial structure    1: scale =     0.3752, B  =   46.4203
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.034    2117 100.00   484.3   488.0  0.16  0.17      94   472.2   484.3  0.20  0.22
 0.101    3558 100.00   399.1   380.7  0.16  0.15     180   397.9   370.4  0.22  0.21
 0.168    4473  99.96   253.1   249.8  0.16  0.13     262   270.5   259.8  0.22  0.19
 0.235    5242 100.00   198.6   198.0  0.16  0.13     289   205.3   206.9  0.22  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0341   1453   0.919    664   0.820   2117   0.888  0.958  0.9630  0.9710  0.9162  0.9426
  0.1010   2885   0.884    673   0.768   3558   0.862  0.999  0.9466  0.9630  0.8797  0.9444
  0.1680   3801   0.861    672   0.771   4473   0.848  0.971  0.9446  0.9561  0.8879  0.9389
  0.2350   4569   0.869    680   0.745   5249   0.853  0.962  0.9450  0.9582  0.8742  0.9407
 $$
Resolution limits                    =     41.964     1.930
Number of used reflections           =      15397
Percentage observed                  =    99.9815
Percentage of free reflections       =     5.0974
Overall R factor                     =     0.1586
Free R factor                        =     0.2160
Average Fourier shell correlation    =     0.9604
AverageFree Fourier shell correlation=     0.9473
Overall weighted R factor            =     0.1490
Free weighted R factor               =     0.2010
Overall weighted R2 factor           =     0.1814
Free weighted R2 factor              =     0.2432
Average correlation coefficient      =     0.9413
Overall correlation coefficient      =     0.9550
Free correlation coefficient         =     0.9108
Cruickshanks DPI for coordinate error=     0.1487
DPI based on free R factor           =     0.1465
Overall figure of merit              =     0.8585
ML based su of positional parameters =     0.0901
ML based su of thermal parameters    =     3.0344
-----------------------------------------------------------------------------
  Time in seconds: CPU =        17.46
             Elapsed =           0.00

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


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS: vs cycle :N:1,2,3:
:FOM vs cycle :N:1,4:
:-LL vs cycle :N:1,5:
:-LLfree vs cycle :N:1,6:
:Geometry vs cycle:N:1,7,8,9,10,11:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1593   0.2161   0.855       84461.    4697.9   0.0111  0.818   1.694  0.985   0.083
       1   0.1591   0.2156   0.859       84276.    4696.0   0.0109  0.799   1.675  0.974   0.084
       2   0.1587   0.2157   0.859       84255.    4695.8   0.0111  0.819   1.688  0.981   0.084
       3   0.1586   0.2158   0.859       84252.    4696.0   0.0111  0.821   1.692  0.983   0.084
       4   0.1586   0.2160   0.859       84246.    4696.0   0.0112  0.822   1.694  0.984   0.084
       5   0.1586   0.2160   0.859       84250.    4696.4   0.0112  0.822   1.695  0.985   0.084
       6   0.1585   0.2160   0.859       84249.    4696.5   0.0112  0.822   1.695  0.985   0.084
       7   0.1586   0.2161   0.859       84252.    4696.9   0.0111  0.822   1.695  0.985   0.084
       8   0.1586   0.2161   0.859       84250.    4696.8   0.0111  0.821   1.696  0.986   0.084
       9   0.1586   0.2160   0.859       84254.    4697.0   0.0111  0.821   1.696  0.986   0.084
      10   0.1586   0.2160   0.858       84255.    4697.1   0.0111  0.821   1.697  0.986   0.084
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1593   0.1586
             R free    0.2161   0.2160
     Rms BondLength    0.0111   0.0111
      Rms BondAngle    1.6938   1.6966
     Rms ChirVolume    0.0834   0.0837
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      49.7s System:    0.1s Elapsed:     0:50