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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: 23:16:23 


 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 1.56     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_1-57A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-56A.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_1-56A.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       0.1027
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.5600
  Estimated number of reflections :      37852
  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  1.5600

  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_1-57A.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=   2.053 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=   2.190 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=   1.824 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=   2.215 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=   2.410 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=   2.388 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=   2.126 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       1531
Number of   all  reflections      30222
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          30222

   Current auto weighting coefficient =    6.3996348    

 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   0.28488833    
 Actual weight    6.3996348      is applied to the X-ray term
Norm of X_ray positional gradient                36.7
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     -0.145E+08
 Cosine of angle between them                      -0.494
Product of X_ray and Geom B-fact gradients     -0.322E+08
 Cosine of angle between them                      -0.867


Residuals: XRAY=     0.9139E+06 GEOM=     0.1354E+05 TOTAL=     0.9274E+06
 function value    927411.25    

-------------------------------------------------------------------------------
             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     1.868     1.644
Bond angles  : others                          3238     2.368     1.580
Torsion angles, period  1. refined              185     6.785     5.000
Torsion angles, period  2. refined               90    34.749    22.778
Torsion angles, period  3. refined              268    13.297    15.000
Torsion angles, period  4. refined                9    12.595    15.000
Chiral centres: refined atoms                   196     0.091     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.018     0.020
VDW repulsions: refined_atoms                   305     0.245     0.200
VDW repulsions.others                          1338     0.221     0.200
VDW; torsion: refined_atoms                     730     0.174     0.200
VDW; torsion.others                             727     0.082     0.200
HBOND: refined_atoms                            211     0.200     0.200
HBOND.others                                      1     0.067     0.200
VDW repulsions: symmetry: refined_atoms           7     0.218     0.200
VDW repulsions: symmetry: others                 22     0.206     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     3.200     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    21.317
Long range B values: others                    1762     7.061    19.925
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0447, B  =    0.1219
Partial structure    1: scale =     0.3874, B  =   40.2499
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.39 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.052    3885 100.00   423.7   433.0  0.17  0.17     182   420.3   426.6  0.21  0.21
 0.154    6576  99.97   245.8   228.7  0.18  0.16     373   254.6   233.3  0.22  0.20
 0.257    8381 100.00   149.8   136.0  0.19  0.17     443   153.0   139.8  0.23  0.20
 0.360    9836 100.00    61.6    75.4  0.35  0.29     533    61.2    75.5  0.39  0.33
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0519   2855   0.907   1030   0.799   3885   0.878  0.948  0.9604  0.9688  0.9031  0.9370
  0.1544   5552   0.865   1024   0.769   6576   0.850  1.032  0.9432  0.9538  0.8842  0.9342
  0.2570   7354   0.856   1027   0.759   8381   0.844  1.046  0.9437  0.9535  0.8921  0.9363
  0.3596   8809   0.618   1038   0.544   9847   0.610  0.651  0.8214  0.8345  0.7837  0.8413
 $$
Resolution limits                    =     41.964     1.560
Number of used reflections           =      28689
Percentage observed                  =    99.9901
Percentage of free reflections       =     5.0662
Overall R factor                     =     0.1979
Free R factor                        =     0.2395
Average Fourier shell correlation    =     0.9148
AverageFree Fourier shell correlation=     0.9030
Overall weighted R factor            =     0.1709
Free weighted R factor               =     0.2094
Overall weighted R2 factor           =     0.2014
Free weighted R2 factor              =     0.2458
Average correlation coefficient      =     0.9033
Overall correlation coefficient      =     0.9587
Free correlation coefficient         =     0.9361
Cruickshanks DPI for coordinate error=     0.0921
DPI based on free R factor           =     0.0962
Overall figure of merit              =     0.7697
ML based su of positional parameters =     0.0726
ML based su of thermal parameters    =     2.1511
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    142800.75       13538.629       927411.25      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.36801168    
 Actual weight    6.3996348      is applied to the X-ray term


 function value    914249.13    

-------------------------------------------------------------------------------
             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 =     0.0447, B  =   -0.0597
Partial structure    1: scale =     0.3874, B  =   40.4168
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.39 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1983
Free R factor                        =     0.2385
Average Fourier shell correlation    =     0.9306
AverageFree Fourier shell correlation=     0.9203
Average correlation coefficient      =     0.9018
Overall figure of merit              =     0.8122
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    141540.02       8444.7188       914249.13       927411.25    


     CGMAT cycle number =      3

 Weight matrix   0.38263878    
 Actual weight    6.3996348      is applied to the X-ray term


 function value    913003.63    

-------------------------------------------------------------------------------
             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 =     0.0447, B  =   -0.0023
Partial structure    1: scale =     0.3874, B  =   40.4156
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.39 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1977
Free R factor                        =     0.2386
Average Fourier shell correlation    =     0.9342
AverageFree Fourier shell correlation=     0.9237
Average correlation coefficient      =     0.9029
Overall figure of merit              =     0.8229
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    141287.52       8815.1289       913003.63       914249.13    


     CGMAT cycle number =      4

 Weight matrix   0.38664964    
 Actual weight    6.3996348      is applied to the X-ray term


 function value    912723.31    

-------------------------------------------------------------------------------
             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 =     0.0447, B  =   -0.0020
Partial structure    1: scale =     0.3875, B  =   40.4335
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.39 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1977
Free R factor                        =     0.2386
Average Fourier shell correlation    =     0.9351
AverageFree Fourier shell correlation=     0.9245
Average correlation coefficient      =     0.9034
Overall figure of merit              =     0.8258
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    141227.55       8918.5811       912723.31       913003.63    


     CGMAT cycle number =      5

 Weight matrix   0.38749504    
 Actual weight    6.3996348      is applied to the X-ray term


 function value    912644.19    

-------------------------------------------------------------------------------
             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 =     0.0447, B  =    0.0000
Partial structure    1: scale =     0.3875, B  =   40.4335
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.39 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1977
Free R factor                        =     0.2387
Average Fourier shell correlation    =     0.9353
AverageFree Fourier shell correlation=     0.9247
Average correlation coefficient      =     0.9037
Overall figure of merit              =     0.8264
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    141207.14       8970.0850       912644.19       912723.31    


     CGMAT cycle number =      6

 Weight matrix   0.38730890    
 Actual weight    6.3996348      is applied to the X-ray term


 function value    912655.19    

-------------------------------------------------------------------------------
             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 =     0.0447, B  =    0.0050
Partial structure    1: scale =     0.3876, B  =   40.4404
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.39 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1976
Free R factor                        =     0.2387
Average Fourier shell correlation    =     0.9353
AverageFree Fourier shell correlation=     0.9246
Average correlation coefficient      =     0.9038
Overall figure of merit              =     0.8264
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    141208.34       8990.1279       912675.88       912644.19    

 fvalues    141208.34       8990.1279       912661.06       912671.94    
 fvalues    141208.34       8990.1279       912661.06       912671.94    


     CGMAT cycle number =      7

 Weight matrix   0.38708124    
 Actual weight    6.3996348      is applied to the X-ray term


 function value    912671.81    

-------------------------------------------------------------------------------
             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 =     0.0447, B  =    0.0070
Partial structure    1: scale =     0.3877, B  =   40.4677
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.39 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1977
Free R factor                        =     0.2386
Average Fourier shell correlation    =     0.9353
AverageFree Fourier shell correlation=     0.9246
Average correlation coefficient      =     0.9038
Overall figure of merit              =     0.8264
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    141208.27       8990.5137       912671.81       912671.94    


     CGMAT cycle number =      8

 Weight matrix   0.38746411    
 Actual weight    6.3996348      is applied to the X-ray term


 function value    912664.94    

-------------------------------------------------------------------------------
             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 =     0.0447, B  =    0.0007
Partial structure    1: scale =     0.3877, B  =   40.4627
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.39 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1977
Free R factor                        =     0.2386
Average Fourier shell correlation    =     0.9353
AverageFree Fourier shell correlation=     0.9246
Average correlation coefficient      =     0.9038
Overall figure of merit              =     0.8264
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    141207.67       8987.3789       912664.94       912671.81    


     CGMAT cycle number =      9

 Weight matrix   0.38708928    
 Actual weight    6.3996348      is applied to the X-ray term


 function value    912662.50    

-------------------------------------------------------------------------------
             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 =     0.0447, B  =    0.0062
Partial structure    1: scale =     0.3877, B  =   40.4705
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.39 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1977
Free R factor                        =     0.2386
Average Fourier shell correlation    =     0.9353
AverageFree Fourier shell correlation=     0.9246
Average correlation coefficient      =     0.9038
Overall figure of merit              =     0.8264
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    141207.13       8988.4414       912662.50       912664.94    


     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   0.38735956    
 Actual weight    6.3996348      is applied to the X-ray term
Norm of X_ray positional gradient                44.0
Norm of Geom. positional gradient                44.0
Norm of X_ray B-factor gradient                  116.
Norm of Geom. B-factor gradient                  116.
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     -0.435E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.9037E+06 GEOM=      8989.     TOTAL=     0.9127E+06
 function value    912663.19    

-------------------------------------------------------------------------------
             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     1.872     1.644
Bond angles  : others                          3238     1.522     1.580
Torsion angles, period  1. refined              185     6.763     5.000
Torsion angles, period  2. refined               90    34.717    22.778
Torsion angles, period  3. refined              268    13.300    15.000
Torsion angles, period  4. refined                9    12.594    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                   304     0.246     0.200
VDW repulsions.others                          1376     0.193     0.200
VDW; torsion: refined_atoms                     731     0.174     0.200
VDW; torsion.others                             774     0.085     0.200
HBOND: refined_atoms                            211     0.199     0.200
HBOND.others                                      1     0.015     0.200
VDW repulsions: symmetry: refined_atoms           8     0.204     0.200
VDW repulsions: symmetry: others                 22     0.193     0.200
HBOND: symmetry: refined_atoms                   21     0.220     0.200
M. chain bond B values: refined atoms           746     1.776     1.550
M. chain bond B values: others                  746     1.771     1.550
M. chain angle B values: refined atoms          929     2.757     2.316
M. chain angle B values: others                 930     2.755     2.316
S. chain bond B values: refined atoms           811     3.211     1.958
S. chain bond B values: others                  810     3.206     1.958
S. chain angle B values: refined atoms         1177     4.871     2.768
S. chain angle B values: others                1178     4.868     2.768
Long range B values: refined atoms             1849     7.402    21.433
Long range B values: others                    1762     7.081    20.025
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0447, B  =    0.0017
Partial structure    1: scale =     0.3877, B  =   40.4943
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.39 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.052    3885 100.00   424.1   433.6  0.17  0.17     182   420.7   427.5  0.21  0.21
 0.154    6576  99.97   246.0   228.9  0.18  0.16     373   254.8   233.7  0.22  0.20
 0.257    8381 100.00   149.9   136.4  0.19  0.17     443   153.2   140.1  0.23  0.20
 0.360    9836 100.00    61.7    75.4  0.35  0.29     533    61.3    75.7  0.39  0.33
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0519   2855   0.922   1030   0.821   3885   0.895  0.950  0.9642  0.9722  0.9034  0.9370
  0.1544   5552   0.872   1024   0.776   6576   0.857  1.032  0.9451  0.9554  0.8860  0.9342
  0.2570   7354   0.871   1027   0.776   8381   0.859  1.046  0.9487  0.9582  0.8937  0.9368
  0.3596   8809   0.759   1038   0.683   9847   0.751  0.718  0.8767  0.8879  0.7834  0.8423
 $$
Resolution limits                    =     41.964     1.560
Number of used reflections           =      28689
Percentage observed                  =    99.9901
Percentage of free reflections       =     5.0662
Overall R factor                     =     0.1977
Free R factor                        =     0.2386
Average Fourier shell correlation    =     0.9353
AverageFree Fourier shell correlation=     0.9246
Overall weighted R factor            =     0.1708
Free weighted R factor               =     0.2086
Overall weighted R2 factor           =     0.2012
Free weighted R2 factor              =     0.2453
Average correlation coefficient      =     0.9038
Overall correlation coefficient      =     0.9588
Free correlation coefficient         =     0.9366
Cruickshanks DPI for coordinate error=     0.0920
DPI based on free R factor           =     0.0958
Overall figure of merit              =     0.8264
ML based su of positional parameters =     0.0622
ML based su of thermal parameters    =     1.7934
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02

 fvalues    141206.84       8989.1113       912661.38       912662.50    

    ****                              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_1-56A.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     1.873     1.644
Bond angles  : others                          3238     1.522     1.580
Torsion angles, period  1. refined              185     6.762     5.000
Torsion angles, period  2. refined               90    34.712    22.778
Torsion angles, period  3. refined              268    13.303    15.000
Torsion angles, period  4. refined                9    12.590    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                   304     0.246     0.200
VDW repulsions.others                          1378     0.193     0.200
VDW; torsion: refined_atoms                     731     0.174     0.200
VDW; torsion.others                             779     0.085     0.200
HBOND: refined_atoms                            212     0.199     0.200
HBOND.others                                      1     0.016     0.200
VDW repulsions: symmetry: refined_atoms           8     0.204     0.200
VDW repulsions: symmetry: others                 22     0.193     0.200
HBOND: symmetry: refined_atoms                   21     0.217     0.200
M. chain bond B values: refined atoms           746     1.776     1.550
M. chain bond B values: others                  746     1.771     1.550
M. chain angle B values: refined atoms          929     2.756     2.316
M. chain angle B values: others                 930     2.755     2.316
S. chain bond B values: refined atoms           811     3.211     1.958
S. chain bond B values: others                  810     3.207     1.958
S. chain angle B values: refined atoms         1177     4.872     2.768
S. chain angle B values: others                1178     4.869     2.768
Long range B values: refined atoms             1850     7.505    21.461
Long range B values: others                    1763     7.191    20.055
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0447, B  =    0.0063
Partial structure    1: scale =     0.3877, B  =   40.5932
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.39 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.052    3885 100.00   424.1   433.5  0.17  0.17     182   420.7   427.6  0.21  0.21
 0.154    6576  99.97   246.0   228.9  0.18  0.16     373   254.8   233.6  0.22  0.20
 0.257    8381 100.00   149.9   136.3  0.19  0.17     443   153.2   140.0  0.23  0.20
 0.360    9836 100.00    61.7    75.4  0.35  0.29     533    61.3    75.7  0.39  0.33
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0519   2855   0.922   1030   0.821   3885   0.895  0.950  0.9641  0.9722  0.9033  0.9370
  0.1544   5552   0.872   1024   0.776   6576   0.857  1.032  0.9451  0.9554  0.8859  0.9342
  0.2570   7354   0.871   1027   0.776   8381   0.859  1.046  0.9487  0.9582  0.8936  0.9368
  0.3596   8809   0.758   1038   0.682   9847   0.750  0.718  0.8767  0.8879  0.7835  0.8423
 $$
Resolution limits                    =     41.964     1.560
Number of used reflections           =      28689
Percentage observed                  =    99.9901
Percentage of free reflections       =     5.0662
Overall R factor                     =     0.1977
Free R factor                        =     0.2387
Average Fourier shell correlation    =     0.9353
AverageFree Fourier shell correlation=     0.9246
Overall weighted R factor            =     0.1708
Free weighted R factor               =     0.2087
Overall weighted R2 factor           =     0.2012
Free weighted R2 factor              =     0.2455
Average correlation coefficient      =     0.9038
Overall correlation coefficient      =     0.9588
Free correlation coefficient         =     0.9365
Cruickshanks DPI for coordinate error=     0.0920
DPI based on free R factor           =     0.0958
Overall figure of merit              =     0.8264
ML based su of positional parameters =     0.0622
ML based su of thermal parameters    =     1.7934
-----------------------------------------------------------------------------
  Time in seconds: CPU =        19.52
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1979   0.2395   0.770      142801.    7794.0   0.0133  0.998   1.868  1.087   0.091
       1   0.1983   0.2385   0.812      141540.    7748.7   0.0120  0.905   1.797  1.043   0.087
       2   0.1977   0.2386   0.823      141288.    7739.7   0.0130  0.979   1.835  1.067   0.089
       3   0.1977   0.2386   0.826      141228.    7738.0   0.0132  0.990   1.852  1.077   0.090
       4   0.1977   0.2387   0.826      141207.    7737.8   0.0133  0.995   1.862  1.083   0.090
       5   0.1976   0.2387   0.826      141206.    7738.2   0.0133  0.997   1.867  1.086   0.090
       6   0.1977   0.2386   0.826      141208.    7738.4   0.0133  0.997   1.869  1.087   0.090
       7   0.1977   0.2386   0.826      141208.    7738.6   0.0133  0.997   1.870  1.088   0.090
       8   0.1977   0.2386   0.826      141207.    7738.6   0.0133  0.998   1.871  1.088   0.090
       9   0.1977   0.2386   0.826      141207.    7738.7   0.0133  0.998   1.872  1.089   0.090
      10   0.1977   0.2387   0.826      141208.    7738.9   0.0133  0.998   1.873  1.089   0.090
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1979   0.1977
             R free    0.2395   0.2387
     Rms BondLength    0.0133   0.0133
      Rms BondAngle    1.8685   1.8726
     Rms ChirVolume    0.0905   0.0903
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      50.6s System:    0.2s Elapsed:     0:50