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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: 13:01:05 


 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 1.99     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_2-00A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-99A.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_1-99A.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       0.0631
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.9900
  Estimated number of reflections :      18249
  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  1.9900

  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_2-00A.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=   1.990 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=   2.198 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=   1.846 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=   2.205 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=   2.385 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=   2.449 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=   2.091 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        751
Number of   all  reflections      14833
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          14833

   Current auto weighting coefficient =    7.4745178    

 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.= 0.911 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  224
 Maximuum H,K,L                 :    30   30   62
 Minimum acceptable grid spacing:    70   70  149
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  224
 Maximuum H,K,L                 :    30   30   62
 Minimum acceptable grid spacing:    70   70  149
 Weight matrix   0.17629682    
 Actual weight    7.4745178      is applied to the X-ray term
Norm of X_ray positional gradient                29.5
Norm of Geom. positional gradient                77.5
Norm of X_ray B-factor gradient                  97.2
Norm of Geom. B-factor gradient                  99.1
Product of X_ray and Geom posit. gradients     -0.793E+07
 Cosine of angle between them                      -0.359
Product of X_ray and Geom B-fact gradients     -0.280E+08
 Cosine of angle between them                      -0.902


Residuals: XRAY=     0.5826E+06 GEOM=     0.1261E+05 TOTAL=     0.5952E+06
 function value    595229.75    

-------------------------------------------------------------------------------
             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     1.739     1.644
Bond angles  : others                          3238     2.346     1.580
Torsion angles, period  1. refined              185     7.161     5.000
Torsion angles, period  2. refined               90    36.168    22.778
Torsion angles, period  3. refined              268    14.753    15.000
Torsion angles, period  4. refined                9    12.089    15.000
Chiral centres: refined atoms                   196     0.084     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.015     0.020
VDW repulsions: refined_atoms                   301     0.247     0.200
VDW repulsions.others                          1341     0.222     0.200
VDW; torsion: refined_atoms                     709     0.171     0.200
VDW; torsion.others                             702     0.080     0.200
HBOND: refined_atoms                            232     0.206     0.200
HBOND.others                                      2     0.061     0.200
Metal-ion: refined_atoms                          1     0.010     0.200
VDW repulsions: symmetry: refined_atoms           9     0.231     0.200
VDW repulsions: symmetry: others                 25     0.191     0.200
HBOND: symmetry: refined_atoms                   15     0.230     0.200
M. chain bond B values: refined atoms           746     1.481     1.186
M. chain bond B values: others                  746     1.480     1.187
M. chain angle B values: refined atoms          929     2.433     1.766
M. chain angle B values: others                 930     2.432     1.765
S. chain bond B values: refined atoms           811     2.367     1.505
S. chain bond B values: others                  810     2.362     1.504
S. chain angle B values: refined atoms         1177     3.791     2.116
S. chain angle B values: others                1178     3.789     2.115
Long range B values: refined atoms             1853     6.602    16.469
Long range B values: others                    1753     6.237    15.042
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0398, B  =   -0.1300
Partial structure    1: scale =     0.3744, B  =   47.9317
Overall anisotropic scale factors
   B11 =  -0.28 B22 =  -0.28 B33 =   0.57 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.032    1948 100.00   482.5   485.3  0.16  0.17      89   473.6   483.1  0.20  0.22
 0.095    3253 100.00   419.1   400.2  0.16  0.15     164   417.2   387.2  0.21  0.20
 0.158    4087  99.95   263.8   262.0  0.16  0.13     242   276.1   271.9  0.23  0.20
 0.221    4787 100.00   215.0   212.8  0.16  0.13     256   219.0   219.4  0.22  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0321   1320   0.906    628   0.809   1948   0.875  0.962  0.9612  0.9687  0.9178  0.9420
  0.0951   2618   0.892    635   0.768   3253   0.868  1.002  0.9492  0.9644  0.8858  0.9451
  0.1580   3458   0.850    629   0.764   4087   0.836  0.963  0.9367  0.9533  0.8680  0.9414
  0.2210   4161   0.867    631   0.750   4792   0.851  0.966  0.9440  0.9573  0.8792  0.9409
 $$
Resolution limits                    =     41.964     1.990
Number of used reflections           =      14078
Percentage observed                  =    99.9798
Percentage of free reflections       =     5.0644
Overall R factor                     =     0.1569
Free R factor                        =     0.2182
Average Fourier shell correlation    =     0.9593
AverageFree Fourier shell correlation=     0.9448
Overall weighted R factor            =     0.1480
Free weighted R factor               =     0.2021
Overall weighted R2 factor           =     0.1808
Free weighted R2 factor              =     0.2417
Average correlation coefficient      =     0.9422
Overall correlation coefficient      =     0.9543
Free correlation coefficient         =     0.9080
Cruickshanks DPI for coordinate error=     0.1658
DPI based on free R factor           =     0.1595
Overall figure of merit              =     0.8541
ML based su of positional parameters =     0.0998
ML based su of thermal parameters    =     3.4657
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    77947.406       12610.502       595229.75      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.18463589    
 Actual weight    7.4745178      is applied to the X-ray term


 function value    589187.94    

-------------------------------------------------------------------------------
             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 =     0.0398, B  =   -0.1734
Partial structure    1: scale =     0.3743, B  =   48.2898
Overall anisotropic scale factors
   B11 =  -0.28 B22 =  -0.28 B33 =   0.57 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1572
Free R factor                        =     0.2180
Average Fourier shell correlation    =     0.9606
AverageFree Fourier shell correlation=     0.9462
Average correlation coefficient      =     0.9425
Overall figure of merit              =     0.8584
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    77760.125       7968.5103       589187.94       595229.75    


     CGMAT cycle number =      3

 Weight matrix   0.18474987    
 Actual weight    7.4745178      is applied to the X-ray term


 function value    589095.00    

-------------------------------------------------------------------------------
             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 =     0.0398, B  =   -0.1426
Partial structure    1: scale =     0.3746, B  =   48.3711
Overall anisotropic scale factors
   B11 =  -0.28 B22 =  -0.28 B33 =   0.57 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1569
Free R factor                        =     0.2184
Average Fourier shell correlation    =     0.9607
AverageFree Fourier shell correlation=     0.9462
Average correlation coefficient      =     0.9426
Overall figure of merit              =     0.8583
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    77744.750       7990.5186       589095.00       589187.94    


     CGMAT cycle number =      4

 Weight matrix   0.18406343    
 Actual weight    7.4745178      is applied to the X-ray term


 function value    589133.13    

-------------------------------------------------------------------------------
             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 =     0.0398, B  =   -0.1458
Partial structure    1: scale =     0.3746, B  =   48.2899
Overall anisotropic scale factors
   B11 =  -0.28 B22 =  -0.28 B33 =   0.57 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1570
Free R factor                        =     0.2189
Average Fourier shell correlation    =     0.9606
AverageFree Fourier shell correlation=     0.9460
Average correlation coefficient      =     0.9425
Overall figure of merit              =     0.8579
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02


 fvalues    77754.578       7955.4395       589130.25       589095.00    
 fvalues    77754.578       7955.4395       589130.25       589133.44    


     CGMAT cycle number =      5

 Weight matrix   0.18371998    
 Actual weight    7.4745178      is applied to the X-ray term


 function value    589152.81    

-------------------------------------------------------------------------------
             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 =     0.0398, B  =   -0.1556
Partial structure    1: scale =     0.3744, B  =   48.2680
Overall anisotropic scale factors
   B11 =  -0.28 B22 =  -0.28 B33 =   0.57 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1571
Free R factor                        =     0.2194
Average Fourier shell correlation    =     0.9605
AverageFree Fourier shell correlation=     0.9459
Average correlation coefficient      =     0.9424
Overall figure of merit              =     0.8577
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03


 fvalues    77764.133       7916.6006       589190.19       589133.44    

 fvalues    77764.133       7916.6006       589176.25       589166.00    
 fvalues    77764.133       7916.6006       589176.25       589166.00    


     CGMAT cycle number =      6

 Weight matrix   0.18357815    
 Actual weight    7.4745178      is applied to the X-ray term


 function value    589169.00    

-------------------------------------------------------------------------------
             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 =     0.0398, B  =   -0.1582
Partial structure    1: scale =     0.3745, B  =   48.2303
Overall anisotropic scale factors
   B11 =  -0.28 B22 =  -0.28 B33 =   0.57 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1572
Free R factor                        =     0.2195
Average Fourier shell correlation    =     0.9605
AverageFree Fourier shell correlation=     0.9458
Average correlation coefficient      =     0.9424
Overall figure of merit              =     0.8576
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    77765.547       7907.7524       589181.56       589166.00    

 fvalues    77765.547       7907.7524       589174.06       589167.69    
 fvalues    77765.547       7907.7524       589174.06       589167.69    


     CGMAT cycle number =      7

 Weight matrix   0.18358262    
 Actual weight    7.4745178      is applied to the X-ray term


 function value    589150.81    

-------------------------------------------------------------------------------
             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 =     0.0398, B  =   -0.1583
Partial structure    1: scale =     0.3745, B  =   48.2380
Overall anisotropic scale factors
   B11 =  -0.28 B22 =  -0.28 B33 =   0.57 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1572
Free R factor                        =     0.2196
Average Fourier shell correlation    =     0.9605
AverageFree Fourier shell correlation=     0.9458
Average correlation coefficient      =     0.9424
Overall figure of merit              =     0.8576
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    77763.875       7903.3384       589150.81       589167.69    


     CGMAT cycle number =      8

 Weight matrix   0.18329319    
 Actual weight    7.4745178      is applied to the X-ray term


 function value    589182.44    

-------------------------------------------------------------------------------
             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 =     0.0398, B  =   -0.1606
Partial structure    1: scale =     0.3746, B  =   48.3156
Overall anisotropic scale factors
   B11 =  -0.28 B22 =  -0.28 B33 =   0.57 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1572
Free R factor                        =     0.2197
Average Fourier shell correlation    =     0.9604
AverageFree Fourier shell correlation=     0.9458
Average correlation coefficient      =     0.9424
Overall figure of merit              =     0.8574
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    77769.570       7893.2695       589211.56       589150.81    

 fvalues    77769.570       7893.2695       589206.94       589183.31    
 fvalues    77769.570       7893.2695       589206.94       589183.31    


     CGMAT cycle number =      9

 Weight matrix   0.18311600    
 Actual weight    7.4745178      is applied to the X-ray term


 function value    589211.06    

-------------------------------------------------------------------------------
             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 =     0.0398, B  =   -0.1572
Partial structure    1: scale =     0.3745, B  =   48.2991
Overall anisotropic scale factors
   B11 =  -0.28 B22 =  -0.28 B33 =   0.57 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1572
Free R factor                        =     0.2197
Average Fourier shell correlation    =     0.9604
AverageFree Fourier shell correlation=     0.9458
Average correlation coefficient      =     0.9424
Overall figure of merit              =     0.8574
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02

 fvalues    77766.820       7892.3350       589161.81       589183.31    


     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.= 0.931 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  224
 Maximuum H,K,L                 :    30   30   62
 Minimum acceptable grid spacing:    70   70  149
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  224
 Maximuum H,K,L                 :    30   30   62
 Minimum acceptable grid spacing:    70   70  149
 Weight matrix   0.18332203    
 Actual weight    7.4745178      is applied to the X-ray term
Norm of X_ray positional gradient                29.3
Norm of Geom. positional gradient                29.4
Norm of X_ray B-factor gradient                  95.9
Norm of Geom. B-factor gradient                  102.
Product of X_ray and Geom posit. gradients     -0.831E+07
 Cosine of angle between them                      -0.998
Product of X_ray and Geom B-fact gradients     -0.308E+08
 Cosine of angle between them                      -0.979


Residuals: XRAY=     0.5813E+06 GEOM=      7891.     TOTAL=     0.5892E+06
 function value    589175.63    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2106     1.702     1.644
Bond angles  : others                          3238     1.401     1.580
Torsion angles, period  1. refined              185     7.179     5.000
Torsion angles, period  2. refined               90    36.139    22.778
Torsion angles, period  3. refined              268    14.678    15.000
Torsion angles, period  4. refined                9    12.126    15.000
Chiral centres: refined atoms                   196     0.082     0.200
Planar groups: refined atoms                   1743     0.009     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   304     0.244     0.200
VDW repulsions.others                          1350     0.197     0.200
VDW; torsion: refined_atoms                     711     0.170     0.200
VDW; torsion.others                             737     0.084     0.200
HBOND: refined_atoms                            237     0.205     0.200
HBOND.others                                      2     0.068     0.200
Metal-ion: refined_atoms                          1     0.006     0.200
VDW repulsions: symmetry: refined_atoms           9     0.228     0.200
VDW repulsions: symmetry: others                 21     0.189     0.200
HBOND: symmetry: refined_atoms                   15     0.232     0.200
HBOND: symmetry: others                           1     0.003     0.200
M. chain bond B values: refined atoms           746     1.465     1.189
M. chain bond B values: others                  746     1.464     1.189
M. chain angle B values: refined atoms          929     2.405     1.770
M. chain angle B values: others                 930     2.404     1.769
S. chain bond B values: refined atoms           811     2.332     1.500
S. chain bond B values: others                  810     2.327     1.500
S. chain angle B values: refined atoms         1177     3.727     2.112
S. chain angle B values: others                1178     3.725     2.111
Long range B values: refined atoms             1864     6.707    16.656
Long range B values: others                    1762     6.348    15.224
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0398, B  =   -0.1603
Partial structure    1: scale =     0.3745, B  =   48.2988
Overall anisotropic scale factors
   B11 =  -0.28 B22 =  -0.28 B33 =   0.57 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.032    1948 100.00   483.1   485.7  0.16  0.17      89   474.3   483.7  0.20  0.22
 0.095    3253 100.00   419.7   400.6  0.16  0.15     164   417.8   386.6  0.22  0.20
 0.158    4087  99.95   264.2   262.3  0.16  0.14     242   276.5   271.6  0.23  0.20
 0.221    4787 100.00   215.3   213.1  0.15  0.12     256   219.3   219.7  0.22  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0321   1320   0.919    628   0.823   1948   0.888  0.962  0.9634  0.9714  0.9153  0.9418
  0.0951   2618   0.893    635   0.770   3253   0.869  1.002  0.9492  0.9649  0.8835  0.9451
  0.1580   3458   0.850    629   0.762   4087   0.837  0.963  0.9371  0.9531  0.8692  0.9395
  0.2210   4161   0.870    631   0.751   4792   0.855  0.966  0.9456  0.9591  0.8811  0.9432
 $$
Resolution limits                    =     41.964     1.990
Number of used reflections           =      14078
Percentage observed                  =    99.9798
Percentage of free reflections       =     5.0644
Overall R factor                     =     0.1572
Free R factor                        =     0.2197
Average Fourier shell correlation    =     0.9604
AverageFree Fourier shell correlation=     0.9458
Overall weighted R factor            =     0.1483
Free weighted R factor               =     0.2035
Overall weighted R2 factor           =     0.1809
Free weighted R2 factor              =     0.2422
Average correlation coefficient      =     0.9424
Overall correlation coefficient      =     0.9542
Free correlation coefficient         =     0.9072
Cruickshanks DPI for coordinate error=     0.1662
DPI based on free R factor           =     0.1607
Overall figure of merit              =     0.8574
ML based su of positional parameters =     0.0978
ML based su of thermal parameters    =     3.4015
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    77768.930       7890.5078       589194.31       589161.81    

 fvalues    77768.930       7890.5078       589170.88       589175.75    
 fvalues    77768.930       7890.5078       589170.88       589175.75    

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.931 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_1-99A.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     1.702     1.644
Bond angles  : others                          3238     1.401     1.580
Torsion angles, period  1. refined              185     7.179     5.000
Torsion angles, period  2. refined               90    36.139    22.778
Torsion angles, period  3. refined              268    14.678    15.000
Torsion angles, period  4. refined                9    12.125    15.000
Chiral centres: refined atoms                   196     0.082     0.200
Planar groups: refined atoms                   1743     0.009     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   304     0.244     0.200
VDW repulsions.others                          1350     0.197     0.200
VDW; torsion: refined_atoms                     711     0.170     0.200
VDW; torsion.others                             737     0.084     0.200
HBOND: refined_atoms                            238     0.204     0.200
HBOND.others                                      2     0.068     0.200
Metal-ion: refined_atoms                          1     0.006     0.200
VDW repulsions: symmetry: refined_atoms           9     0.228     0.200
VDW repulsions: symmetry: others                 21     0.189     0.200
HBOND: symmetry: refined_atoms                   15     0.232     0.200
HBOND: symmetry: others                           1     0.003     0.200
M. chain bond B values: refined atoms           746     1.465     1.189
M. chain bond B values: others                  746     1.464     1.189
M. chain angle B values: refined atoms          929     2.405     1.770
M. chain angle B values: others                 930     2.404     1.769
S. chain bond B values: refined atoms           811     2.332     1.500
S. chain bond B values: others                  810     2.327     1.500
S. chain angle B values: refined atoms         1177     3.727     2.112
S. chain angle B values: others                1178     3.725     2.111
Long range B values: refined atoms             1865     6.709    16.678
Long range B values: others                    1762     6.347    15.224
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0398, B  =   -0.1601
Partial structure    1: scale =     0.3745, B  =   48.2964
Overall anisotropic scale factors
   B11 =  -0.28 B22 =  -0.28 B33 =   0.57 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.032    1948 100.00   483.1   485.7  0.16  0.17      89   474.3   483.7  0.20  0.22
 0.095    3253 100.00   419.7   400.6  0.16  0.15     164   417.8   386.6  0.22  0.20
 0.158    4087  99.95   264.2   262.3  0.16  0.14     242   276.5   271.6  0.23  0.20
 0.221    4787 100.00   215.3   213.1  0.15  0.12     256   219.3   219.7  0.22  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0321   1320   0.919    628   0.823   1948   0.888  0.962  0.9634  0.9714  0.9153  0.9418
  0.0951   2618   0.893    635   0.770   3253   0.869  1.002  0.9491  0.9649  0.8834  0.9451
  0.1580   3458   0.850    629   0.762   4087   0.837  0.963  0.9371  0.9531  0.8692  0.9395
  0.2210   4161   0.870    631   0.751   4792   0.855  0.966  0.9456  0.9591  0.8810  0.9432
 $$
Resolution limits                    =     41.964     1.990
Number of used reflections           =      14078
Percentage observed                  =    99.9798
Percentage of free reflections       =     5.0644
Overall R factor                     =     0.1572
Free R factor                        =     0.2198
Average Fourier shell correlation    =     0.9604
AverageFree Fourier shell correlation=     0.9458
Overall weighted R factor            =     0.1483
Free weighted R factor               =     0.2035
Overall weighted R2 factor           =     0.1809
Free weighted R2 factor              =     0.2423
Average correlation coefficient      =     0.9424
Overall correlation coefficient      =     0.9542
Free correlation coefficient         =     0.9072
Cruickshanks DPI for coordinate error=     0.1662
DPI based on free R factor           =     0.1607
Overall figure of merit              =     0.8574
ML based su of positional parameters =     0.0978
ML based su of thermal parameters    =     3.4015
-----------------------------------------------------------------------------
  Time in seconds: CPU =        18.31
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1569   0.2182   0.854       77947.    4313.7   0.0111  0.816   1.739  1.003   0.084
       1   0.1572   0.2180   0.858       77760.    4311.5   0.0108  0.790   1.704  0.982   0.083
       2   0.1569   0.2184   0.858       77745.    4311.3   0.0111  0.812   1.711  0.987   0.083
       3   0.1570   0.2189   0.858       77755.    4312.3   0.0111  0.812   1.709  0.986   0.083
       4   0.1571   0.2194   0.858       77762.    4312.8   0.0111  0.809   1.705  0.984   0.082
       5   0.1572   0.2195   0.858       77766.    4313.1   0.0110  0.809   1.704  0.983   0.082
       6   0.1572   0.2196   0.858       77764.    4313.1   0.0110  0.808   1.703  0.983   0.082
       7   0.1572   0.2197   0.857       77769.    4313.6   0.0110  0.808   1.703  0.983   0.082
       8   0.1572   0.2197   0.857       77773.    4313.7   0.0110  0.808   1.702  0.983   0.082
       9   0.1572   0.2197   0.857       77769.    4313.5   0.0110  0.808   1.702  0.983   0.082
      10   0.1572   0.2198   0.857       77769.    4313.6   0.0110  0.808   1.702  0.982   0.082
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1569   0.1572
             R free    0.2182   0.2198
     Rms BondLength    0.0111   0.0110
      Rms BondAngle    1.7392   1.7021
     Rms ChirVolume    0.0837   0.0821
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      50.5s System:    0.1s Elapsed:     0:51