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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 26/ 5/2020 Run time: 10:34:57 


 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 1.90     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- bins 4
  Data line--- ncyc 10
  Data line--- monitor MEDIum
  Data line--- free 0
  Data line--- END

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN   Filename: CDO_R.mtz 

 LABIN FP=FP SIGFP=SIGFP FREE=FreeR_flag

    ****                     Input and Default parameters#                      ****


Input coordinate file.  Logical name - XYZIN actual file name  - CDO_step0-10A_R00_2-00A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-10A_R00_1-90A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_step0-10A_R00_1-90A.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       0.0693
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.9000
  Estimated number of reflections :      21862
  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  1.9000

  Damping factors:     1.0000  1.0000  1.0000


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


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

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

 Chiral centers
          Weight= 1.00

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

 TORSION ANGLES
          Weight= 1.00

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

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

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

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

 Input file :CDO_step0-10A_R00_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        864
Number of   all  reflections      16986
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          16986

   Current auto weighting coefficient =    7.2495699    

 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  240
 Maximuum H,K,L                 :    31   31   65
 Minimum acceptable grid spacing:    73   73  154
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    31   31   65
 Minimum acceptable grid spacing:    73   73  154
 Weight matrix   0.20570168    
 Actual weight    7.2495699      is applied to the X-ray term
Norm of X_ray positional gradient                37.6
Norm of Geom. positional gradient                77.5
Norm of X_ray B-factor gradient                  128.
Norm of Geom. B-factor gradient                  99.1
Product of X_ray and Geom posit. gradients     -0.678E+07
 Cosine of angle between them                      -0.241
Product of X_ray and Geom B-fact gradients     -0.300E+08
 Cosine of angle between them                      -0.732


Residuals: XRAY=     0.6409E+06 GEOM=     0.1261E+05 TOTAL=     0.6535E+06
 function value    653531.31    

-------------------------------------------------------------------------------
             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 =     0.0403, B  =    0.3463
Partial structure    1: scale =     0.3753, B  =   46.3030
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2213 100.00   480.8   485.3  0.16  0.17      98   477.0   485.5  0.20  0.22
 0.104    3735 100.00   385.9   369.4  0.16  0.15     189   387.0   363.4  0.22  0.20
 0.173    4666  99.96   247.1   241.5  0.15  0.13     276   264.7   258.4  0.23  0.19
 0.242    5503 100.00   188.4   189.7  0.19  0.14     301   190.2   190.1  0.23  0.20
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1524   0.910    689   0.805   2213   0.878  0.959  0.9623  0.9687  0.9174  0.9417
  0.1042   3040   0.879    695   0.771   3735   0.859  0.996  0.9459  0.9622  0.8755  0.9454
  0.1733   3977   0.858    689   0.761   4666   0.844  0.979  0.9412  0.9553  0.8772  0.9423
  0.2425   4801   0.860    705   0.741   5506   0.845  0.946  0.9351  0.9490  0.8564  0.9188
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16120
Percentage observed                  =    99.9823
Percentage of free reflections       =     5.0871
Overall R factor                     =     0.1632
Free R factor                        =     0.2192
Average Fourier shell correlation    =     0.9566
AverageFree Fourier shell correlation=     0.9425
Overall weighted R factor            =     0.1504
Free weighted R factor               =     0.2026
Overall weighted R2 factor           =     0.1821
Free weighted R2 factor              =     0.2424
Average correlation coefficient      =     0.9349
Overall correlation coefficient      =     0.9542
Free correlation coefficient         =     0.9111
Cruickshanks DPI for coordinate error=     0.1443
DPI based on free R factor           =     0.1431
Overall figure of merit              =     0.8523
ML based su of positional parameters =     0.0910
ML based su of thermal parameters    =     3.0295
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    88408.117       12610.502       653531.31      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.21796259    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    645593.94    

-------------------------------------------------------------------------------
             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 =     0.0402, B  =   -0.1349
Partial structure    1: scale =     0.3751, B  =   46.8981
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1614
Free R factor                        =     0.2161
Average Fourier shell correlation    =     0.9590
AverageFree Fourier shell correlation=     0.9448
Average correlation coefficient      =     0.9384
Overall figure of merit              =     0.8577
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    87955.156       7956.9043       645593.94       653531.31    


     CGMAT cycle number =      3

 Weight matrix   0.22145483    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    644844.13    

-------------------------------------------------------------------------------
             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 =     0.0402, B  =   -0.0772
Partial structure    1: scale =     0.3753, B  =   46.8451
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1603
Free R factor                        =     0.2150
Average Fourier shell correlation    =     0.9597
AverageFree Fourier shell correlation=     0.9456
Average correlation coefficient      =     0.9395
Overall figure of merit              =     0.8589
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    87820.367       8184.2793       644844.13       645593.94    


     CGMAT cycle number =      4

 Weight matrix   0.22292538    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    644503.50    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.0698
Partial structure    1: scale =     0.3759, B  =   46.6317
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1599
Free R factor                        =     0.2145
Average Fourier shell correlation    =     0.9599
AverageFree Fourier shell correlation=     0.9459
Average correlation coefficient      =     0.9399
Overall figure of merit              =     0.8593
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    87763.914       8252.8848       644503.50       644844.13    


     CGMAT cycle number =      5

 Weight matrix   0.22490954    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    644340.56    

-------------------------------------------------------------------------------
             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 =     0.0402, B  =   -0.0701
Partial structure    1: scale =     0.3759, B  =   46.6942
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1597
Free R factor                        =     0.2143
Average Fourier shell correlation    =     0.9601
AverageFree Fourier shell correlation=     0.9462
Average correlation coefficient      =     0.9401
Overall figure of merit              =     0.8598
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    87737.094       8284.3516       644340.56       644503.50    


     CGMAT cycle number =      6

 Weight matrix   0.22656435    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    644115.31    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.1249
Partial structure    1: scale =     0.3761, B  =   46.5434
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1596
Free R factor                        =     0.2139
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9464
Average correlation coefficient      =     0.9402
Overall figure of merit              =     0.8603
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    87707.445       8274.0488       644115.31       644340.56    


     CGMAT cycle number =      7

 Weight matrix   0.22686866    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    644038.63    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.1094
Partial structure    1: scale =     0.3766, B  =   46.6382
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1596
Free R factor                        =     0.2138
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9465
Average correlation coefficient      =     0.9403
Overall figure of merit              =     0.8603
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    87692.664       8304.4922       644038.63       644115.31    


     CGMAT cycle number =      8

 Weight matrix   0.22671826    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    644030.00    

-------------------------------------------------------------------------------
             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 =     0.0402, B  =   -0.1209
Partial structure    1: scale =     0.3763, B  =   46.5593
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1596
Free R factor                        =     0.2139
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9465
Average correlation coefficient      =     0.9404
Overall figure of merit              =     0.8603
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    87691.570       8303.7842       644030.00       644038.63    


     CGMAT cycle number =      9

 Weight matrix   0.22666846    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    644071.50    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.1066
Partial structure    1: scale =     0.3758, B  =   46.5464
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1597
Free R factor                        =     0.2138
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9466
Average correlation coefficient      =     0.9404
Overall figure of merit              =     0.8604
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    87698.688       8304.7490       644038.50       644030.00    
 fvalues    87698.688       8304.7490       644038.50       644082.50    


     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.= 0.943 id.= 3.000 dev= -2.06 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    31   31   65
 Minimum acceptable grid spacing:    73   73  154
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    31   31   65
 Minimum acceptable grid spacing:    73   73  154
 Weight matrix   0.22680278    
 Actual weight    7.2495699      is applied to the X-ray term
Norm of X_ray positional gradient                32.1
Norm of Geom. positional gradient                32.0
Norm of X_ray B-factor gradient                  108.
Norm of Geom. B-factor gradient                  112.
Product of X_ray and Geom posit. gradients     -0.994E+07
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.384E+08
 Cosine of angle between them                      -0.987


Residuals: XRAY=     0.6357E+06 GEOM=      8307.     TOTAL=     0.6440E+06
 function value    644046.06    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2106     1.725     1.644
Bond angles  : others                          3238     1.432     1.580
Torsion angles, period  1. refined              185     7.000     5.000
Torsion angles, period  2. refined               90    36.460    22.778
Torsion angles, period  3. refined              268    14.379    15.000
Torsion angles, period  4. refined                9    11.603    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                   295     0.247     0.200
VDW repulsions.others                          1371     0.192     0.200
VDW; torsion: refined_atoms                     718     0.170     0.200
VDW; torsion.others                             782     0.083     0.200
HBOND: refined_atoms                            228     0.202     0.200
HBOND.others                                      1     0.025     0.200
VDW repulsions: symmetry: refined_atoms           9     0.224     0.200
VDW repulsions: symmetry: others                 22     0.198     0.200
HBOND: symmetry: refined_atoms                   20     0.211     0.200
M. chain bond B values: refined atoms           746     1.542     1.215
M. chain bond B values: others                  746     1.541     1.215
M. chain angle B values: refined atoms          929     2.481     1.808
M. chain angle B values: others                 930     2.480     1.807
S. chain bond B values: refined atoms           811     2.538     1.555
S. chain bond B values: others                  810     2.535     1.555
S. chain angle B values: refined atoms         1177     4.011     2.185
S. chain angle B values: others                1178     4.009     2.184
Long range B values: refined atoms             1850     6.725    16.938
Long range B values: others                    1754     6.436    15.574
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.1002
Partial structure    1: scale =     0.3759, B  =   46.6608
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2213 100.00   481.6   485.8  0.16  0.17      98   477.8   483.4  0.19  0.21
 0.104    3735 100.00   386.5   369.2  0.16  0.15     189   387.6   361.7  0.21  0.20
 0.173    4666  99.96   247.5   242.1  0.16  0.13     276   265.1   256.8  0.22  0.19
 0.242    5503 100.00   188.7   189.5  0.16  0.13     301   190.5   190.4  0.23  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1524   0.925    689   0.826   2213   0.894  0.959  0.9657  0.9719  0.9180  0.9414
  0.1042   3040   0.885    695   0.777   3735   0.864  0.996  0.9485  0.9638  0.8811  0.9450
  0.1733   3977   0.867    689   0.767   4666   0.852  0.979  0.9465  0.9574  0.8911  0.9395
  0.2425   4801   0.866    705   0.748   5506   0.851  0.951  0.9392  0.9559  0.8619  0.9377
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16120
Percentage observed                  =    99.9823
Percentage of free reflections       =     5.0871
Overall R factor                     =     0.1597
Free R factor                        =     0.2138
Average Fourier shell correlation    =     0.9604
AverageFree Fourier shell correlation=     0.9466
Overall weighted R factor            =     0.1493
Free weighted R factor               =     0.1977
Overall weighted R2 factor           =     0.1820
Free weighted R2 factor              =     0.2376
Average correlation coefficient      =     0.9404
Overall correlation coefficient      =     0.9553
Free correlation coefficient         =     0.9155
Cruickshanks DPI for coordinate error=     0.1412
DPI based on free R factor           =     0.1395
Overall figure of merit              =     0.8604
ML based su of positional parameters =     0.0866
ML based su of thermal parameters    =     2.8868
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    87693.422       8306.5059       644046.06       644082.50    

    ****                              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.= 0.943 id.= 3.000 dev= -2.06 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_step0-10A_R00_1-90A.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     1.725     1.644
Bond angles  : others                          3238     1.432     1.580
Torsion angles, period  1. refined              185     6.998     5.000
Torsion angles, period  2. refined               90    36.496    22.778
Torsion angles, period  3. refined              268    14.369    15.000
Torsion angles, period  4. refined                9    11.562    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                   295     0.247     0.200
VDW repulsions.others                          1374     0.192     0.200
VDW; torsion: refined_atoms                     718     0.170     0.200
VDW; torsion.others                             783     0.083     0.200
HBOND: refined_atoms                            226     0.203     0.200
HBOND.others                                      1     0.020     0.200
VDW repulsions: symmetry: refined_atoms           9     0.224     0.200
VDW repulsions: symmetry: others                 22     0.199     0.200
HBOND: symmetry: refined_atoms                   20     0.211     0.200
M. chain bond B values: refined atoms           746     1.542     1.215
M. chain bond B values: others                  746     1.541     1.215
M. chain angle B values: refined atoms          929     2.481     1.808
M. chain angle B values: others                 930     2.479     1.808
S. chain bond B values: refined atoms           811     2.538     1.555
S. chain bond B values: others                  810     2.535     1.555
S. chain angle B values: refined atoms         1177     4.009     2.185
S. chain angle B values: others                1178     4.007     2.185
Long range B values: refined atoms             1848     6.659    16.875
Long range B values: others                    1752     6.363    15.506
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.0998
Partial structure    1: scale =     0.3762, B  =   46.5154
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2213 100.00   481.4   485.6  0.16  0.17      98   477.7   483.4  0.19  0.21
 0.104    3735 100.00   386.4   369.2  0.16  0.15     189   387.5   361.5  0.21  0.20
 0.173    4666  99.96   247.4   242.1  0.16  0.13     276   265.0   256.7  0.22  0.19
 0.242    5503 100.00   188.7   189.5  0.16  0.13     301   190.5   190.4  0.23  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1524   0.925    689   0.826   2213   0.894  0.959  0.9656  0.9718  0.9179  0.9414
  0.1042   3040   0.884    695   0.777   3735   0.865  0.996  0.9485  0.9638  0.8811  0.9450
  0.1733   3977   0.867    689   0.767   4666   0.852  0.979  0.9465  0.9573  0.8909  0.9394
  0.2425   4801   0.866    705   0.748   5506   0.851  0.951  0.9393  0.9560  0.8621  0.9378
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16120
Percentage observed                  =    99.9823
Percentage of free reflections       =     5.0871
Overall R factor                     =     0.1596
Free R factor                        =     0.2139
Average Fourier shell correlation    =     0.9604
AverageFree Fourier shell correlation=     0.9466
Overall weighted R factor            =     0.1493
Free weighted R factor               =     0.1979
Overall weighted R2 factor           =     0.1819
Free weighted R2 factor              =     0.2379
Average correlation coefficient      =     0.9404
Overall correlation coefficient      =     0.9553
Free correlation coefficient         =     0.9155
Cruickshanks DPI for coordinate error=     0.1412
DPI based on free R factor           =     0.1396
Overall figure of merit              =     0.8604
ML based su of positional parameters =     0.0866
ML based su of thermal parameters    =     2.8868
-----------------------------------------------------------------------------
  Time in seconds: CPU =        14.16
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1632   0.2192   0.852       88408.    4898.9   0.0111  0.816   1.739  1.003   0.084
       1   0.1614   0.2161   0.858       87955.    4885.2   0.0108  0.802   1.708  0.985   0.082
       2   0.1603   0.2150   0.859       87820.    4878.9   0.0112  0.828   1.718  0.991   0.082
       3   0.1599   0.2145   0.859       87764.    4875.9   0.0113  0.834   1.720  0.994   0.082
       4   0.1597   0.2143   0.860       87737.    4873.9   0.0113  0.836   1.721  0.994   0.082
       5   0.1596   0.2139   0.860       87707.    4872.7   0.0113  0.839   1.722  0.995   0.082
       6   0.1596   0.2138   0.860       87693.    4871.8   0.0113  0.839   1.723  0.996   0.082
       7   0.1596   0.2139   0.860       87692.    4872.0   0.0113  0.839   1.724  0.996   0.082
       8   0.1597   0.2138   0.860       87697.    4872.1   0.0113  0.839   1.725  0.997   0.082
       9   0.1597   0.2138   0.860       87693.    4871.7   0.0113  0.840   1.725  0.997   0.082
      10   0.1596   0.2139   0.860       87689.    4871.6   0.0113  0.840   1.725  0.997   0.082
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1632   0.1596
             R free    0.2192   0.2139
     Rms BondLength    0.0111   0.0113
      Rms BondAngle    1.7392   1.7254
     Rms ChirVolume    0.0837   0.0824
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      46.0s System:    1.2s Elapsed:     0:47