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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 27/ 5/2020 Run time: 00:37:30 


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

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

 LABIN FP=FP SIGFP=SIGFP FREE=FreeR_flag

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


Input coordinate file.  Logical name - XYZIN actual file name  - CDO_step0-01A_R00_1-54A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-53A.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_1-53A.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       0.1068
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.5300
  Estimated number of reflections :      40432
  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  1.5300

  Damping factors:     1.0000  1.0000  1.0000


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


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

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

 Chiral centers
          Weight= 1.00

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

 TORSION ANGLES
          Weight= 1.00

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

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

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

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

 Input file :CDO_step0-01A_R00_1-54A.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.51
 _lib_update       11/07/18
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 24624
                with complete description    : 24624
  NUMBER OF MODIFICATIONS                    :    70
  NUMBER OF LINKS                            :    77
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  Number of atoms    :    1836
  Number of residues :     502
  Number of chains   :       4
  I am reading library. Please wait.
                mon_lib.cif
  INFO:     link is found (not be used) dist=   2.059 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=   2.192 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=   1.828 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=   2.218 ideal_dist=   2.090
            ch:AAA  res: 140  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.408 ideal_dist=   1.945
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:N   .
  INFO:     link is found (not be used) dist=   2.390 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=   2.125 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       1603
Number of   all  reflections      31992
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          31992

   Current auto weighting coefficient =    6.3246508    

 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.= 0.895 id.= 3.000 dev= -2.11 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    38   38   81
 Minimum acceptable grid spacing:    86   86  181
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    38   38   81
 Minimum acceptable grid spacing:    86   86  181
 Weight matrix   0.28167662    
 Actual weight    6.3246508      is applied to the X-ray term
Norm of X_ray positional gradient                36.9
Norm of Geom. positional gradient                82.9
Norm of X_ray B-factor gradient                  98.5
Norm of Geom. B-factor gradient                  108.
Product of X_ray and Geom posit. gradients     -0.148E+08
 Cosine of angle between them                      -0.501
Product of X_ray and Geom B-fact gradients     -0.305E+08
 Cosine of angle between them                      -0.888


Residuals: XRAY=     0.9454E+06 GEOM=     0.1345E+05 TOTAL=     0.9588E+06
 function value    958825.19    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.035     0.017
Bond angles  : refined atoms                   2106     1.869     1.644
Bond angles  : others                          3238     2.369     1.580
Torsion angles, period  1. refined              185     6.753     5.000
Torsion angles, period  2. refined               90    34.739    22.778
Torsion angles, period  3. refined              268    13.310    15.000
Torsion angles, period  4. refined                9    12.442    15.000
Chiral centres: refined atoms                   196     0.091     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.018     0.020
VDW repulsions: refined_atoms                   304     0.245     0.200
VDW repulsions.others                          1336     0.221     0.200
VDW; torsion: refined_atoms                     731     0.174     0.200
VDW; torsion.others                             726     0.082     0.200
HBOND: refined_atoms                            211     0.201     0.200
HBOND.others                                      1     0.035     0.200
VDW repulsions: symmetry: refined_atoms           8     0.205     0.200
VDW repulsions: symmetry: others                 23     0.202     0.200
HBOND: symmetry: refined_atoms                   22     0.173     0.200
M. chain bond B values: refined atoms           746     1.786     1.573
M. chain bond B values: others                  746     1.781     1.573
M. chain angle B values: refined atoms          929     2.764     2.350
M. chain angle B values: others                 930     2.763     2.349
S. chain bond B values: refined atoms           811     3.220     1.982
S. chain bond B values: others                  810     3.215     1.981
S. chain angle B values: refined atoms         1177     4.888     2.803
S. chain angle B values: others                1178     4.886     2.803
Long range B values: refined atoms             1848     7.861    21.755
Long range B values: others                    1760     7.578    20.329
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0452, B  =    0.1106
Partial structure    1: scale =     0.3918, B  =   38.9946
Overall anisotropic scale factors
   B11 =  -0.19 B22 =  -0.19 B33 =   0.37 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.054    4097 100.00   415.6   425.3  0.17  0.17     194   409.6   417.0  0.20  0.21
 0.161    6961  99.97   237.0   218.5  0.18  0.16     398   246.1   224.0  0.22  0.20
 0.267    8879 100.00   136.7   124.9  0.20  0.18     477   137.2   126.2  0.24  0.21
 0.374   10439 100.00    55.4    68.4  0.38  0.32     533    54.9    68.8  0.41  0.37
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0539   3029   0.907   1068   0.797   4097   0.878  0.947  0.9605  0.9686  0.9044  0.9366
  0.1606   5899   0.867   1062   0.772   6961   0.852  1.045  0.9446  0.9545  0.8879  0.9336
  0.2672   7800   0.843   1079   0.751   8879   0.831  1.034  0.9398  0.9494  0.8953  0.9340
  0.3739   9371   0.577   1079   0.502  10450   0.569  0.599  0.7863  0.8071  0.7580  0.8186
 $$
Resolution limits                    =     41.964     1.530
Number of used reflections           =      30387
Percentage observed                  =    99.9906
Percentage of free reflections       =     5.0109
Overall R factor                     =     0.2023
Free R factor                        =     0.2403
Average Fourier shell correlation    =     0.9042
AverageFree Fourier shell correlation=     0.8924
Overall weighted R factor            =     0.1732
Free weighted R factor               =     0.2083
Overall weighted R2 factor           =     0.2029
Free weighted R2 factor              =     0.2442
Average correlation coefficient      =     0.8946
Overall correlation coefficient      =     0.9591
Free correlation coefficient         =     0.9379
Cruickshanks DPI for coordinate error=     0.0889
DPI based on free R factor           =     0.0919
Overall figure of merit              =     0.7523
ML based su of positional parameters =     0.0726
ML based su of thermal parameters    =     2.1313
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    149474.06       13453.910       958825.19      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.36370245    
 Actual weight    6.3246508      is applied to the X-ray term


 function value    945931.31    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0451, B  =   -0.0692
Partial structure    1: scale =     0.3921, B  =   38.9604
Overall anisotropic scale factors
   B11 =  -0.19 B22 =  -0.19 B33 =   0.37 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2026
Free R factor                        =     0.2393
Average Fourier shell correlation    =     0.9204
AverageFree Fourier shell correlation=     0.9104
Average correlation coefficient      =     0.8928
Overall figure of merit              =     0.7908
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    148236.06       8389.9834       945931.31       958825.19    


     CGMAT cycle number =      3

 Weight matrix   0.37580907    
 Actual weight    6.3246508      is applied to the X-ray term


 function value    944844.31    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0451, B  =    0.0032
Partial structure    1: scale =     0.3922, B  =   38.9703
Overall anisotropic scale factors
   B11 =  -0.19 B22 =  -0.19 B33 =   0.37 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2019
Free R factor                        =     0.2399
Average Fourier shell correlation    =     0.9241
AverageFree Fourier shell correlation=     0.9139
Average correlation coefficient      =     0.8940
Overall figure of merit              =     0.7998
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    148000.92       8790.1914       944844.31       945931.31    


     CGMAT cycle number =      4

 Weight matrix   0.37760559    
 Actual weight    6.3246508      is applied to the X-ray term


 function value    944567.44    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0451, B  =    0.0079
Partial structure    1: scale =     0.3922, B  =   39.0539
Overall anisotropic scale factors
   B11 =  -0.19 B22 =  -0.19 B33 =   0.37 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2018
Free R factor                        =     0.2400
Average Fourier shell correlation    =     0.9248
AverageFree Fourier shell correlation=     0.9144
Average correlation coefficient      =     0.8945
Overall figure of merit              =     0.8016
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    147942.02       8885.8584       944567.44       944844.31    


     CGMAT cycle number =      5

 Weight matrix   0.37710634    
 Actual weight    6.3246508      is applied to the X-ray term


 function value    944568.88    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0451, B  =    0.0227
Partial structure    1: scale =     0.3921, B  =   39.0575
Overall anisotropic scale factors
   B11 =  -0.19 B22 =  -0.19 B33 =   0.37 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2018
Free R factor                        =     0.2400
Average Fourier shell correlation    =     0.9248
AverageFree Fourier shell correlation=     0.9144
Average correlation coefficient      =     0.8947
Overall figure of merit              =     0.8015
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03

 fvalues    147929.83       8926.7275       944531.25       944567.44    


     CGMAT cycle number =      6

 Weight matrix   0.34298897    
 Actual weight    5.7496824      is applied to the X-ray term


 function value    859494.31    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0451, B  =    0.0183
Partial structure    1: scale =     0.3921, B  =   39.0381
Overall anisotropic scale factors
   B11 =  -0.19 B22 =  -0.19 B33 =   0.37 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2018
Free R factor                        =     0.2401
Average Fourier shell correlation    =     0.9248
AverageFree Fourier shell correlation=     0.9143
Average correlation coefficient      =     0.8947
Overall figure of merit              =     0.8015
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    147931.67       8934.1699       859494.31       944531.25    


     CGMAT cycle number =      7

 Weight matrix   0.31088349    
 Actual weight    5.2269840      is applied to the X-ray term


 function value    782224.25    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0451, B  =    0.0150
Partial structure    1: scale =     0.3921, B  =   39.0308
Overall anisotropic scale factors
   B11 =  -0.19 B22 =  -0.19 B33 =   0.37 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2023
Free R factor                        =     0.2400
Average Fourier shell correlation    =     0.9246
AverageFree Fourier shell correlation=     0.9142
Average correlation coefficient      =     0.8943
Overall figure of merit              =     0.8013
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    147997.39       8644.2705       782224.25       859494.31    


     CGMAT cycle number =      8

 Weight matrix   0.30954814    
 Actual weight    5.2269840      is applied to the X-ray term


 function value    782374.19    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0451, B  =    0.0139
Partial structure    1: scale =     0.3920, B  =   38.8794
Overall anisotropic scale factors
   B11 =  -0.19 B22 =  -0.19 B33 =   0.37 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2028
Free R factor                        =     0.2400
Average Fourier shell correlation    =     0.9243
AverageFree Fourier shell correlation=     0.9139
Average correlation coefficient      =     0.8936
Overall figure of merit              =     0.8010
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    148096.14       8301.0830       782433.13       782224.25    

 fvalues    148096.14       8301.0830       782413.56       782397.25    
 fvalues    148096.14       8301.0830       782413.56       782397.25    


     CGMAT cycle number =      9

 Weight matrix   0.30944344    
 Actual weight    5.2269840      is applied to the X-ray term


 function value    782397.50    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0451, B  =    0.0137
Partial structure    1: scale =     0.3920, B  =   38.8654
Overall anisotropic scale factors
   B11 =  -0.19 B22 =  -0.19 B33 =   0.37 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2028
Free R factor                        =     0.2400
Average Fourier shell correlation    =     0.9242
AverageFree Fourier shell correlation=     0.9139
Average correlation coefficient      =     0.8936
Overall figure of merit              =     0.8010
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02

 fvalues    148098.23       8277.2217       782384.38       782397.25    


     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.= 0.912 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        :   144  144  280
 Maximuum H,K,L                 :    38   38   81
 Minimum acceptable grid spacing:    86   86  181
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    38   38   81
 Minimum acceptable grid spacing:    86   86  181
 Weight matrix   0.31035343    
 Actual weight    5.2269840      is applied to the X-ray term
Norm of X_ray positional gradient                37.9
Norm of Geom. positional gradient                38.2
Norm of X_ray B-factor gradient                  101.
Norm of Geom. B-factor gradient                  103.
Product of X_ray and Geom posit. gradients     -0.140E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.334E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.7741E+06 GEOM=      8245.     TOTAL=     0.7824E+06
 function value    782362.56    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.788     1.644
Bond angles  : others                          3238     1.499     1.580
Torsion angles, period  1. refined              185     6.772     5.000
Torsion angles, period  2. refined               90    34.736    22.778
Torsion angles, period  3. refined              268    13.306    15.000
Torsion angles, period  4. refined                9    12.218    15.000
Chiral centres: refined atoms                   196     0.086     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   303     0.244     0.200
VDW repulsions.others                          1376     0.191     0.200
VDW; torsion: refined_atoms                     732     0.172     0.200
VDW; torsion.others                             775     0.084     0.200
HBOND: refined_atoms                            207     0.199     0.200
HBOND.others                                      1     0.012     0.200
VDW repulsions: symmetry: refined_atoms           8     0.200     0.200
VDW repulsions: symmetry: others                 24     0.183     0.200
HBOND: symmetry: refined_atoms                   22     0.164     0.200
M. chain bond B values: refined atoms           746     1.715     1.588
M. chain bond B values: others                  746     1.710     1.588
M. chain angle B values: refined atoms          929     2.694     2.372
M. chain angle B values: others                 930     2.692     2.372
S. chain bond B values: refined atoms           811     3.032     1.983
S. chain bond B values: others                  810     3.027     1.983
S. chain angle B values: refined atoms         1177     4.661     2.811
S. chain angle B values: others                1178     4.659     2.810
Long range B values: refined atoms             1845     7.562    21.754
Long range B values: others                    1761     7.266    20.394
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0451, B  =    0.0000
Partial structure    1: scale =     0.3920, B  =   38.8676
Overall anisotropic scale factors
   B11 =  -0.19 B22 =  -0.19 B33 =   0.37 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.054    4097 100.00   416.3   426.0  0.17  0.17     194   410.3   417.3  0.20  0.21
 0.161    6961  99.97   237.4   219.0  0.18  0.16     398   246.5   224.4  0.22  0.20
 0.267    8879 100.00   136.9   125.3  0.20  0.18     477   137.4   126.4  0.24  0.21
 0.374   10439 100.00    55.5    68.5  0.38  0.32     533    55.0    68.9  0.41  0.36
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0539   3029   0.923   1068   0.822   4097   0.897  0.950  0.9645  0.9724  0.9038  0.9364
  0.1606   5899   0.876   1062   0.780   6961   0.861  1.045  0.9467  0.9563  0.8894  0.9328
  0.2672   7800   0.859   1079   0.770   8879   0.848  1.034  0.9454  0.9546  0.8956  0.9332
  0.3739   9371   0.692   1079   0.617  10450   0.684  0.655  0.8434  0.8585  0.7561  0.8167
 $$
Resolution limits                    =     41.964     1.530
Number of used reflections           =      30387
Percentage observed                  =    99.9906
Percentage of free reflections       =     5.0109
Overall R factor                     =     0.2029
Free R factor                        =     0.2401
Average Fourier shell correlation    =     0.9243
AverageFree Fourier shell correlation=     0.9140
Overall weighted R factor            =     0.1736
Free weighted R factor               =     0.2083
Overall weighted R2 factor           =     0.2032
Free weighted R2 factor              =     0.2440
Average correlation coefficient      =     0.8935
Overall correlation coefficient      =     0.9589
Free correlation coefficient         =     0.9380
Cruickshanks DPI for coordinate error=     0.0891
DPI based on free R factor           =     0.0918
Overall figure of merit              =     0.8012
ML based su of positional parameters =     0.0628
ML based su of thermal parameters    =     1.8066
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    148100.25       8244.9297       782362.56       782384.38    

    ****                              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.= 0.912 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

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

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_step0-01A_R00_1-53A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.785     1.644
Bond angles  : others                          3238     1.498     1.580
Torsion angles, period  1. refined              185     6.773     5.000
Torsion angles, period  2. refined               90    34.735    22.778
Torsion angles, period  3. refined              268    13.301    15.000
Torsion angles, period  4. refined                9    12.201    15.000
Chiral centres: refined atoms                   196     0.086     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   303     0.244     0.200
VDW repulsions.others                          1373     0.191     0.200
VDW; torsion: refined_atoms                     731     0.172     0.200
VDW; torsion.others                             778     0.084     0.200
HBOND: refined_atoms                            208     0.198     0.200
HBOND.others                                      1     0.013     0.200
VDW repulsions: symmetry: refined_atoms           8     0.200     0.200
VDW repulsions: symmetry: others                 24     0.183     0.200
HBOND: symmetry: refined_atoms                   22     0.165     0.200
M. chain bond B values: refined atoms           746     1.712     1.588
M. chain bond B values: others                  746     1.707     1.588
M. chain angle B values: refined atoms          929     2.690     2.372
M. chain angle B values: others                 930     2.689     2.372
S. chain bond B values: refined atoms           811     3.026     1.982
S. chain bond B values: others                  810     3.022     1.982
S. chain angle B values: refined atoms         1177     4.653     2.810
S. chain angle B values: others                1178     4.651     2.810
Long range B values: refined atoms             1845     7.561    21.772
Long range B values: others                    1760     7.264    20.392
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0451, B  =    0.0177
Partial structure    1: scale =     0.3920, B  =   38.8603
Overall anisotropic scale factors
   B11 =  -0.19 B22 =  -0.19 B33 =   0.37 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.054    4097 100.00   416.3   425.9  0.17  0.17     194   410.4   417.2  0.20  0.21
 0.161    6961  99.97   237.4   218.9  0.18  0.16     398   246.6   224.3  0.22  0.20
 0.267    8879 100.00   137.0   125.2  0.20  0.18     477   137.4   126.3  0.24  0.21
 0.374   10439 100.00    55.5    68.4  0.38  0.32     533    55.0    68.8  0.41  0.36
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0539   3029   0.923   1068   0.822   4097   0.897  0.950  0.9645  0.9724  0.9037  0.9364
  0.1606   5899   0.876   1062   0.780   6961   0.861  1.045  0.9466  0.9562  0.8893  0.9328
  0.2672   7800   0.859   1079   0.770   8879   0.848  1.034  0.9453  0.9545  0.8956  0.9332
  0.3739   9371   0.691   1079   0.616  10450   0.683  0.655  0.8431  0.8582  0.7561  0.8167
 $$
Resolution limits                    =     41.964     1.530
Number of used reflections           =      30387
Percentage observed                  =    99.9906
Percentage of free reflections       =     5.0109
Overall R factor                     =     0.2029
Free R factor                        =     0.2401
Average Fourier shell correlation    =     0.9242
AverageFree Fourier shell correlation=     0.9139
Overall weighted R factor            =     0.1737
Free weighted R factor               =     0.2086
Overall weighted R2 factor           =     0.2032
Free weighted R2 factor              =     0.2442
Average correlation coefficient      =     0.8935
Overall correlation coefficient      =     0.9589
Free correlation coefficient         =     0.9380
Cruickshanks DPI for coordinate error=     0.0891
DPI based on free R factor           =     0.0919
Overall figure of merit              =     0.8009
ML based su of positional parameters =     0.0628
ML based su of thermal parameters    =     1.8066
-----------------------------------------------------------------------------
  Time in seconds: CPU =        23.30
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2023   0.2403   0.752      149474.    8070.7   0.0133  0.999   1.869  1.087   0.091
       1   0.2026   0.2393   0.791      148236.    8029.4   0.0121  0.910   1.797  1.045   0.087
       2   0.2019   0.2399   0.800      148001.    8022.2   0.0132  0.988   1.838  1.070   0.090
       3   0.2018   0.2400   0.802      147942.    8021.0   0.0133  0.997   1.855  1.080   0.091
       4   0.2018   0.2400   0.802      147936.    8021.2   0.0133  1.001   1.863  1.085   0.091
       5   0.2018   0.2401   0.802      147932.    8021.5   0.0133  1.001   1.867  1.087   0.091
       6   0.2023   0.2400   0.801      147997.    8022.8   0.0127  0.957   1.836  1.068   0.089
       7   0.2028   0.2400   0.801      148092.    8025.3   0.0121  0.911   1.795  1.044   0.086
       8   0.2028   0.2400   0.801      148101.    8025.6   0.0121  0.910   1.792  1.043   0.086
       9   0.2029   0.2401   0.801      148100.    8025.8   0.0121  0.908   1.788  1.041   0.086
      10   0.2029   0.2401   0.801      148117.    8026.1   0.0121  0.907   1.785  1.039   0.086
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2023   0.2029
             R free    0.2403   0.2401
     Rms BondLength    0.0133   0.0121
      Rms BondAngle    1.8692   1.7850
     Rms ChirVolume    0.0912   0.0860
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      55.2s System:    0.2s Elapsed:     0:56