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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: 01:05:49 


 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 1.52     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_1-53A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-52A.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_1-52A.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       0.1082
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.5200
  Estimated number of reflections :      40937
  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  1.5200

  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_1-53A.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=   2.060 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=   2.193 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=   1.830 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=   2.217 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=   2.404 ideal_dist=   1.945
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:N   .
  INFO:     link is found (not be used) dist=   2.388 ideal_dist=   2.235
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:SG  .
  INFO:     link is found (not be used) dist=   2.115 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       1622
Number of   all  reflections      32594
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          32594

   Current auto weighting coefficient =    6.2996802    

 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  182
 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  182
 Weight matrix   0.27393207    
 Actual weight    6.2996802      is applied to the X-ray term
Norm of X_ray positional gradient                38.1
Norm of Geom. positional gradient                79.8
Norm of X_ray B-factor gradient                  105.
Norm of Geom. B-factor gradient                  97.8
Product of X_ray and Geom posit. gradients     -0.130E+08
 Cosine of angle between them                      -0.443
Product of X_ray and Geom B-fact gradients     -0.296E+08
 Cosine of angle between them                      -0.894


Residuals: XRAY=     0.9570E+06 GEOM=     0.1268E+05 TOTAL=     0.9697E+06
 function value    969698.88    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.035     0.017
Bond angles  : refined atoms                   2106     1.785     1.644
Bond angles  : others                          3238     2.352     1.580
Torsion angles, period  1. refined              185     6.774     5.000
Torsion angles, period  2. refined               90    34.736    22.778
Torsion angles, period  3. refined              268    13.300    15.000
Torsion angles, period  4. refined                9    12.193    15.000
Chiral centres: refined atoms                   196     0.086     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.015     0.020
VDW repulsions: refined_atoms                   303     0.244     0.200
VDW repulsions.others                          1338     0.219     0.200
VDW; torsion: refined_atoms                     731     0.172     0.200
VDW; torsion.others                             721     0.080     0.200
HBOND: refined_atoms                            207     0.199     0.200
HBOND.others                                      1     0.060     0.200
VDW repulsions: symmetry: refined_atoms           8     0.200     0.200
VDW repulsions: symmetry: others                 24     0.195     0.200
HBOND: symmetry: refined_atoms                   22     0.164     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     3.027     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             1844     7.562    21.770
Long range B values: others                    1759     7.265    20.389
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0453, B  =    0.1254
Partial structure    1: scale =     0.3916, B  =   38.6406
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.055    4172 100.00   413.4   422.9  0.17  0.17     199   408.0   414.3  0.21  0.21
 0.163    7086  99.97   234.2   215.3  0.18  0.16     404   243.4   220.4  0.22  0.20
 0.271    9069 100.00   132.6   121.3  0.20  0.18     482   132.4   122.5  0.24  0.21
 0.379   10639 100.00    53.4    66.2  0.39  0.33     537    53.6    66.7  0.41  0.37
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0546   3094   0.904   1078   0.791   4172   0.875  0.946  0.9595  0.9679  0.9032  0.9362
  0.1627   6008   0.867   1078   0.774   7086   0.853  1.048  0.9446  0.9544  0.8863  0.9322
  0.2707   7973   0.842   1096   0.751   9069   0.831  1.031  0.9387  0.9486  0.8927  0.9319
  0.3788   9557   0.548   1086   0.479  10643   0.541  0.574  0.7733  0.7869  0.7525  0.8050
 $$
Resolution limits                    =     41.964     1.520
Number of used reflections           =      30969
Percentage observed                  =    99.9908
Percentage of free reflections       =     4.9768
Overall R factor                     =     0.2047
Free R factor                        =     0.2414
Average Fourier shell correlation    =     0.8970
AverageFree Fourier shell correlation=     0.8880
Overall weighted R factor            =     0.1747
Free weighted R factor               =     0.2096
Overall weighted R2 factor           =     0.2041
Free weighted R2 factor              =     0.2453
Average correlation coefficient      =     0.8890
Overall correlation coefficient      =     0.9589
Free correlation coefficient         =     0.9379
Cruickshanks DPI for coordinate error=     0.0882
DPI based on free R factor           =     0.0909
Overall figure of merit              =     0.7422
ML based su of positional parameters =     0.0735
ML based su of thermal parameters    =     2.1577
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    151915.86       12677.583       969698.88      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.35355887    
 Actual weight    6.2996802      is applied to the X-ray term


 function value    956757.13    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0453, B  =   -0.0557
Partial structure    1: scale =     0.3918, B  =   38.8070
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.37 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2044
Free R factor                        =     0.2404
Average Fourier shell correlation    =     0.9146
AverageFree Fourier shell correlation=     0.9070
Average correlation coefficient      =     0.8878
Overall figure of merit              =     0.7811
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    150577.81       8165.0322       956757.13       969698.88    


     CGMAT cycle number =      3

 Weight matrix   0.36409900    
 Actual weight    6.2996802      is applied to the X-ray term


 function value    955678.38    

-------------------------------------------------------------------------------
             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 =     0.0453, B  =    0.0005
Partial structure    1: scale =     0.3918, B  =   38.8099
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.37 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2037
Free R factor                        =     0.2405
Average Fourier shell correlation    =     0.9182
AverageFree Fourier shell correlation=     0.9102
Average correlation coefficient      =     0.8891
Overall figure of merit              =     0.7887
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    150333.02       8628.4102       955678.38       956757.13    


     CGMAT cycle number =      4

 Weight matrix   0.36502895    
 Actual weight    6.2996802      is applied to the X-ray term


 function value    955518.94    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0453, B  =    0.0275
Partial structure    1: scale =     0.3919, B  =   38.7789
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.37 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2037
Free R factor                        =     0.2405
Average Fourier shell correlation    =     0.9187
AverageFree Fourier shell correlation=     0.9106
Average correlation coefficient      =     0.8896
Overall figure of merit              =     0.7896
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    150286.42       8762.5684       955518.94       955678.38    


     CGMAT cycle number =      5

 Weight matrix   0.36542153    
 Actual weight    6.2996802      is applied to the X-ray term


 function value    955488.13    

-------------------------------------------------------------------------------
             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 =     0.0453, B  =    0.0258
Partial structure    1: scale =     0.3919, B  =   38.7449
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.37 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2036
Free R factor                        =     0.2406
Average Fourier shell correlation    =     0.9187
AverageFree Fourier shell correlation=     0.9106
Average correlation coefficient      =     0.8898
Overall figure of merit              =     0.7897
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    150273.41       8813.6904       955488.13       955518.94    


     CGMAT cycle number =      6

 Weight matrix   0.36477560    
 Actual weight    6.2996802      is applied to the X-ray term


 function value    955510.38    

-------------------------------------------------------------------------------
             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 =     0.0453, B  =    0.0306
Partial structure    1: scale =     0.3920, B  =   38.6667
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.37 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2036
Free R factor                        =     0.2407
Average Fourier shell correlation    =     0.9187
AverageFree Fourier shell correlation=     0.9105
Average correlation coefficient      =     0.8899
Overall figure of merit              =     0.7896
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    150273.73       8832.2480       955504.13       955488.13    
 fvalues    150273.73       8832.2480       955504.13       955508.75    


     CGMAT cycle number =      7

 Weight matrix   0.36462453    
 Actual weight    6.2996802      is applied to the X-ray term


 function value    955515.94    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0453, B  =    0.0291
Partial structure    1: scale =     0.3920, B  =   38.6856
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.37 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2036
Free R factor                        =     0.2408
Average Fourier shell correlation    =     0.9187
AverageFree Fourier shell correlation=     0.9104
Average correlation coefficient      =     0.8899
Overall figure of merit              =     0.7896
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    150273.59       8834.4434       955545.75       955508.75    

 fvalues    150273.59       8834.4434       955522.75       955510.00    
 fvalues    150273.59       8834.4434       955522.75       955510.00    


     CGMAT cycle number =      8

 Weight matrix   0.36512759    
 Actual weight    6.2996802      is applied to the X-ray term


 function value    955485.00    

-------------------------------------------------------------------------------
             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 =     0.0453, B  =    0.0219
Partial structure    1: scale =     0.3920, B  =   38.7571
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.37 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2037
Free R factor                        =     0.2408
Average Fourier shell correlation    =     0.9187
AverageFree Fourier shell correlation=     0.9105
Average correlation coefficient      =     0.8899
Overall figure of merit              =     0.7897
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    150269.98       8832.1113       955485.00       955510.00    


     CGMAT cycle number =      9

 Weight matrix   0.36439595    
 Actual weight    6.2996802      is applied to the X-ray term


 function value    955523.38    

-------------------------------------------------------------------------------
             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 =     0.0453, B  =    0.0301
Partial structure    1: scale =     0.3920, B  =   38.7850
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.37 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2036
Free R factor                        =     0.2407
Average Fourier shell correlation    =     0.9187
AverageFree Fourier shell correlation=     0.9104
Average correlation coefficient      =     0.8899
Overall figure of merit              =     0.7895
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    150276.22       8833.1543       955529.06       955485.00    

 fvalues    150276.22       8833.1543       955517.75       955525.25    
 fvalues    150276.22       8833.1543       955517.75       955525.25    


     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.= 0.909 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  182
 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  182
 Weight matrix   0.36511168    
 Actual weight    6.2996802      is applied to the X-ray term
Norm of X_ray positional gradient                43.6
Norm of Geom. positional gradient                43.5
Norm of X_ray B-factor gradient                  113.
Norm of Geom. B-factor gradient                  111.
Product of X_ray and Geom posit. gradients     -0.184E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.401E+08
 Cosine of angle between them                      -0.998


Residuals: XRAY=     0.9467E+06 GEOM=      8833.     TOTAL=     0.9555E+06
 function value    955483.81    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.856     1.644
Bond angles  : others                          3238     1.518     1.580
Torsion angles, period  1. refined              185     6.755     5.000
Torsion angles, period  2. refined               90    34.646    22.778
Torsion angles, period  3. refined              268    13.311    15.000
Torsion angles, period  4. refined                9    12.434    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   305     0.245     0.200
VDW repulsions.others                          1378     0.193     0.200
VDW; torsion: refined_atoms                     730     0.174     0.200
VDW; torsion.others                             768     0.085     0.200
HBOND: refined_atoms                            209     0.200     0.200
HBOND.others                                      1     0.026     0.200
VDW repulsions: symmetry: refined_atoms           8     0.202     0.200
VDW repulsions: symmetry: others                 25     0.179     0.200
HBOND: symmetry: refined_atoms                   22     0.166     0.200
M. chain bond B values: refined atoms           746     1.799     1.596
M. chain bond B values: others                  746     1.794     1.596
M. chain angle B values: refined atoms          929     2.787     2.383
M. chain angle B values: others                 930     2.786     2.383
S. chain bond B values: refined atoms           811     3.233     2.009
S. chain bond B values: others                  810     3.229     2.009
S. chain angle B values: refined atoms         1177     4.923     2.842
S. chain angle B values: others                1178     4.921     2.842
Long range B values: refined atoms             1847     7.702    21.919
Long range B values: others                    1762     7.429    20.547
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0453, B  =    0.0208
Partial structure    1: scale =     0.3920, B  =   38.7898
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.055    4172 100.00   413.4   423.1  0.17  0.17     199   408.1   415.3  0.21  0.21
 0.163    7086  99.97   234.2   215.5  0.18  0.16     404   243.4   220.5  0.22  0.20
 0.271    9069 100.00   132.6   121.6  0.20  0.18     482   132.5   122.8  0.24  0.21
 0.379   10639 100.00    53.4    66.3  0.39  0.34     537    53.6    66.9  0.41  0.37
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0546   3094   0.920   1078   0.815   4172   0.893  0.949  0.9636  0.9717  0.9032  0.9363
  0.1627   6008   0.877   1078   0.785   7086   0.863  1.048  0.9475  0.9573  0.8886  0.9338
  0.2707   7973   0.858   1096   0.769   9069   0.847  1.031  0.9443  0.9547  0.8932  0.9339
  0.3788   9557   0.658   1086   0.590  10643   0.651  0.624  0.8327  0.8417  0.7527  0.8049
 $$
Resolution limits                    =     41.964     1.520
Number of used reflections           =      30969
Percentage observed                  =    99.9908
Percentage of free reflections       =     4.9768
Overall R factor                     =     0.2037
Free R factor                        =     0.2407
Average Fourier shell correlation    =     0.9187
AverageFree Fourier shell correlation=     0.9105
Overall weighted R factor            =     0.1737
Free weighted R factor               =     0.2091
Overall weighted R2 factor           =     0.2033
Free weighted R2 factor              =     0.2456
Average correlation coefficient      =     0.8899
Overall correlation coefficient      =     0.9593
Free correlation coefficient         =     0.9383
Cruickshanks DPI for coordinate error=     0.0878
DPI based on free R factor           =     0.0906
Overall figure of merit              =     0.7897
ML based su of positional parameters =     0.0636
ML based su of thermal parameters    =     1.8326
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    150269.61       8833.2832       955483.81       955525.25    

    ****                              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.= 0.909 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_1-52A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.857     1.644
Bond angles  : others                          3238     1.518     1.580
Torsion angles, period  1. refined              185     6.755     5.000
Torsion angles, period  2. refined               90    34.644    22.778
Torsion angles, period  3. refined              268    13.312    15.000
Torsion angles, period  4. refined                9    12.435    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   305     0.245     0.200
VDW repulsions.others                          1380     0.193     0.200
VDW; torsion: refined_atoms                     730     0.174     0.200
VDW; torsion.others                             768     0.085     0.200
HBOND: refined_atoms                            209     0.200     0.200
HBOND.others                                      1     0.026     0.200
VDW repulsions: symmetry: refined_atoms           8     0.202     0.200
VDW repulsions: symmetry: others                 25     0.179     0.200
HBOND: symmetry: refined_atoms                   22     0.166     0.200
M. chain bond B values: refined atoms           746     1.799     1.596
M. chain bond B values: others                  746     1.794     1.596
M. chain angle B values: refined atoms          929     2.787     2.383
M. chain angle B values: others                 930     2.786     2.383
S. chain bond B values: refined atoms           811     3.234     2.009
S. chain bond B values: others                  810     3.229     2.009
S. chain angle B values: refined atoms         1177     4.923     2.842
S. chain angle B values: others                1178     4.921     2.842
Long range B values: refined atoms             1847     7.704    21.920
Long range B values: others                    1762     7.431    20.547
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0453, B  =    0.0246
Partial structure    1: scale =     0.3920, B  =   38.8001
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.055    4172 100.00   413.4   423.1  0.17  0.17     199   408.1   415.3  0.21  0.21
 0.163    7086  99.97   234.2   215.4  0.18  0.16     404   243.4   220.5  0.22  0.20
 0.271    9069 100.00   132.6   121.6  0.20  0.18     482   132.4   122.8  0.24  0.21
 0.379   10639 100.00    53.4    66.3  0.39  0.34     537    53.6    66.9  0.41  0.37
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0546   3094   0.920   1078   0.815   4172   0.893  0.949  0.9636  0.9717  0.9032  0.9363
  0.1627   6008   0.877   1078   0.785   7086   0.863  1.048  0.9475  0.9573  0.8886  0.9338
  0.2707   7973   0.858   1096   0.769   9069   0.847  1.031  0.9443  0.9547  0.8933  0.9339
  0.3788   9557   0.658   1086   0.590  10643   0.651  0.624  0.8327  0.8416  0.7527  0.8049
 $$
Resolution limits                    =     41.964     1.520
Number of used reflections           =      30969
Percentage observed                  =    99.9908
Percentage of free reflections       =     4.9768
Overall R factor                     =     0.2037
Free R factor                        =     0.2407
Average Fourier shell correlation    =     0.9187
AverageFree Fourier shell correlation=     0.9105
Overall weighted R factor            =     0.1737
Free weighted R factor               =     0.2091
Overall weighted R2 factor           =     0.2033
Free weighted R2 factor              =     0.2456
Average correlation coefficient      =     0.8899
Overall correlation coefficient      =     0.9593
Free correlation coefficient         =     0.9383
Cruickshanks DPI for coordinate error=     0.0878
DPI based on free R factor           =     0.0906
Overall figure of merit              =     0.7896
ML based su of positional parameters =     0.0636
ML based su of thermal parameters    =     1.8326
-----------------------------------------------------------------------------
  Time in seconds: CPU =        27.46
             Elapsed =           0.00

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


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS: vs cycle :N:1,2,3:
:FOM vs cycle :N:1,4:
:-LL vs cycle :N:1,5:
:-LLfree vs cycle :N:1,6:
:Geometry vs cycle:N:1,7,8,9,10,11:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2047   0.2414   0.742      151916.    8146.9   0.0121  0.908   1.785  1.039   0.086
       1   0.2044   0.2404   0.781      150578.    8102.9   0.0119  0.893   1.762  1.025   0.086
       2   0.2037   0.2405   0.789      150333.    8096.0   0.0130  0.973   1.814  1.056   0.089
       3   0.2037   0.2405   0.790      150286.    8094.8   0.0131  0.985   1.836  1.069   0.090
       4   0.2036   0.2406   0.790      150273.    8094.9   0.0132  0.989   1.847  1.075   0.090
       5   0.2036   0.2407   0.790      150274.    8095.3   0.0132  0.990   1.852  1.078   0.090
       6   0.2036   0.2408   0.790      150275.    8095.8   0.0132  0.990   1.855  1.079   0.090
       7   0.2037   0.2408   0.790      150270.    8095.8   0.0132  0.990   1.855  1.079   0.090
       8   0.2036   0.2407   0.790      150276.    8095.9   0.0132  0.990   1.856  1.080   0.090
       9   0.2037   0.2407   0.790      150270.    8095.8   0.0132  0.990   1.856  1.080   0.090
      10   0.2037   0.2407   0.790      150269.    8095.7   0.0132  0.990   1.857  1.080   0.090
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2047   0.2037
             R free    0.2414   0.2407
     Rms BondLength    0.0121   0.0132
      Rms BondAngle    1.7847   1.8565
     Rms ChirVolume    0.0863   0.0902
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      59.1s System:    0.3s Elapsed:     1:00