###############################################################
 ###############################################################
 ###############################################################
 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 26/ 5/2020 Run time: 19:24:03 


 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 1.50     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 8
  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_complete_R08_1-60A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R08_1-50A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R08_1-50A.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       0.1111
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.5000
  Estimated number of reflections :      43652
  Free R exclusion - flag equals:     8
  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  1.5000

  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_complete_R08_1-60A.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=   2.058 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=   2.185 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=   1.826 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=   2.204 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=   2.393 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=   2.054 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:26-MAY-20
  --------------------------------
  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                            8
Number of "free" reflections       1680
Number of   all  reflections      33910
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          33910

   Current auto weighting coefficient =    6.2496691    

 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.= 0.893 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                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Weight matrix   0.29669902    
 Actual weight    6.2496691      is applied to the X-ray term
Norm of X_ray positional gradient                40.6
Norm of Geom. positional gradient                80.2
Norm of X_ray B-factor gradient                  116.
Norm of Geom. B-factor gradient                  106.
Product of X_ray and Geom posit. gradients     -0.146E+08
 Cosine of angle between them                      -0.462
Product of X_ray and Geom B-fact gradients     -0.350E+08
 Cosine of angle between them                      -0.888


Residuals: XRAY=     0.9769E+06 GEOM=     0.1292E+05 TOTAL=     0.9898E+06
 function value    989836.38    

-------------------------------------------------------------------------------
             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     1.770     1.644
Bond angles  : others                          3238     2.353     1.580
Torsion angles, period  1. refined              185     6.882     5.000
Torsion angles, period  2. refined               90    35.875    22.778
Torsion angles, period  3. refined              268    13.098    15.000
Torsion angles, period  4. refined                9    11.327    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.015     0.020
VDW repulsions: refined_atoms                   294     0.246     0.200
VDW repulsions.others                          1328     0.221     0.200
VDW; torsion: refined_atoms                     721     0.173     0.200
VDW; torsion.others                             714     0.080     0.200
HBOND: refined_atoms                            215     0.199     0.200
HBOND.others                                      1     0.032     0.200
VDW repulsions: symmetry: refined_atoms           9     0.189     0.200
VDW repulsions: symmetry: others                 25     0.188     0.200
HBOND: symmetry: refined_atoms                   23     0.173     0.200
M. chain bond B values: refined atoms           746     1.712     1.511
M. chain bond B values: others                  746     1.708     1.511
M. chain angle B values: refined atoms          929     2.688     2.259
M. chain angle B values: others                 930     2.687     2.259
S. chain bond B values: refined atoms           811     3.052     1.902
S. chain bond B values: others                  810     3.044     1.901
S. chain angle B values: refined atoms         1177     4.664     2.688
S. chain angle B values: others                1178     4.662     2.687
Long range B values: refined atoms             1834     7.011    20.807
Long range B values: others                    1739     6.702    19.285
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    1.1480
Partial structure    1: scale =     0.3898, B  =   39.2346
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4314 100.00   406.3   416.6  0.17  0.18     233   404.7   412.8  0.21  0.21
 0.167    7406  99.97   228.5   208.5  0.18  0.16     392   222.8   203.5  0.22  0.19
 0.278    9425 100.00   124.0   114.2  0.21  0.18     485   124.4   114.3  0.24  0.21
 0.389   11073 100.00    50.2    62.5  0.41  0.36     568    50.9    63.0  0.41  0.36
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3202   0.910   1112   0.802   4314   0.882  0.946  0.9618  0.9688  0.9067  0.9353
  0.1670   6276   0.876   1130   0.774   7406   0.860  1.060  0.9458  0.9587  0.8924  0.9342
  0.2780   8301   0.841   1124   0.757   9425   0.831  1.022  0.9368  0.9466  0.8941  0.9304
  0.3890   9961   0.541   1122   0.479  11083   0.535  0.547  0.7647  0.7740  0.7533  0.7738
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32228
Percentage observed                  =    99.9912
Percentage of free reflections       =     4.9546
Overall R factor                     =     0.2080
Free R factor                        =     0.2399
Average Fourier shell correlation    =     0.8930
AverageFree Fourier shell correlation=     0.8840
Overall weighted R factor            =     0.1769
Free weighted R factor               =     0.2104
Overall weighted R2 factor           =     0.2080
Free weighted R2 factor              =     0.2423
Average correlation coefficient      =     0.8781
Overall correlation coefficient      =     0.9589
Free correlation coefficient         =     0.9421
Cruickshanks DPI for coordinate error=     0.0862
DPI based on free R factor           =     0.0874
Overall figure of merit              =     0.7427
ML based su of positional parameters =     0.0703
ML based su of thermal parameters    =     2.0526
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    156315.33       12917.300       989836.38      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.36194646    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    978700.25    

-------------------------------------------------------------------------------
             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 =     0.0456, B  =   -0.0819
Partial structure    1: scale =     0.3899, B  =   39.2839
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2077
Free R factor                        =     0.2395
Average Fourier shell correlation    =     0.9040
AverageFree Fourier shell correlation=     0.8949
Average correlation coefficient      =     0.8787
Overall figure of merit              =     0.7657
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    155306.08       8088.6602       978700.25       989836.38    


     CGMAT cycle number =      3

 Weight matrix   0.36935312    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    977965.69    

-------------------------------------------------------------------------------
             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 =     0.0456, B  =   -0.0219
Partial structure    1: scale =     0.3901, B  =   39.2345
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2066
Free R factor                        =     0.2393
Average Fourier shell correlation    =     0.9065
AverageFree Fourier shell correlation=     0.8967
Average correlation coefficient      =     0.8803
Overall figure of merit              =     0.7695
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    155092.56       8688.4902       977965.69       978700.25    


     CGMAT cycle number =      4

 Weight matrix   0.33727044    
 Actual weight    5.6815171      is applied to the X-ray term


 function value    889784.44    

-------------------------------------------------------------------------------
             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 =     0.0456, B  =   -0.0114
Partial structure    1: scale =     0.3908, B  =   39.3206
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2064
Free R factor                        =     0.2394
Average Fourier shell correlation    =     0.9071
AverageFree Fourier shell correlation=     0.8971
Average correlation coefficient      =     0.8809
Overall figure of merit              =     0.7705
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    155051.38       8857.3545       889784.44       977965.69    


     CGMAT cycle number =      5

 Weight matrix   0.30619684    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    809694.81    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =   -0.0057
Partial structure    1: scale =     0.3910, B  =   39.4035
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2066
Free R factor                        =     0.2392
Average Fourier shell correlation    =     0.9070
AverageFree Fourier shell correlation=     0.8970
Average correlation coefficient      =     0.8807
Overall figure of merit              =     0.7705
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    155091.16       8646.6406       809694.81       889784.44    


     CGMAT cycle number =      6

 Weight matrix   0.30580872    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    809734.56    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =   -0.0089
Partial structure    1: scale =     0.3911, B  =   39.5142
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2070
Free R factor                        =     0.2393
Average Fourier shell correlation    =     0.9068
AverageFree Fourier shell correlation=     0.8969
Average correlation coefficient      =     0.8803
Overall figure of merit              =     0.7704
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    155162.38       8336.1143       809222.75       809694.81    
 fvalues    155162.38       8336.1143       809222.75       809752.13    


     CGMAT cycle number =      7

 Weight matrix   0.30856532    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    809224.81    

-------------------------------------------------------------------------------
             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 =     0.0456, B  =   -0.0077
Partial structure    1: scale =     0.3911, B  =   39.4939
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2071
Free R factor                        =     0.2394
Average Fourier shell correlation    =     0.9084
AverageFree Fourier shell correlation=     0.8993
Average correlation coefficient      =     0.8802
Overall figure of merit              =     0.7769
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    155074.88       8260.7207       809224.81       809752.13    


     CGMAT cycle number =      8

 Weight matrix   0.30705082    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    809417.06    

-------------------------------------------------------------------------------
             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 =     0.0456, B  =   -0.0001
Partial structure    1: scale =     0.3911, B  =   39.4943
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2072
Free R factor                        =     0.2394
Average Fourier shell correlation    =     0.9074
AverageFree Fourier shell correlation=     0.8978
Average correlation coefficient      =     0.8802
Overall figure of merit              =     0.7735
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    155155.09       8230.6504       809765.63       809224.81    

 fvalues    155155.09       8230.6504       809776.00       809609.06    
 fvalues    155155.09       8230.6504       809776.00       809609.06    


     CGMAT cycle number =      9

 Weight matrix   0.30589408    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    809766.75    

-------------------------------------------------------------------------------
             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 =     0.0455, B  =   -0.0023
Partial structure    1: scale =     0.3911, B  =   39.5103
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2072
Free R factor                        =     0.2394
Average Fourier shell correlation    =     0.9067
AverageFree Fourier shell correlation=     0.8967
Average correlation coefficient      =     0.8802
Overall figure of merit              =     0.7704
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    155188.44       8224.2109       809790.19       809609.06    

 fvalues    155188.44       8224.2109       809783.88       809774.81    
 fvalues    155188.44       8224.2109       809783.88       809774.81    


     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.= 0.910 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                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Weight matrix   0.30600163    
 Actual weight    5.1650152      is applied to the X-ray term
Norm of X_ray positional gradient                38.9
Norm of Geom. positional gradient                39.0
Norm of X_ray B-factor gradient                  101.
Norm of Geom. B-factor gradient                  101.
Product of X_ray and Geom posit. gradients     -0.146E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.331E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.8016E+06 GEOM=      8222.     TOTAL=     0.8098E+06
 function value    809784.25    

-------------------------------------------------------------------------------
             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     1.757     1.644
Bond angles  : others                          3238     1.496     1.580
Torsion angles, period  1. refined              185     6.861     5.000
Torsion angles, period  2. refined               90    35.706    22.778
Torsion angles, period  3. refined              268    13.003    15.000
Torsion angles, period  4. refined                9    11.402    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   293     0.246     0.200
VDW repulsions.others                          1339     0.194     0.200
VDW; torsion: refined_atoms                     725     0.172     0.200
VDW; torsion.others                             788     0.083     0.200
HBOND: refined_atoms                            213     0.198     0.200
HBOND.others                                      1     0.064     0.200
VDW repulsions: symmetry: refined_atoms           9     0.189     0.200
VDW repulsions: symmetry: others                 25     0.177     0.200
HBOND: symmetry: refined_atoms                   24     0.170     0.200
M. chain bond B values: refined atoms           746     1.757     1.624
M. chain bond B values: others                  746     1.754     1.624
M. chain angle B values: refined atoms          929     2.740     2.428
M. chain angle B values: others                 930     2.739     2.427
S. chain bond B values: refined atoms           811     3.124     2.024
S. chain bond B values: others                  810     3.117     2.024
S. chain angle B values: refined atoms         1177     4.767     2.869
S. chain angle B values: others                1178     4.765     2.868
Long range B values: refined atoms             1833     6.999    22.181
Long range B values: others                    1738     6.726    20.623
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0455, B  =   -0.0055
Partial structure    1: scale =     0.3911, B  =   39.5319
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4314 100.00   406.7   416.9  0.17  0.18     233   405.1   413.7  0.21  0.21
 0.167    7406  99.97   228.8   208.7  0.18  0.16     392   223.1   203.9  0.22  0.19
 0.278    9425 100.00   124.1   114.5  0.21  0.18     485   124.5   114.6  0.24  0.21
 0.389   11073 100.00    50.2    62.5  0.41  0.36     568    51.0    62.9  0.41  0.36
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3202   0.926   1112   0.832   4314   0.902  0.949  0.9662  0.9730  0.9046  0.9352
  0.1670   6276   0.888   1130   0.787   7406   0.873  1.062  0.9495  0.9617  0.8941  0.9354
  0.2780   8301   0.861   1124   0.778   9425   0.851  1.025  0.9439  0.9533  0.8963  0.9306
  0.3890   9961   0.589   1122   0.528  11083   0.583  0.565  0.7919  0.8045  0.7501  0.7788
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32228
Percentage observed                  =    99.9912
Percentage of free reflections       =     4.9546
Overall R factor                     =     0.2072
Free R factor                        =     0.2395
Average Fourier shell correlation    =     0.9067
AverageFree Fourier shell correlation=     0.8967
Overall weighted R factor            =     0.1763
Free weighted R factor               =     0.2099
Overall weighted R2 factor           =     0.2071
Free weighted R2 factor              =     0.2409
Average correlation coefficient      =     0.8802
Overall correlation coefficient      =     0.9591
Free correlation coefficient         =     0.9420
Cruickshanks DPI for coordinate error=     0.0859
DPI based on free R factor           =     0.0872
Overall figure of merit              =     0.7705
ML based su of positional parameters =     0.0629
ML based su of thermal parameters    =     1.8219
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    155191.47       8222.1377       809797.00       809774.81    

 fvalues    155191.47       8222.1377       809798.31       809788.44    
 fvalues    155191.47       8222.1377       809798.31       809788.44    

    ****                              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.= 0.910 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_complete_R08_1-50A.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     1.757     1.644
Bond angles  : others                          3238     1.496     1.580
Torsion angles, period  1. refined              185     6.861     5.000
Torsion angles, period  2. refined               90    35.705    22.778
Torsion angles, period  3. refined              268    13.002    15.000
Torsion angles, period  4. refined                9    11.401    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   293     0.246     0.200
VDW repulsions.others                          1338     0.194     0.200
VDW; torsion: refined_atoms                     725     0.172     0.200
VDW; torsion.others                             789     0.083     0.200
HBOND: refined_atoms                            213     0.198     0.200
HBOND.others                                      1     0.064     0.200
VDW repulsions: symmetry: refined_atoms           9     0.189     0.200
VDW repulsions: symmetry: others                 25     0.177     0.200
HBOND: symmetry: refined_atoms                   24     0.170     0.200
M. chain bond B values: refined atoms           746     1.757     1.624
M. chain bond B values: others                  746     1.754     1.624
M. chain angle B values: refined atoms          929     2.740     2.428
M. chain angle B values: others                 930     2.739     2.427
S. chain bond B values: refined atoms           811     3.124     2.024
S. chain bond B values: others                  810     3.116     2.024
S. chain angle B values: refined atoms         1177     4.766     2.868
S. chain angle B values: others                1178     4.764     2.868
Long range B values: refined atoms             1833     6.999    22.181
Long range B values: others                    1738     6.726    20.623
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0455, B  =   -0.0071
Partial structure    1: scale =     0.3910, B  =   39.5642
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4314 100.00   406.8   417.0  0.17  0.18     233   405.2   413.7  0.21  0.21
 0.167    7406  99.97   228.8   208.7  0.18  0.16     392   223.1   204.0  0.22  0.19
 0.278    9425 100.00   124.1   114.5  0.21  0.18     485   124.5   114.6  0.24  0.21
 0.389   11073 100.00    50.2    62.5  0.41  0.36     568    51.0    62.9  0.41  0.36
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3202   0.926   1112   0.832   4314   0.902  0.949  0.9662  0.9730  0.9047  0.9352
  0.1670   6276   0.888   1130   0.787   7406   0.873  1.062  0.9495  0.9617  0.8940  0.9354
  0.2780   8301   0.861   1124   0.778   9425   0.851  1.025  0.9439  0.9533  0.8963  0.9306
  0.3890   9961   0.589   1122   0.528  11083   0.583  0.565  0.7919  0.8045  0.7501  0.7788
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32228
Percentage observed                  =    99.9912
Percentage of free reflections       =     4.9546
Overall R factor                     =     0.2072
Free R factor                        =     0.2395
Average Fourier shell correlation    =     0.9067
AverageFree Fourier shell correlation=     0.8967
Overall weighted R factor            =     0.1763
Free weighted R factor               =     0.2099
Overall weighted R2 factor           =     0.2071
Free weighted R2 factor              =     0.2409
Average correlation coefficient      =     0.8802
Overall correlation coefficient      =     0.9591
Free correlation coefficient         =     0.9420
Cruickshanks DPI for coordinate error=     0.0859
DPI based on free R factor           =     0.0872
Overall figure of merit              =     0.7705
ML based su of positional parameters =     0.0629
ML based su of thermal parameters    =     1.8219
-----------------------------------------------------------------------------
  Time in seconds: CPU =        29.27
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2080   0.2399   0.743      156315.    8312.8   0.0123  0.920   1.770  1.033   0.087
       1   0.2077   0.2395   0.766      155306.    8285.5   0.0124  0.923   1.758  1.025   0.088
       2   0.2066   0.2393   0.769      155093.    8281.1   0.0134  1.001   1.810  1.056   0.091
       3   0.2064   0.2394   0.771      155051.    8279.7   0.0135  1.010   1.830  1.068   0.092
       4   0.2066   0.2392   0.770      155091.    8280.1   0.0129  0.969   1.809  1.055   0.090
       5   0.2070   0.2393   0.770      155159.    8281.2   0.0123  0.924   1.774  1.034   0.088
       6   0.2071   0.2394   0.777      155075.    8276.6   0.0122  0.919   1.763  1.028   0.088
       7   0.2072   0.2394   0.774      155118.    8278.6   0.0122  0.917   1.758  1.025   0.088
       8   0.2072   0.2394   0.770      155187.    8281.8   0.0122  0.917   1.758  1.025   0.088
       9   0.2072   0.2395   0.770      155191.    8282.0   0.0122  0.917   1.757  1.025   0.088
      10   0.2072   0.2395   0.770      155192.    8282.1   0.0122  0.917   1.757  1.025   0.088
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2080   0.2072
             R free    0.2399   0.2395
     Rms BondLength    0.0123   0.0122
      Rms BondAngle    1.7699   1.7574
     Rms ChirVolume    0.0868   0.0876
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      61.4s System:    0.2s Elapsed:     1:01