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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 26/ 5/2020 Run time: 19:20:21 


 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 1.66     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_1-67A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-66A.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_1-66A.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       0.0907
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.6600
  Estimated number of reflections :      31727
  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  1.6600

  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_1-67A.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=   2.041 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=   2.199 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=   1.835 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=   2.226 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=   2.422 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=   2.403 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=   2.131 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       1288
Number of   all  reflections      25205
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          25205

   Current auto weighting coefficient =    6.6496506    

 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.= 0.903 id.= 3.000 dev= -2.10 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        :   120  120  256
 Maximuum H,K,L                 :    35   35   74
 Minimum acceptable grid spacing:    80   80  170
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    35   35   74
 Minimum acceptable grid spacing:    80   80  170
 Weight matrix   0.29643604    
 Actual weight    6.6496506      is applied to the X-ray term
Norm of X_ray positional gradient                37.1
Norm of Geom. positional gradient                82.0
Norm of X_ray B-factor gradient                  111.
Norm of Geom. B-factor gradient                  120.
Product of X_ray and Geom posit. gradients     -0.143E+08
 Cosine of angle between them                      -0.484
Product of X_ray and Geom B-fact gradients     -0.379E+08
 Cosine of angle between them                      -0.885


Residuals: XRAY=     0.8161E+06 GEOM=     0.1363E+05 TOTAL=     0.8298E+06
 function value    829776.06    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.035     0.017
Bond angles  : refined atoms                   2106     1.842     1.644
Bond angles  : others                          3238     2.364     1.580
Torsion angles, period  1. refined              185     6.778     5.000
Torsion angles, period  2. refined               90    34.946    22.778
Torsion angles, period  3. refined              268    13.342    15.000
Torsion angles, period  4. refined                9    12.358    15.000
Chiral centres: refined atoms                   196     0.092     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.016     0.020
VDW repulsions: refined_atoms                   293     0.250     0.200
VDW repulsions.others                          1325     0.220     0.200
VDW; torsion: refined_atoms                     722     0.175     0.200
VDW; torsion.others                             724     0.081     0.200
HBOND: refined_atoms                            213     0.202     0.200
HBOND.others                                      2     0.063     0.200
VDW repulsions: symmetry: refined_atoms           8     0.204     0.200
VDW repulsions: symmetry: others                 22     0.201     0.200
HBOND: symmetry: refined_atoms                   22     0.170     0.200
M. chain bond B values: refined atoms           746     1.730     1.428
M. chain bond B values: others                  746     1.727     1.428
M. chain angle B values: refined atoms          929     2.713     2.131
M. chain angle B values: others                 930     2.712     2.131
S. chain bond B values: refined atoms           811     3.087     1.833
S. chain bond B values: others                  810     3.082     1.832
S. chain angle B values: refined atoms         1177     4.737     2.580
S. chain angle B values: others                1178     4.735     2.579
Long range B values: refined atoms             1831     7.101    19.704
Long range B values: others                    1742     6.852    18.313
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0433, B  =    0.0928
Partial structure    1: scale =     0.3884, B  =   43.1562
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.44 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.046    3257 100.00   445.9   455.5  0.16  0.17     145   437.4   450.5  0.20  0.21
 0.136    5480  99.98   280.7   267.4  0.17  0.15     323   290.6   268.5  0.22  0.20
 0.227    6978  99.99   189.4   172.1  0.17  0.15     376   193.8   178.2  0.20  0.17
 0.318    8194 100.00    89.1   102.7  0.28  0.21     444    84.3    99.5  0.34  0.27
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0459   2352   0.911    905   0.811   3257   0.883  0.949  0.9617  0.9702  0.9050  0.9394
  0.1364   4571   0.869    909   0.763   5480   0.851  1.005  0.9457  0.9569  0.8938  0.9402
  0.2270   6061   0.880    917   0.768   6978   0.866  1.055  0.9550  0.9607  0.9132  0.9424
  0.3176   7299   0.734    901   0.666   8200   0.726  0.781  0.8877  0.9073  0.8445  0.8932
 $$
Resolution limits                    =     41.964     1.660
Number of used reflections           =      23915
Percentage observed                  =    99.9881
Percentage of free reflections       =     5.1105
Overall R factor                     =     0.1834
Free R factor                        =     0.2279
Average Fourier shell correlation    =     0.9428
AverageFree Fourier shell correlation=     0.9302
Overall weighted R factor            =     0.1622
Free weighted R factor               =     0.2012
Overall weighted R2 factor           =     0.1933
Free weighted R2 factor              =     0.2380
Average correlation coefficient      =     0.9246
Overall correlation coefficient      =     0.9583
Free correlation coefficient         =     0.9336
Cruickshanks DPI for coordinate error=     0.1031
DPI based on free R factor           =     0.1067
Overall figure of merit              =     0.8170
ML based su of positional parameters =     0.0726
ML based su of thermal parameters    =     2.2140
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    122734.52       13634.405       829776.06      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.36798212    
 Actual weight    6.6496506      is applied to the X-ray term


 function value    818931.56    

-------------------------------------------------------------------------------
             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 =     0.0432, B  =   -0.0637
Partial structure    1: scale =     0.3885, B  =   43.2475
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.44 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1835
Free R factor                        =     0.2273
Average Fourier shell correlation    =     0.9508
AverageFree Fourier shell correlation=     0.9394
Average correlation coefficient      =     0.9239
Overall figure of merit              =     0.8486
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    121848.70       8680.3184       818931.56       829776.06    


     CGMAT cycle number =      3

 Weight matrix   0.37243190    
 Actual weight    6.6496506      is applied to the X-ray term


 function value    818615.94    

-------------------------------------------------------------------------------
             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 =     0.0432, B  =   -0.0364
Partial structure    1: scale =     0.3888, B  =   42.9849
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.44 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1832
Free R factor                        =     0.2277
Average Fourier shell correlation    =     0.9513
AverageFree Fourier shell correlation=     0.9398
Average correlation coefficient      =     0.9249
Overall figure of merit              =     0.8504
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    121750.92       9014.9053       818615.94       818931.56    


     CGMAT cycle number =      4

 Weight matrix   0.37171948    
 Actual weight    6.6496506      is applied to the X-ray term


 function value    818576.81    

-------------------------------------------------------------------------------
             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 =     0.0432, B  =   -0.0025
Partial structure    1: scale =     0.3889, B  =   42.9878
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.44 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1834
Free R factor                        =     0.2279
Average Fourier shell correlation    =     0.9514
AverageFree Fourier shell correlation=     0.9398
Average correlation coefficient      =     0.9251
Overall figure of merit              =     0.8504
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    121728.55       9124.5020       818576.81       818615.94    


     CGMAT cycle number =      5

 Weight matrix   0.37090644    
 Actual weight    6.6496506      is applied to the X-ray term


 function value    818577.38    

-------------------------------------------------------------------------------
             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 =     0.0432, B  =   -0.0022
Partial structure    1: scale =     0.3889, B  =   42.9526
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.44 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1834
Free R factor                        =     0.2281
Average Fourier shell correlation    =     0.9514
AverageFree Fourier shell correlation=     0.9397
Average correlation coefficient      =     0.9252
Overall figure of merit              =     0.8503
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03

 fvalues    121725.51       9141.8574       818573.94       818576.81    


     CGMAT cycle number =      6

 Weight matrix   0.37034512    
 Actual weight    6.6496506      is applied to the X-ray term


 function value    818599.19    

-------------------------------------------------------------------------------
             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 =     0.0432, B  =   -0.0040
Partial structure    1: scale =     0.3888, B  =   42.9444
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.44 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1835
Free R factor                        =     0.2282
Average Fourier shell correlation    =     0.9514
AverageFree Fourier shell correlation=     0.9397
Average correlation coefficient      =     0.9252
Overall figure of merit              =     0.8501
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    121730.30       9141.7510       818633.56       818573.94    

 fvalues    121730.30       9141.7510       818617.56       818605.69    
 fvalues    121730.30       9141.7510       818617.56       818605.69    


     CGMAT cycle number =      7

 Weight matrix   0.37012702    
 Actual weight    6.6496506      is applied to the X-ray term


 function value    818608.06    

-------------------------------------------------------------------------------
             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 =     0.0432, B  =   -0.0033
Partial structure    1: scale =     0.3888, B  =   42.9375
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.44 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1835
Free R factor                        =     0.2283
Average Fourier shell correlation    =     0.9513
AverageFree Fourier shell correlation=     0.9397
Average correlation coefficient      =     0.9252
Overall figure of merit              =     0.8501
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    121731.09       9139.7139       818627.75       818605.69    

 fvalues    121731.09       9139.7139       818621.88       818608.88    
 fvalues    121731.09       9139.7139       818621.88       818608.88    


     CGMAT cycle number =      8

 Weight matrix   0.37011036    
 Actual weight    6.6496506      is applied to the X-ray term


 function value    818609.75    

-------------------------------------------------------------------------------
             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 =     0.0432, B  =   -0.0044
Partial structure    1: scale =     0.3888, B  =   42.9469
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.44 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1835
Free R factor                        =     0.2283
Average Fourier shell correlation    =     0.9513
AverageFree Fourier shell correlation=     0.9397
Average correlation coefficient      =     0.9252
Overall figure of merit              =     0.8501
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    121732.13       9137.5576       818621.75       818608.88    

 fvalues    121732.13       9137.5576       818619.81       818613.69    
 fvalues    121732.13       9137.5576       818619.81       818613.69    


     CGMAT cycle number =      9

 Weight matrix   0.36984366    
 Actual weight    6.6496506      is applied to the X-ray term


 function value    818616.88    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0432, B  =   -0.0005
Partial structure    1: scale =     0.3888, B  =   42.9468
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.44 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1835
Free R factor                        =     0.2283
Average Fourier shell correlation    =     0.9513
AverageFree Fourier shell correlation=     0.9397
Average correlation coefficient      =     0.9252
Overall figure of merit              =     0.8501
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    121732.74       9137.3984       818620.00       818613.69    

 fvalues    121732.74       9137.3984       818616.06       818617.56    
 fvalues    121732.74       9137.3984       818616.06       818617.56    


     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.= 0.916 id.= 3.000 dev= -2.08 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        :   120  120  256
 Maximuum H,K,L                 :    35   35   74
 Minimum acceptable grid spacing:    80   80  170
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    35   35   74
 Minimum acceptable grid spacing:    80   80  170
 Weight matrix   0.36999848    
 Actual weight    6.6496506      is applied to the X-ray term
Norm of X_ray positional gradient                43.1
Norm of Geom. positional gradient                43.1
Norm of X_ray B-factor gradient                  123.
Norm of Geom. B-factor gradient                  123.
Product of X_ray and Geom posit. gradients     -0.180E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.490E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.8095E+06 GEOM=      9137.     TOTAL=     0.8186E+06
 function value    818616.06    

-------------------------------------------------------------------------------
             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     1.844     1.644
Bond angles  : others                          3238     1.522     1.580
Torsion angles, period  1. refined              185     6.776     5.000
Torsion angles, period  2. refined               90    34.991    22.778
Torsion angles, period  3. refined              268    13.244    15.000
Torsion angles, period  4. refined                9    12.590    15.000
Chiral centres: refined atoms                   196     0.091     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   298     0.247     0.200
VDW repulsions.others                          1336     0.196     0.200
VDW; torsion: refined_atoms                     726     0.174     0.200
VDW; torsion.others                             745     0.086     0.200
HBOND: refined_atoms                            212     0.201     0.200
HBOND.others                                      1     0.054     0.200
VDW repulsions: symmetry: refined_atoms           8     0.207     0.200
VDW repulsions: symmetry: others                 23     0.188     0.200
HBOND: symmetry: refined_atoms                   21     0.171     0.200
M. chain bond B values: refined atoms           746     1.725     1.440
M. chain bond B values: others                  746     1.722     1.440
M. chain angle B values: refined atoms          929     2.711     2.149
M. chain angle B values: others                 930     2.710     2.149
S. chain bond B values: refined atoms           811     3.103     1.842
S. chain bond B values: others                  810     3.098     1.841
S. chain angle B values: refined atoms         1177     4.743     2.595
S. chain angle B values: others                1178     4.741     2.594
Long range B values: refined atoms             1838     7.083    19.887
Long range B values: others                    1751     6.840    18.536
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0432, B  =   -0.0041
Partial structure    1: scale =     0.3888, B  =   42.9505
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.44 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.046    3257 100.00   446.4   456.0  0.16  0.17     145   437.9   452.9  0.20  0.21
 0.136    5480  99.98   281.0   267.4  0.17  0.15     323   291.0   268.0  0.22  0.20
 0.227    6978  99.99   189.7   172.3  0.18  0.15     376   194.0   178.6  0.20  0.18
 0.318    8194 100.00    89.2   102.8  0.27  0.21     444    84.4    99.4  0.34  0.27
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0459   2352   0.927    905   0.833   3257   0.901  0.952  0.9659  0.9734  0.9059  0.9392
  0.1364   4571   0.869    909   0.762   5480   0.851  1.005  0.9455  0.9568  0.8931  0.9398
  0.2270   6061   0.888    917   0.776   6978   0.873  1.055  0.9571  0.9626  0.9134  0.9419
  0.3176   7299   0.817    901   0.747   8200   0.810  0.810  0.9121  0.9293  0.8458  0.8958
 $$
Resolution limits                    =     41.964     1.660
Number of used reflections           =      23915
Percentage observed                  =    99.9881
Percentage of free reflections       =     5.1105
Overall R factor                     =     0.1835
Free R factor                        =     0.2283
Average Fourier shell correlation    =     0.9513
AverageFree Fourier shell correlation=     0.9397
Overall weighted R factor            =     0.1625
Free weighted R factor               =     0.2015
Overall weighted R2 factor           =     0.1934
Free weighted R2 factor              =     0.2376
Average correlation coefficient      =     0.9252
Overall correlation coefficient      =     0.9582
Free correlation coefficient         =     0.9336
Cruickshanks DPI for coordinate error=     0.1032
DPI based on free R factor           =     0.1069
Overall figure of merit              =     0.8501
ML based su of positional parameters =     0.0649
ML based su of thermal parameters    =     1.9267
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    121732.54       9137.1934       818616.06       818617.56    

    ****                              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.= 0.916 id.= 3.000 dev= -2.08 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_1-66A.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     1.844     1.644
Bond angles  : others                          3238     1.522     1.580
Torsion angles, period  1. refined              185     6.776     5.000
Torsion angles, period  2. refined               90    34.991    22.778
Torsion angles, period  3. refined              268    13.244    15.000
Torsion angles, period  4. refined                9    12.592    15.000
Chiral centres: refined atoms                   196     0.091     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   298     0.247     0.200
VDW repulsions.others                          1335     0.196     0.200
VDW; torsion: refined_atoms                     726     0.174     0.200
VDW; torsion.others                             745     0.086     0.200
HBOND: refined_atoms                            212     0.201     0.200
HBOND.others                                      1     0.054     0.200
VDW repulsions: symmetry: refined_atoms           8     0.207     0.200
VDW repulsions: symmetry: others                 23     0.188     0.200
HBOND: symmetry: refined_atoms                   21     0.171     0.200
M. chain bond B values: refined atoms           746     1.725     1.440
M. chain bond B values: others                  746     1.722     1.440
M. chain angle B values: refined atoms          929     2.711     2.149
M. chain angle B values: others                 930     2.709     2.149
S. chain bond B values: refined atoms           811     3.103     1.842
S. chain bond B values: others                  810     3.098     1.841
S. chain angle B values: refined atoms         1177     4.743     2.595
S. chain angle B values: others                1178     4.741     2.594
Long range B values: refined atoms             1838     7.083    19.887
Long range B values: others                    1751     6.840    18.536
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0432, B  =   -0.0001
Partial structure    1: scale =     0.3888, B  =   42.9503
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.44 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.046    3257 100.00   446.4   456.0  0.16  0.17     145   437.9   452.8  0.20  0.21
 0.136    5480  99.98   281.0   267.4  0.17  0.15     323   291.0   268.0  0.22  0.20
 0.227    6978  99.99   189.7   172.3  0.18  0.15     376   194.0   178.6  0.20  0.18
 0.318    8194 100.00    89.2   102.7  0.27  0.21     444    84.4    99.4  0.34  0.27
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0459   2352   0.927    905   0.833   3257   0.901  0.952  0.9659  0.9734  0.9060  0.9392
  0.1364   4571   0.869    909   0.762   5480   0.851  1.005  0.9455  0.9568  0.8931  0.9398
  0.2270   6061   0.888    917   0.776   6978   0.873  1.055  0.9571  0.9626  0.9134  0.9419
  0.3176   7299   0.817    901   0.747   8200   0.810  0.810  0.9121  0.9293  0.8458  0.8958
 $$
Resolution limits                    =     41.964     1.660
Number of used reflections           =      23915
Percentage observed                  =    99.9881
Percentage of free reflections       =     5.1105
Overall R factor                     =     0.1835
Free R factor                        =     0.2283
Average Fourier shell correlation    =     0.9513
AverageFree Fourier shell correlation=     0.9397
Overall weighted R factor            =     0.1625
Free weighted R factor               =     0.2015
Overall weighted R2 factor           =     0.1935
Free weighted R2 factor              =     0.2376
Average correlation coefficient      =     0.9252
Overall correlation coefficient      =     0.9582
Free correlation coefficient         =     0.9336
Cruickshanks DPI for coordinate error=     0.1032
DPI based on free R factor           =     0.1069
Overall figure of merit              =     0.8500
ML based su of positional parameters =     0.0649
ML based su of thermal parameters    =     1.9267
-----------------------------------------------------------------------------
  Time in seconds: CPU =        22.27
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1834   0.2279   0.817      122735.    6776.2   0.0132  0.990   1.842  1.071   0.092
       1   0.1835   0.2273   0.849      121849.    6747.8   0.0121  0.913   1.784  1.036   0.087
       2   0.1832   0.2277   0.850      121751.    6747.0   0.0131  0.982   1.821  1.059   0.091
       3   0.1834   0.2279   0.850      121729.    6747.3   0.0132  0.992   1.836  1.069   0.091
       4   0.1834   0.2281   0.850      121726.    6747.9   0.0133  0.994   1.842  1.072   0.091
       5   0.1835   0.2282   0.850      121729.    6748.6   0.0133  0.995   1.844  1.074   0.091
       6   0.1835   0.2283   0.850      121731.    6748.8   0.0133  0.995   1.844  1.074   0.091
       7   0.1835   0.2283   0.850      121732.    6748.8   0.0133  0.995   1.844  1.074   0.091
       8   0.1835   0.2283   0.850      121733.    6748.8   0.0133  0.995   1.844  1.074   0.091
       9   0.1835   0.2283   0.850      121733.    6748.9   0.0133  0.995   1.844  1.074   0.091
      10   0.1835   0.2283   0.850      121733.    6748.9   0.0133  0.995   1.844  1.074   0.091
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1834   0.1835
             R free    0.2279   0.2283
     Rms BondLength    0.0132   0.0133
      Rms BondAngle    1.8422   1.8442
     Rms ChirVolume    0.0917   0.0912
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      54.4s System:    1.2s Elapsed:     0:55