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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: 19:41:25 


 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 1.65     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_1-66A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-65A.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_1-65A.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       0.0918
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.6500
  Estimated number of reflections :      32156
  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  1.6500

  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_1-66A.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=   2.048 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=   2.194 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=   2.218 ideal_dist=   2.090
            ch:AAA  res: 140  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.436 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=   2.401 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=   2.139 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       1306
Number of   all  reflections      25627
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          25627

   Current auto weighting coefficient =    6.6246233    

 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.= 0.901 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        :   128  128  256
 Maximuum H,K,L                 :    35   35   75
 Minimum acceptable grid spacing:    81   81  171
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  256
 Maximuum H,K,L                 :    35   35   75
 Minimum acceptable grid spacing:    81   81  171
 Weight matrix   0.29298401    
 Actual weight    6.6246233      is applied to the X-ray term
Norm of X_ray positional gradient                36.7
Norm of Geom. positional gradient                82.4
Norm of X_ray B-factor gradient                  110.
Norm of Geom. B-factor gradient                  118.
Product of X_ray and Geom posit. gradients     -0.140E+08
 Cosine of angle between them                      -0.478
Product of X_ray and Geom B-fact gradients     -0.366E+08
 Cosine of angle between them                      -0.869


Residuals: XRAY=     0.8245E+06 GEOM=     0.1364E+05 TOTAL=     0.8382E+06
 function value    838178.06    

-------------------------------------------------------------------------------
             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     1.845     1.644
Bond angles  : others                          3238     2.367     1.580
Torsion angles, period  1. refined              185     6.774     5.000
Torsion angles, period  2. refined               90    34.988    22.778
Torsion angles, period  3. refined              268    13.246    15.000
Torsion angles, period  4. refined                9    12.606    15.000
Chiral centres: refined atoms                   196     0.091     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.018     0.020
VDW repulsions: refined_atoms                   298     0.247     0.200
VDW repulsions.others                          1322     0.220     0.200
VDW; torsion: refined_atoms                     725     0.174     0.200
VDW; torsion.others                             723     0.081     0.200
HBOND: refined_atoms                            212     0.201     0.200
HBOND.others                                      2     0.075     0.200
VDW repulsions: symmetry: refined_atoms           8     0.207     0.200
VDW repulsions: symmetry: others                 22     0.203     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     1.721     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             1837     7.083    19.884
Long range B values: others                    1750     6.840    18.533
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0435, B  =    0.1257
Partial structure    1: scale =     0.3847, B  =   42.8128
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.43 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.046    3313 100.00   443.3   452.5  0.16  0.17     149   435.9   447.0  0.21  0.21
 0.138    5574  99.98   276.1   262.8  0.17  0.15     325   285.6   263.8  0.22  0.20
 0.230    7114  99.99   186.2   168.7  0.18  0.16     383   191.3   174.9  0.20  0.18
 0.321    8309 100.00    85.5    99.3  0.28  0.22     449    81.1    96.6  0.35  0.27
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0464   2391   0.911    922   0.811   3313   0.884  0.949  0.9614  0.9698  0.9051  0.9378
  0.1381   4659   0.866    915   0.758   5574   0.849  1.006  0.9434  0.9557  0.8880  0.9396
  0.2298   6185   0.878    929   0.769   7114   0.864  1.056  0.9546  0.9601  0.9143  0.9413
  0.3215   7410   0.727    908   0.654   8318   0.719  0.771  0.8816  0.9026  0.8373  0.8907
 $$
Resolution limits                    =     41.964     1.650
Number of used reflections           =      24319
Percentage observed                  =    99.9883
Percentage of free reflections       =     5.0966
Overall R factor                     =     0.1855
Free R factor                        =     0.2303
Average Fourier shell correlation    =     0.9407
AverageFree Fourier shell correlation=     0.9275
Overall weighted R factor            =     0.1640
Free weighted R factor               =     0.2038
Overall weighted R2 factor           =     0.1957
Free weighted R2 factor              =     0.2387
Average correlation coefficient      =     0.9231
Overall correlation coefficient      =     0.9579
Free correlation coefficient         =     0.9332
Cruickshanks DPI for coordinate error=     0.1024
DPI based on free R factor           =     0.1063
Overall figure of merit              =     0.8136
ML based su of positional parameters =     0.0729
ML based su of thermal parameters    =     2.2147
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    124465.47       13641.201       838178.06      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.36216241    
 Actual weight    6.6246233      is applied to the X-ray term


 function value    827184.00    

-------------------------------------------------------------------------------
             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 =     0.0434, B  =   -0.0734
Partial structure    1: scale =     0.3851, B  =   43.1971
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.43 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1857
Free R factor                        =     0.2295
Average Fourier shell correlation    =     0.9487
AverageFree Fourier shell correlation=     0.9369
Average correlation coefficient      =     0.9221
Overall figure of merit              =     0.8445
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    123567.71       8594.4102       827184.00       838178.06    


     CGMAT cycle number =      3

 Weight matrix   0.37085322    
 Actual weight    6.6246233      is applied to the X-ray term


 function value    826635.56    

-------------------------------------------------------------------------------
             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 =     0.0434, B  =   -0.0371
Partial structure    1: scale =     0.3853, B  =   43.3298
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.43 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1852
Free R factor                        =     0.2294
Average Fourier shell correlation    =     0.9496
AverageFree Fourier shell correlation=     0.9377
Average correlation coefficient      =     0.9230
Overall figure of merit              =     0.8477
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    123437.59       8908.0879       826635.56       827184.00    


     CGMAT cycle number =      4

 Weight matrix   0.37125975    
 Actual weight    6.6246233      is applied to the X-ray term


 function value    826586.25    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0434, B  =   -0.0273
Partial structure    1: scale =     0.3851, B  =   43.3936
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.43 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1852
Free R factor                        =     0.2294
Average Fourier shell correlation    =     0.9497
AverageFree Fourier shell correlation=     0.9377
Average correlation coefficient      =     0.9233
Overall figure of merit              =     0.8479
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    123413.55       9017.9326       826586.25       826635.56    


     CGMAT cycle number =      5

 Weight matrix   0.37103376    
 Actual weight    6.6246233      is applied to the X-ray term


 function value    826583.00    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0434, B  =   -0.0199
Partial structure    1: scale =     0.3850, B  =   43.3167
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.43 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1852
Free R factor                        =     0.2295
Average Fourier shell correlation    =     0.9497
AverageFree Fourier shell correlation=     0.9377
Average correlation coefficient      =     0.9234
Overall figure of merit              =     0.8478
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    123407.32       9055.9961       826583.00       826586.25    


     CGMAT cycle number =      6

 Weight matrix   0.37075678    
 Actual weight    6.6246233      is applied to the X-ray term


 function value    826580.63    

-------------------------------------------------------------------------------
             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 =     0.0434, B  =   -0.0188
Partial structure    1: scale =     0.3851, B  =   43.3254
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.43 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1852
Free R factor                        =     0.2295
Average Fourier shell correlation    =     0.9497
AverageFree Fourier shell correlation=     0.9377
Average correlation coefficient      =     0.9234
Overall figure of merit              =     0.8478
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    123405.68       9064.5254       826580.63       826583.00    


     CGMAT cycle number =      7

 Weight matrix   0.37001234    
 Actual weight    6.6246233      is applied to the X-ray term


 function value    826609.81    

-------------------------------------------------------------------------------
             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 =     0.0434, B  =   -0.0146
Partial structure    1: scale =     0.3849, B  =   43.2734
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.43 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1852
Free R factor                        =     0.2295
Average Fourier shell correlation    =     0.9496
AverageFree Fourier shell correlation=     0.9377
Average correlation coefficient      =     0.9234
Overall figure of merit              =     0.8476
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    123410.71       9062.5684       826635.69       826580.63    

 fvalues    123410.71       9062.5684       826592.56       826612.06    
 fvalues    123410.71       9062.5684       826592.56       826612.06    


     CGMAT cycle number =      8

 Weight matrix   0.36989388    
 Actual weight    6.6246233      is applied to the X-ray term


 function value    826616.38    

-------------------------------------------------------------------------------
             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 =     0.0434, B  =   -0.0191
Partial structure    1: scale =     0.3850, B  =   43.2522
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.43 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1852
Free R factor                        =     0.2296
Average Fourier shell correlation    =     0.9496
AverageFree Fourier shell correlation=     0.9377
Average correlation coefficient      =     0.9234
Overall figure of merit              =     0.8476
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    123412.06       9056.3027       826628.44       826612.06    

 fvalues    123412.06       9056.3027       826610.75       826614.75    
 fvalues    123412.06       9056.3027       826610.75       826614.75    


     CGMAT cycle number =      9

 Weight matrix   0.36990887    
 Actual weight    6.6246233      is applied to the X-ray term


 function value    826618.06    

-------------------------------------------------------------------------------
             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 =     0.0434, B  =   -0.0199
Partial structure    1: scale =     0.3850, B  =   43.2761
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.43 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1852
Free R factor                        =     0.2296
Average Fourier shell correlation    =     0.9496
AverageFree Fourier shell correlation=     0.9377
Average correlation coefficient      =     0.9234
Overall figure of merit              =     0.8476
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    123412.63       9054.7246       826607.44       826614.75    
 fvalues    123412.63       9054.7246       826607.44       826616.88    


     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.= 0.918 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        :   128  128  256
 Maximuum H,K,L                 :    35   35   75
 Minimum acceptable grid spacing:    81   81  171
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  256
 Maximuum H,K,L                 :    35   35   75
 Minimum acceptable grid spacing:    81   81  171
 Weight matrix   0.36975193    
 Actual weight    6.6246233      is applied to the X-ray term
Norm of X_ray positional gradient                42.9
Norm of Geom. positional gradient                42.9
Norm of X_ray B-factor gradient                  121.
Norm of Geom. B-factor gradient                  122.
Product of X_ray and Geom posit. gradients     -0.178E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.476E+08
 Cosine of angle between them                      -0.998


Residuals: XRAY=     0.8176E+06 GEOM=      9053.     TOTAL=     0.8266E+06
 function value    826623.13    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.843     1.644
Bond angles  : others                          3238     1.518     1.580
Torsion angles, period  1. refined              185     6.765     5.000
Torsion angles, period  2. refined               90    34.959    22.778
Torsion angles, period  3. refined              268    13.148    15.000
Torsion angles, period  4. refined                9    12.610    15.000
Chiral centres: refined atoms                   196     0.091     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   298     0.248     0.200
VDW repulsions.others                          1353     0.193     0.200
VDW; torsion: refined_atoms                     729     0.174     0.200
VDW; torsion.others                             776     0.085     0.200
HBOND: refined_atoms                            214     0.205     0.200
HBOND.others                                      1     0.061     0.200
VDW repulsions: symmetry: refined_atoms           8     0.213     0.200
VDW repulsions: symmetry: others                 24     0.184     0.200
HBOND: symmetry: refined_atoms                   21     0.175     0.200
M. chain bond B values: refined atoms           746     1.733     1.452
M. chain bond B values: others                  746     1.731     1.452
M. chain angle B values: refined atoms          929     2.707     2.168
M. chain angle B values: others                 930     2.706     2.168
S. chain bond B values: refined atoms           811     3.089     1.852
S. chain bond B values: others                  810     3.084     1.851
S. chain angle B values: refined atoms         1177     4.717     2.611
S. chain angle B values: others                1178     4.715     2.610
Long range B values: refined atoms             1842     7.157    20.090
Long range B values: others                    1753     6.889    18.696
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0434, B  =   -0.0194
Partial structure    1: scale =     0.3849, B  =   43.2382
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.43 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.046    3313 100.00   443.9   453.0  0.16  0.17     149   436.5   447.7  0.21  0.21
 0.138    5574  99.98   276.5   263.0  0.17  0.15     325   286.0   264.3  0.22  0.20
 0.230    7114  99.99   186.5   169.0  0.18  0.15     383   191.5   175.1  0.20  0.18
 0.321    8309 100.00    85.6    99.4  0.28  0.22     449    81.2    96.8  0.35  0.27
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0464   2391   0.925    922   0.829   3313   0.898  0.952  0.9646  0.9726  0.9045  0.9378
  0.1381   4659   0.869    915   0.760   5574   0.851  1.006  0.9441  0.9562  0.8885  0.9396
  0.2298   6185   0.887    929   0.779   7114   0.873  1.056  0.9573  0.9629  0.9152  0.9421
  0.3215   7410   0.812    908   0.738   8318   0.804  0.803  0.9073  0.9247  0.8385  0.8908
 $$
Resolution limits                    =     41.964     1.650
Number of used reflections           =      24319
Percentage observed                  =    99.9883
Percentage of free reflections       =     5.0966
Overall R factor                     =     0.1853
Free R factor                        =     0.2296
Average Fourier shell correlation    =     0.9496
AverageFree Fourier shell correlation=     0.9377
Overall weighted R factor            =     0.1639
Free weighted R factor               =     0.2035
Overall weighted R2 factor           =     0.1956
Free weighted R2 factor              =     0.2394
Average correlation coefficient      =     0.9234
Overall correlation coefficient      =     0.9580
Free correlation coefficient         =     0.9333
Cruickshanks DPI for coordinate error=     0.1023
DPI based on free R factor           =     0.1059
Overall figure of merit              =     0.8475
ML based su of positional parameters =     0.0648
ML based su of thermal parameters    =     1.9174
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    123414.01       9053.0781       826642.31       826616.88    

 fvalues    123414.01       9053.0781       826622.44       826624.38    
 fvalues    123414.01       9053.0781       826622.44       826624.38    

    ****                              VDW outliers                              ****

VDW deviations from the ideal >10.000Sigma or dist <  1.000 will be monitored

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.918 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_1-65A.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     1.843     1.644
Bond angles  : others                          3238     1.518     1.580
Torsion angles, period  1. refined              185     6.764     5.000
Torsion angles, period  2. refined               90    34.957    22.778
Torsion angles, period  3. refined              268    13.148    15.000
Torsion angles, period  4. refined                9    12.609    15.000
Chiral centres: refined atoms                   196     0.091     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   298     0.248     0.200
VDW repulsions.others                          1354     0.193     0.200
VDW; torsion: refined_atoms                     729     0.174     0.200
VDW; torsion.others                             777     0.085     0.200
HBOND: refined_atoms                            214     0.205     0.200
HBOND.others                                      1     0.062     0.200
VDW repulsions: symmetry: refined_atoms           8     0.214     0.200
VDW repulsions: symmetry: others                 24     0.184     0.200
HBOND: symmetry: refined_atoms                   21     0.175     0.200
M. chain bond B values: refined atoms           746     1.733     1.452
M. chain bond B values: others                  746     1.730     1.452
M. chain angle B values: refined atoms          929     2.707     2.168
M. chain angle B values: others                 930     2.705     2.168
S. chain bond B values: refined atoms           811     3.089     1.852
S. chain bond B values: others                  810     3.084     1.851
S. chain angle B values: refined atoms         1177     4.717     2.611
S. chain angle B values: others                1178     4.715     2.610
Long range B values: refined atoms             1842     7.158    20.090
Long range B values: others                    1753     6.890    18.696
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0434, B  =   -0.0207
Partial structure    1: scale =     0.3848, B  =   43.2289
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.43 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.046    3313 100.00   443.9   453.0  0.16  0.17     149   436.5   447.7  0.21  0.21
 0.138    5574  99.98   276.5   263.0  0.17  0.15     325   286.0   264.3  0.22  0.20
 0.230    7114  99.99   186.5   169.1  0.18  0.15     383   191.5   175.1  0.20  0.18
 0.321    8309 100.00    85.6    99.4  0.28  0.22     449    81.2    96.8  0.35  0.27
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0464   2391   0.925    922   0.829   3313   0.898  0.952  0.9646  0.9726  0.9046  0.9378
  0.1381   4659   0.869    915   0.760   5574   0.851  1.006  0.9441  0.9562  0.8885  0.9396
  0.2298   6185   0.887    929   0.779   7114   0.873  1.056  0.9573  0.9629  0.9152  0.9421
  0.3215   7410   0.812    908   0.738   8318   0.804  0.803  0.9073  0.9247  0.8385  0.8908
 $$
Resolution limits                    =     41.964     1.650
Number of used reflections           =      24319
Percentage observed                  =    99.9883
Percentage of free reflections       =     5.0966
Overall R factor                     =     0.1853
Free R factor                        =     0.2296
Average Fourier shell correlation    =     0.9496
AverageFree Fourier shell correlation=     0.9377
Overall weighted R factor            =     0.1639
Free weighted R factor               =     0.2035
Overall weighted R2 factor           =     0.1955
Free weighted R2 factor              =     0.2394
Average correlation coefficient      =     0.9234
Overall correlation coefficient      =     0.9580
Free correlation coefficient         =     0.9333
Cruickshanks DPI for coordinate error=     0.1023
DPI based on free R factor           =     0.1059
Overall figure of merit              =     0.8475
ML based su of positional parameters =     0.0648
ML based su of thermal parameters    =     1.9174
-----------------------------------------------------------------------------
  Time in seconds: CPU =        23.40
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1855   0.2303   0.814      124465.    6850.7   0.0133  0.996   1.845  1.074   0.091
       1   0.1857   0.2295   0.844      123568.    6820.7   0.0121  0.908   1.779  1.034   0.087
       2   0.1852   0.2294   0.848      123438.    6816.8   0.0129  0.971   1.814  1.055   0.089
       3   0.1852   0.2294   0.848      123414.    6816.5   0.0130  0.981   1.830  1.065   0.090
       4   0.1852   0.2295   0.848      123407.    6816.8   0.0131  0.984   1.837  1.069   0.091
       5   0.1852   0.2295   0.848      123406.    6817.0   0.0131  0.985   1.841  1.071   0.091
       6   0.1852   0.2295   0.848      123410.    6817.5   0.0131  0.985   1.842  1.072   0.091
       7   0.1852   0.2296   0.848      123412.    6817.9   0.0131  0.985   1.843  1.072   0.091
       8   0.1852   0.2296   0.848      123413.    6817.9   0.0131  0.985   1.843  1.072   0.091
       9   0.1853   0.2296   0.848      123414.    6817.9   0.0131  0.984   1.843  1.072   0.091
      10   0.1853   0.2296   0.848      123414.    6818.0   0.0131  0.984   1.843  1.072   0.091
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1855   0.1853
             R free    0.2303   0.2296
     Rms BondLength    0.0133   0.0131
      Rms BondAngle    1.8447   1.8428
     Rms ChirVolume    0.0911   0.0907
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      55.0s System:    0.7s Elapsed:     0:55