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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 27/ 5/2020 Run time: 04:40:35 


 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 1.45     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_1-46A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-45A.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_1-45A.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       0.1189
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.4500
  Estimated number of reflections :      47600
  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  1.4500

  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_1-46A.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=   2.057 ideal_dist=   2.090
            ch:AAA  res:  86  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.193 ideal_dist=   2.090
            ch:AAA  res:  88  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   1.831 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=   2.406 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=   2.385 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=   2.107 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       1873
Number of   all  reflections      37460
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          37460

   Current auto weighting coefficient =    6.1247458    

 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.= 0.896 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        :   144  144  288
 Maximuum H,K,L                 :    40   40   85
 Minimum acceptable grid spacing:    89   89  189
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  288
 Maximuum H,K,L                 :    40   40   85
 Minimum acceptable grid spacing:    89   89  189
 Weight matrix   0.27365044    
 Actual weight    6.1247458      is applied to the X-ray term
Norm of X_ray positional gradient                36.6
Norm of Geom. positional gradient                83.1
Norm of X_ray B-factor gradient                  92.1
Norm of Geom. B-factor gradient                  101.
Product of X_ray and Geom posit. gradients     -0.149E+08
 Cosine of angle between them                      -0.505
Product of X_ray and Geom B-fact gradients     -0.272E+08
 Cosine of angle between them                      -0.906


Residuals: XRAY=     0.1035E+07 GEOM=     0.1322E+05 TOTAL=     0.1049E+07
 function value    1048518.4    

-------------------------------------------------------------------------------
             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     1.849     1.644
Bond angles  : others                          3238     2.366     1.580
Torsion angles, period  1. refined              185     6.731     5.000
Torsion angles, period  2. refined               90    34.663    22.778
Torsion angles, period  3. refined              268    13.323    15.000
Torsion angles, period  4. refined                9    12.445    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.018     0.020
VDW repulsions: refined_atoms                   304     0.244     0.200
VDW repulsions.others                          1336     0.220     0.200
VDW; torsion: refined_atoms                     731     0.173     0.200
VDW; torsion.others                             722     0.081     0.200
HBOND: refined_atoms                            205     0.200     0.200
HBOND.others                                      1     0.065     0.200
VDW repulsions: symmetry: refined_atoms           8     0.198     0.200
VDW repulsions: symmetry: others                 24     0.197     0.200
HBOND: symmetry: refined_atoms                   21     0.164     0.200
M. chain bond B values: refined atoms           746     1.836     1.659
M. chain bond B values: others                  746     1.830     1.659
M. chain angle B values: refined atoms          929     2.822     2.479
M. chain angle B values: others                 930     2.821     2.479
S. chain bond B values: refined atoms           811     3.267     2.077
S. chain bond B values: others                  810     3.262     2.076
S. chain angle B values: refined atoms         1177     4.970     2.942
S. chain angle B values: others                1178     4.968     2.941
Long range B values: refined atoms             1841     7.728    22.665
Long range B values: others                    1755     7.450    21.246
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0463, B  =    0.0877
Partial structure    1: scale =     0.3944, B  =   37.4080
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.060    4783 100.00   390.7   400.2  0.17  0.18     222   386.5   390.1  0.21  0.22
 0.179    8139  99.98   214.0   191.5  0.19  0.17     462   225.2   202.4  0.22  0.20
 0.297   10396 100.00   103.4    97.6  0.22  0.19     565   103.5    98.4  0.26  0.23
 0.416   12250 100.00    42.8    53.1  0.44  0.41     624    43.1    53.9  0.45  0.42
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0600   3596   0.896   1187   0.786   4783   0.869  0.945  0.9569  0.9660  0.9016  0.9355
  0.1787   6950   0.864   1189   0.766   8139   0.850  1.080  0.9460  0.9549  0.8919  0.9339
  0.2975   9201   0.818   1195   0.732  10396   0.808  0.982  0.9300  0.9394  0.8918  0.9236
  0.4162  11065   0.535   1202   0.475  12267   0.529  0.505  0.7105  0.7060  0.7068  0.7083
 $$
Resolution limits                    =     41.964     1.450
Number of used reflections           =      35585
Percentage observed                  =    99.9920
Percentage of free reflections       =     5.0003
Overall R factor                     =     0.2140
Free R factor                        =     0.2494
Average Fourier shell correlation    =     0.8660
AverageFree Fourier shell correlation=     0.8640
Overall weighted R factor            =     0.1800
Free weighted R factor               =     0.2150
Overall weighted R2 factor           =     0.2088
Free weighted R2 factor              =     0.2506
Average correlation coefficient      =     0.8534
Overall correlation coefficient      =     0.9597
Free correlation coefficient         =     0.9404
Cruickshanks DPI for coordinate error=     0.0805
DPI based on free R factor           =     0.0836
Overall figure of merit              =     0.7294
ML based su of positional parameters =     0.0725
ML based su of thermal parameters    =     2.0693
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    169035.47       13219.080       1048518.4      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.34471738    
 Actual weight    6.1247458      is applied to the X-ray term


 function value    1036781.6    

-------------------------------------------------------------------------------
             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 =     0.0462, B  =   -0.0512
Partial structure    1: scale =     0.3934, B  =   37.4416
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2144
Free R factor                        =     0.2485
Average Fourier shell correlation    =     0.8792
AverageFree Fourier shell correlation=     0.8775
Average correlation coefficient      =     0.8519
Overall figure of merit              =     0.7525
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    167943.08       8172.8701       1036781.6       1048518.4    


     CGMAT cycle number =      3

 Weight matrix   0.35079488    
 Actual weight    6.1247458      is applied to the X-ray term


 function value    1036194.5    

-------------------------------------------------------------------------------
             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 =     0.0462, B  =   -0.0091
Partial structure    1: scale =     0.3934, B  =   37.3550
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2137
Free R factor                        =     0.2486
Average Fourier shell correlation    =     0.8820
AverageFree Fourier shell correlation=     0.8799
Average correlation coefficient      =     0.8527
Overall figure of merit              =     0.7559
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    167782.47       8569.4805       1036194.5       1036781.6    


     CGMAT cycle number =      4

 Weight matrix   0.35140505    
 Actual weight    6.1247458      is applied to the X-ray term


 function value    1036137.2    

-------------------------------------------------------------------------------
             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 =     0.0462, B  =    0.0003
Partial structure    1: scale =     0.3935, B  =   37.3923
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2137
Free R factor                        =     0.2487
Average Fourier shell correlation    =     0.8824
AverageFree Fourier shell correlation=     0.8802
Average correlation coefficient      =     0.8531
Overall figure of merit              =     0.7564
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    167760.14       8648.9600       1036137.2       1036194.5    


     CGMAT cycle number =      5

 Weight matrix   0.35156912    
 Actual weight    6.1247458      is applied to the X-ray term


 function value    1036133.3    

-------------------------------------------------------------------------------
             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 =     0.0462, B  =    0.0000
Partial structure    1: scale =     0.3935, B  =   37.3924
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2137
Free R factor                        =     0.2488
Average Fourier shell correlation    =     0.8825
AverageFree Fourier shell correlation=     0.8802
Average correlation coefficient      =     0.8533
Overall figure of merit              =     0.7565
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    167754.98       8676.6641       1036133.3       1036137.2    


     CGMAT cycle number =      6

 Weight matrix   0.35127673    
 Actual weight    6.1247458      is applied to the X-ray term


 function value    1036144.6    

-------------------------------------------------------------------------------
             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 =     0.0462, B  =    0.0013
Partial structure    1: scale =     0.3935, B  =   37.3839
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2136
Free R factor                        =     0.2488
Average Fourier shell correlation    =     0.8825
AverageFree Fourier shell correlation=     0.8802
Average correlation coefficient      =     0.8533
Overall figure of merit              =     0.7565
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    167755.38       8682.6572       1036168.6       1036133.3    

 fvalues    167755.38       8682.6572       1036144.6       1036141.8    
 fvalues    167755.38       8682.6572       1036144.6       1036141.8    


     CGMAT cycle number =      7

 Weight matrix   0.35107920    
 Actual weight    6.1247458      is applied to the X-ray term


 function value    1036153.1    

-------------------------------------------------------------------------------
             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 =     0.0462, B  =    0.0031
Partial structure    1: scale =     0.3934, B  =   37.3594
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2136
Free R factor                        =     0.2488
Average Fourier shell correlation    =     0.8824
AverageFree Fourier shell correlation=     0.8801
Average correlation coefficient      =     0.8533
Overall figure of merit              =     0.7564
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    167757.84       8681.9316       1036170.3       1036141.8    

 fvalues    167757.84       8681.9316       1036163.3       1036156.1    
 fvalues    167757.84       8681.9316       1036163.3       1036156.1    


     CGMAT cycle number =      8

 Weight matrix   0.35115793    
 Actual weight    6.1247458      is applied to the X-ray term


 function value    1036153.5    

-------------------------------------------------------------------------------
             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 =     0.0462, B  =    0.0006
Partial structure    1: scale =     0.3934, B  =   37.3600
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2136
Free R factor                        =     0.2488
Average Fourier shell correlation    =     0.8824
AverageFree Fourier shell correlation=     0.8801
Average correlation coefficient      =     0.8533
Overall figure of merit              =     0.7564
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    167757.70       8680.1758       1036153.5       1036156.1    


     CGMAT cycle number =      9

 Weight matrix   0.35105243    
 Actual weight    6.1247458      is applied to the X-ray term


 function value    1036160.1    

-------------------------------------------------------------------------------
             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 =     0.0462, B  =    0.0024
Partial structure    1: scale =     0.3934, B  =   37.3710
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2136
Free R factor                        =     0.2488
Average Fourier shell correlation    =     0.8824
AverageFree Fourier shell correlation=     0.8801
Average correlation coefficient      =     0.8533
Overall figure of merit              =     0.7564
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    167758.89       8680.2520       1036172.6       1036153.5    

 fvalues    167758.89       8680.2520       1036163.0       1036160.8    
 fvalues    167758.89       8680.2520       1036163.0       1036160.8    


     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.= 0.913 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  288
 Maximuum H,K,L                 :    40   40   85
 Minimum acceptable grid spacing:    89   89  189
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  288
 Maximuum H,K,L                 :    40   40   85
 Minimum acceptable grid spacing:    89   89  189
 Weight matrix   0.35095757    
 Actual weight    6.1247458      is applied to the X-ray term
Norm of X_ray positional gradient                43.7
Norm of Geom. positional gradient                43.7
Norm of X_ray B-factor gradient                  106.
Norm of Geom. B-factor gradient                  105.
Product of X_ray and Geom posit. gradients     -0.185E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.359E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.1027E+07 GEOM=      8680.     TOTAL=     0.1036E+07
 function value    1036172.1    

-------------------------------------------------------------------------------
             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     1.847     1.644
Bond angles  : others                          3238     1.513     1.580
Torsion angles, period  1. refined              185     6.739     5.000
Torsion angles, period  2. refined               90    34.678    22.778
Torsion angles, period  3. refined              268    13.331    15.000
Torsion angles, period  4. refined                9    12.340    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                   299     0.246     0.200
VDW repulsions.others                          1359     0.195     0.200
VDW; torsion: refined_atoms                     728     0.174     0.200
VDW; torsion.others                             748     0.086     0.200
HBOND: refined_atoms                            203     0.201     0.200
HBOND.others                                      1     0.002     0.200
VDW repulsions: symmetry: refined_atoms           9     0.185     0.200
VDW repulsions: symmetry: others                 24     0.188     0.200
HBOND: symmetry: refined_atoms                   20     0.167     0.200
M. chain bond B values: refined atoms           746     1.840     1.667
M. chain bond B values: others                  746     1.835     1.667
M. chain angle B values: refined atoms          929     2.822     2.491
M. chain angle B values: others                 930     2.821     2.491
S. chain bond B values: refined atoms           811     3.270     2.083
S. chain bond B values: others                  810     3.265     2.083
S. chain angle B values: refined atoms         1177     4.972     2.952
S. chain angle B values: others                1178     4.970     2.951
Long range B values: refined atoms             1833     7.721    22.715
Long range B values: others                    1748     7.440    21.308
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0462, B  =    0.0031
Partial structure    1: scale =     0.3934, B  =   37.3762
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.060    4783 100.00   391.2   400.8  0.17  0.18     222   387.0   390.5  0.21  0.22
 0.179    8139  99.98   214.3   191.8  0.19  0.17     462   225.5   202.6  0.22  0.20
 0.297   10396 100.00   103.6    97.9  0.22  0.19     565   103.6    98.7  0.26  0.23
 0.416   12250 100.00    42.9    53.1  0.44  0.41     624    43.2    53.9  0.45  0.42
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0600   3596   0.912   1187   0.811   4783   0.887  0.948  0.9616  0.9702  0.9021  0.9356
  0.1787   6950   0.881   1189   0.782   8139   0.866  1.082  0.9496  0.9588  0.8927  0.9341
  0.2975   9201   0.842   1195   0.759  10396   0.832  0.989  0.9385  0.9478  0.8927  0.9244
  0.4162  11065   0.574   1202   0.518  12267   0.568  0.524  0.7469  0.7422  0.7061  0.7071
 $$
Resolution limits                    =     41.964     1.450
Number of used reflections           =      35585
Percentage observed                  =    99.9920
Percentage of free reflections       =     5.0003
Overall R factor                     =     0.2136
Free R factor                        =     0.2488
Average Fourier shell correlation    =     0.8824
AverageFree Fourier shell correlation=     0.8801
Overall weighted R factor            =     0.1798
Free weighted R factor               =     0.2145
Overall weighted R2 factor           =     0.2087
Free weighted R2 factor              =     0.2501
Average correlation coefficient      =     0.8533
Overall correlation coefficient      =     0.9598
Free correlation coefficient         =     0.9407
Cruickshanks DPI for coordinate error=     0.0803
DPI based on free R factor           =     0.0834
Overall figure of merit              =     0.7564
ML based su of positional parameters =     0.0640
ML based su of thermal parameters    =     1.8184
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    167760.69       8680.2432       1036169.4       1036160.8    
 fvalues    167760.69       8680.2432       1036169.4       1036171.8    

    ****                              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.= 0.913 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

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

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_step0-01A_R00_1-45A.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     1.847     1.644
Bond angles  : others                          3238     1.513     1.580
Torsion angles, period  1. refined              185     6.739     5.000
Torsion angles, period  2. refined               90    34.678    22.778
Torsion angles, period  3. refined              268    13.332    15.000
Torsion angles, period  4. refined                9    12.339    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                   300     0.246     0.200
VDW repulsions.others                          1359     0.195     0.200
VDW; torsion: refined_atoms                     728     0.174     0.200
VDW; torsion.others                             748     0.086     0.200
HBOND: refined_atoms                            203     0.201     0.200
HBOND.others                                      1     0.001     0.200
VDW repulsions: symmetry: refined_atoms           9     0.185     0.200
VDW repulsions: symmetry: others                 24     0.188     0.200
HBOND: symmetry: refined_atoms                   20     0.167     0.200
M. chain bond B values: refined atoms           746     1.840     1.667
M. chain bond B values: others                  746     1.835     1.667
M. chain angle B values: refined atoms          929     2.822     2.491
M. chain angle B values: others                 930     2.821     2.491
S. chain bond B values: refined atoms           811     3.270     2.083
S. chain bond B values: others                  810     3.265     2.083
S. chain angle B values: refined atoms         1177     4.972     2.952
S. chain angle B values: others                1178     4.970     2.951
Long range B values: refined atoms             1834     7.719    22.717
Long range B values: others                    1749     7.439    21.311
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0462, B  =    0.0030
Partial structure    1: scale =     0.3934, B  =   37.3798
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.060    4783 100.00   391.2   400.8  0.17  0.18     222   387.0   390.5  0.21  0.22
 0.179    8139  99.98   214.3   191.8  0.19  0.17     462   225.5   202.6  0.22  0.20
 0.297   10396 100.00   103.6    97.9  0.22  0.19     565   103.6    98.7  0.26  0.23
 0.416   12250 100.00    42.9    53.1  0.44  0.41     624    43.2    53.9  0.45  0.42
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0600   3596   0.912   1187   0.811   4783   0.887  0.948  0.9616  0.9701  0.9021  0.9356
  0.1787   6950   0.881   1189   0.782   8139   0.866  1.082  0.9496  0.9588  0.8927  0.9341
  0.2975   9201   0.842   1195   0.759  10396   0.832  0.989  0.9385  0.9478  0.8927  0.9245
  0.4162  11065   0.574   1202   0.518  12267   0.568  0.524  0.7469  0.7422  0.7062  0.7071
 $$
Resolution limits                    =     41.964     1.450
Number of used reflections           =      35585
Percentage observed                  =    99.9920
Percentage of free reflections       =     5.0003
Overall R factor                     =     0.2136
Free R factor                        =     0.2488
Average Fourier shell correlation    =     0.8824
AverageFree Fourier shell correlation=     0.8801
Overall weighted R factor            =     0.1798
Free weighted R factor               =     0.2145
Overall weighted R2 factor           =     0.2087
Free weighted R2 factor              =     0.2502
Average correlation coefficient      =     0.8533
Overall correlation coefficient      =     0.9598
Free correlation coefficient         =     0.9407
Cruickshanks DPI for coordinate error=     0.0803
DPI based on free R factor           =     0.0834
Overall figure of merit              =     0.7564
ML based su of positional parameters =     0.0640
ML based su of thermal parameters    =     1.8184
-----------------------------------------------------------------------------
  Time in seconds: CPU =        29.64
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2140   0.2494   0.729      169035.    9080.5   0.0132  0.994   1.849  1.076   0.090
       1   0.2144   0.2485   0.753      167943.    9048.9   0.0119  0.899   1.777  1.035   0.087
       2   0.2137   0.2486   0.756      167782.    9046.0   0.0130  0.980   1.822  1.061   0.090
       3   0.2137   0.2487   0.756      167760.    9045.9   0.0131  0.986   1.837  1.070   0.090
       4   0.2137   0.2488   0.757      167755.    9046.3   0.0131  0.989   1.843  1.073   0.090
       5   0.2136   0.2488   0.756      167756.    9046.7   0.0131  0.989   1.846  1.075   0.090
       6   0.2136   0.2488   0.756      167757.    9046.8   0.0131  0.989   1.847  1.075   0.090
       7   0.2136   0.2488   0.756      167758.    9046.9   0.0131  0.989   1.847  1.075   0.090
       8   0.2136   0.2488   0.756      167759.    9046.9   0.0131  0.989   1.847  1.076   0.091
       9   0.2136   0.2488   0.756      167761.    9047.0   0.0131  0.989   1.847  1.076   0.091
      10   0.2136   0.2488   0.756      167761.    9047.0   0.0131  0.989   1.847  1.076   0.091
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2140   0.2136
             R free    0.2494   0.2488
     Rms BondLength    0.0132   0.0131
      Rms BondAngle    1.8486   1.8474
     Rms ChirVolume    0.0905   0.0905
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      60.7s System:    0.2s Elapsed:     1:01