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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 27/ 5/2020 Run time: 01:34:33 


 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 1.51     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_1-52A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-51A.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_1-51A.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       0.1096
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.5100
  Estimated number of reflections :      43652
  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  1.5100

  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_1-52A.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=   2.056 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=   2.191 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=   1.828 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=   2.216 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=   2.411 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=   2.387 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=   2.112 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       1655
Number of   all  reflections      33241
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          33241

   Current auto weighting coefficient =    6.2748213    

 mode : HKRF


######  TLS Group Definitions ######



     CGMAT cycle number =      1

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.893 id.= 3.000 dev= -2.11 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    86   86  183
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    86   86  183
 Weight matrix   0.27919573    
 Actual weight    6.2748213      is applied to the X-ray term
Norm of X_ray positional gradient                36.5
Norm of Geom. positional gradient                82.6
Norm of X_ray B-factor gradient                  97.1
Norm of Geom. B-factor gradient                  106.
Product of X_ray and Geom posit. gradients     -0.146E+08
 Cosine of angle between them                      -0.500
Product of X_ray and Geom B-fact gradients     -0.296E+08
 Cosine of angle between them                      -0.892


Residuals: XRAY=     0.9661E+06 GEOM=     0.1335E+05 TOTAL=     0.9794E+06
 function value    979442.19    

-------------------------------------------------------------------------------
             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     1.857     1.644
Bond angles  : others                          3238     2.366     1.580
Torsion angles, period  1. refined              185     6.759     5.000
Torsion angles, period  2. refined               90    34.645    22.778
Torsion angles, period  3. refined              268    13.310    15.000
Torsion angles, period  4. refined                9    12.442    15.000
Chiral centres: refined atoms                   196     0.091     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.017     0.020
VDW repulsions: refined_atoms                   305     0.245     0.200
VDW repulsions.others                          1340     0.220     0.200
VDW; torsion: refined_atoms                     730     0.174     0.200
VDW; torsion.others                             729     0.081     0.200
HBOND: refined_atoms                            209     0.200     0.200
HBOND.others                                      1     0.072     0.200
VDW repulsions: symmetry: refined_atoms           8     0.202     0.200
VDW repulsions: symmetry: others                 23     0.199     0.200
HBOND: symmetry: refined_atoms                   22     0.166     0.200
M. chain bond B values: refined atoms           746     1.799     1.596
M. chain bond B values: others                  746     1.794     1.596
M. chain angle B values: refined atoms          929     2.787     2.383
M. chain angle B values: others                 930     2.786     2.383
S. chain bond B values: refined atoms           811     3.234     2.009
S. chain bond B values: others                  810     3.229     2.009
S. chain angle B values: refined atoms         1177     4.924     2.842
S. chain angle B values: others                1178     4.922     2.842
Long range B values: refined atoms             1847     7.704    21.920
Long range B values: others                    1762     7.432    20.549
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0455, B  =    0.1455
Partial structure    1: scale =     0.3917, B  =   38.5505
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.37 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.055    4255 100.00   409.6   419.4  0.17  0.18     202   402.1   409.4  0.21  0.21
 0.165    7230  99.97   230.6   211.3  0.18  0.16     410   243.3   219.5  0.22  0.20
 0.274    9230 100.00   128.3   117.8  0.20  0.18     500   126.1   117.4  0.25  0.22
 0.384   10862 100.00    51.7    64.3  0.40  0.35     542    52.0    65.2  0.42  0.38
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0553   3161   0.903   1094   0.792   4255   0.874  0.946  0.9593  0.9677  0.9049  0.9362
  0.1648   6129   0.867   1101   0.773   7230   0.853  1.053  0.9457  0.9549  0.8860  0.9336
  0.2743   8131   0.837   1099   0.746   9230   0.826  1.025  0.9356  0.9480  0.8912  0.9332
  0.3838   9762   0.575   1107   0.503  10869   0.567  0.582  0.7779  0.7876  0.7537  0.7948
 $$
Resolution limits                    =     41.964     1.510
Number of used reflections           =      31584
Percentage observed                  =    99.9910
Percentage of free reflections       =     4.9791
Overall R factor                     =     0.2054
Free R factor                        =     0.2429
Average Fourier shell correlation    =     0.8970
AverageFree Fourier shell correlation=     0.8892
Overall weighted R factor            =     0.1748
Free weighted R factor               =     0.2105
Overall weighted R2 factor           =     0.2042
Free weighted R2 factor              =     0.2469
Average correlation coefficient      =     0.8861
Overall correlation coefficient      =     0.9593
Free correlation coefficient         =     0.9382
Cruickshanks DPI for coordinate error=     0.0868
DPI based on free R factor           =     0.0900
Overall figure of merit              =     0.7498
ML based su of positional parameters =     0.0727
ML based su of thermal parameters    =     2.1212
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    153963.00       13351.878       979442.19      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.35353607    
 Actual weight    6.2748213      is applied to the X-ray term


 function value    967278.31    

-------------------------------------------------------------------------------
             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 =     0.0454, B  =   -0.0531
Partial structure    1: scale =     0.3918, B  =   38.5449
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.37 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2058
Free R factor                        =     0.2418
Average Fourier shell correlation    =     0.9123
AverageFree Fourier shell correlation=     0.9058
Average correlation coefficient      =     0.8845
Overall figure of merit              =     0.7812
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    152830.94       8291.5176       967278.31       979442.19    


     CGMAT cycle number =      3

 Weight matrix   0.36394718    
 Actual weight    6.2748213      is applied to the X-ray term


 function value    966434.56    

-------------------------------------------------------------------------------
             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 =     0.0454, B  =   -0.0120
Partial structure    1: scale =     0.3921, B  =   38.6352
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2052
Free R factor                        =     0.2420
Average Fourier shell correlation    =     0.9158
AverageFree Fourier shell correlation=     0.9090
Average correlation coefficient      =     0.8857
Overall figure of merit              =     0.7881
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    152637.59       8660.9180       966434.56       967278.31    


     CGMAT cycle number =      4

 Weight matrix   0.36544594    
 Actual weight    6.2748213      is applied to the X-ray term


 function value    966290.25    

-------------------------------------------------------------------------------
             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 =     0.0454, B  =   -0.0087
Partial structure    1: scale =     0.3921, B  =   38.6433
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2051
Free R factor                        =     0.2421
Average Fourier shell correlation    =     0.9165
AverageFree Fourier shell correlation=     0.9095
Average correlation coefficient      =     0.8863
Overall figure of merit              =     0.7894
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    152600.38       8750.1748       966290.25       966434.56    


     CGMAT cycle number =      5

 Weight matrix   0.36541590    
 Actual weight    6.2748213      is applied to the X-ray term


 function value    966295.75    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0454, B  =    0.0009
Partial structure    1: scale =     0.3921, B  =   38.6482
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2051
Free R factor                        =     0.2421
Average Fourier shell correlation    =     0.9165
AverageFree Fourier shell correlation=     0.9095
Average correlation coefficient      =     0.8865
Overall figure of merit              =     0.7895
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03


 fvalues    152594.56       8790.3672       966298.38       966290.25    

 fvalues    152594.56       8790.3672       966301.13       966294.00    
 fvalues    152594.56       8790.3672       966301.13       966294.00    


     CGMAT cycle number =      6

 Weight matrix   0.36528563    
 Actual weight    6.2748213      is applied to the X-ray term


 function value    966292.44    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0454, B  =    0.0028
Partial structure    1: scale =     0.3921, B  =   38.6562
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2051
Free R factor                        =     0.2421
Average Fourier shell correlation    =     0.9165
AverageFree Fourier shell correlation=     0.9094
Average correlation coefficient      =     0.8865
Overall figure of merit              =     0.7894
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    152594.02       8792.2236       966292.44       966294.00    


     CGMAT cycle number =      7

 Weight matrix   0.36518958    
 Actual weight    6.2748213      is applied to the X-ray term


 function value    966296.50    

-------------------------------------------------------------------------------
             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 =     0.0454, B  =    0.0031
Partial structure    1: scale =     0.3921, B  =   38.6153
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2051
Free R factor                        =     0.2421
Average Fourier shell correlation    =     0.9165
AverageFree Fourier shell correlation=     0.9094
Average correlation coefficient      =     0.8865
Overall figure of merit              =     0.7894
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    152594.28       8793.0918       966299.31       966292.44    

 fvalues    152594.28       8793.0918       966297.00       966294.88    
 fvalues    152594.28       8793.0918       966297.00       966294.88    


     CGMAT cycle number =      8

 Weight matrix   0.36534092    
 Actual weight    6.2748213      is applied to the X-ray term


 function value    966289.50    

-------------------------------------------------------------------------------
             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 =     0.0454, B  =    0.0000
Partial structure    1: scale =     0.3921, B  =   38.6146
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2051
Free R factor                        =     0.2421
Average Fourier shell correlation    =     0.9165
AverageFree Fourier shell correlation=     0.9094
Average correlation coefficient      =     0.8865
Overall figure of merit              =     0.7894
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    152593.59       8791.9961       966289.50       966294.88    


     CGMAT cycle number =      9

 Weight matrix   0.36513481    
 Actual weight    6.2748213      is applied to the X-ray term


 function value    966291.13    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0454, B  =    0.0031
Partial structure    1: scale =     0.3921, B  =   38.5672
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2051
Free R factor                        =     0.2421
Average Fourier shell correlation    =     0.9165
AverageFree Fourier shell correlation=     0.9094
Average correlation coefficient      =     0.8865
Overall figure of merit              =     0.7894
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02

 fvalues    152593.34       8793.0078       966288.94       966289.50    


     CGMAT cycle number =     10

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.910 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    86   86  183
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    86   86  183
 Weight matrix   0.36511359    
 Actual weight    6.2748213      is applied to the X-ray term
Norm of X_ray positional gradient                43.5
Norm of Geom. positional gradient                43.4
Norm of X_ray B-factor gradient                  110.
Norm of Geom. B-factor gradient                  109.
Product of X_ray and Geom posit. gradients     -0.183E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.386E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.9575E+06 GEOM=      8794.     TOTAL=     0.9663E+06
 function value    966291.75    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.851     1.644
Bond angles  : others                          3238     1.515     1.580
Torsion angles, period  1. refined              185     6.752     5.000
Torsion angles, period  2. refined               90    34.675    22.778
Torsion angles, period  3. refined              268    13.298    15.000
Torsion angles, period  4. refined                9    12.406    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   303     0.245     0.200
VDW repulsions.others                          1361     0.195     0.200
VDW; torsion: refined_atoms                     729     0.174     0.200
VDW; torsion.others                             746     0.086     0.200
HBOND: refined_atoms                            207     0.200     0.200
HBOND.others                                      1     0.025     0.200
VDW repulsions: symmetry: refined_atoms           8     0.202     0.200
VDW repulsions: symmetry: others                 23     0.189     0.200
HBOND: symmetry: refined_atoms                   22     0.167     0.200
M. chain bond B values: refined atoms           746     1.803     1.609
M. chain bond B values: others                  746     1.798     1.609
M. chain angle B values: refined atoms          929     2.792     2.404
M. chain angle B values: others                 930     2.791     2.404
S. chain bond B values: refined atoms           811     3.242     2.024
S. chain bond B values: others                  810     3.238     2.023
S. chain angle B values: refined atoms         1177     4.932     2.864
S. chain angle B values: others                1178     4.930     2.863
Long range B values: refined atoms             1842     7.715    22.068
Long range B values: others                    1756     7.443    20.674
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0454, B  =    0.0031
Partial structure    1: scale =     0.3921, B  =   38.5652
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10.  v. resln :N:1,6,7,11,12:
:Cycle   10.  and  v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.055    4255 100.00   410.0   419.8  0.17  0.18     202   402.5   410.0  0.21  0.21
 0.165    7230  99.97   230.9   211.6  0.18  0.16     410   243.5   219.7  0.22  0.20
 0.274    9230 100.00   128.4   118.0  0.20  0.18     500   126.3   117.5  0.25  0.22
 0.384   10862 100.00    51.8    64.3  0.40  0.35     542    52.0    65.3  0.42  0.37
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle   10. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0553   3161   0.919   1094   0.817   4255   0.893  0.948  0.9637  0.9716  0.9055  0.9362
  0.1648   6129   0.878   1101   0.784   7230   0.863  1.053  0.9480  0.9573  0.8873  0.9340
  0.2743   8131   0.853   1099   0.763   9230   0.843  1.027  0.9415  0.9534  0.8922  0.9332
  0.3838   9762   0.661   1107   0.594  10869   0.654  0.624  0.8305  0.8365  0.7546  0.7959
 $$
Resolution limits                    =     41.964     1.510
Number of used reflections           =      31584
Percentage observed                  =    99.9910
Percentage of free reflections       =     4.9791
Overall R factor                     =     0.2051
Free R factor                        =     0.2421
Average Fourier shell correlation    =     0.9165
AverageFree Fourier shell correlation=     0.9094
Overall weighted R factor            =     0.1746
Free weighted R factor               =     0.2098
Overall weighted R2 factor           =     0.2040
Free weighted R2 factor              =     0.2460
Average correlation coefficient      =     0.8865
Overall correlation coefficient      =     0.9594
Free correlation coefficient         =     0.9387
Cruickshanks DPI for coordinate error=     0.0867
DPI based on free R factor           =     0.0897
Overall figure of merit              =     0.7894
ML based su of positional parameters =     0.0635
ML based su of thermal parameters    =     1.8227
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    152593.63       8793.6406       966285.88       966288.94    
 fvalues    152593.63       8793.6406       966285.88       966291.38    

    ****                              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.= 0.910 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

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

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_step0-01A_R00_1-51A.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     1.852     1.644
Bond angles  : others                          3238     1.515     1.580
Torsion angles, period  1. refined              185     6.752     5.000
Torsion angles, period  2. refined               90    34.674    22.778
Torsion angles, period  3. refined              268    13.298    15.000
Torsion angles, period  4. refined                9    12.405    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   303     0.245     0.200
VDW repulsions.others                          1364     0.195     0.200
VDW; torsion: refined_atoms                     729     0.174     0.200
VDW; torsion.others                             747     0.086     0.200
HBOND: refined_atoms                            207     0.200     0.200
HBOND.others                                      1     0.025     0.200
VDW repulsions: symmetry: refined_atoms           8     0.202     0.200
VDW repulsions: symmetry: others                 24     0.185     0.200
HBOND: symmetry: refined_atoms                   22     0.167     0.200
M. chain bond B values: refined atoms           746     1.803     1.609
M. chain bond B values: others                  746     1.798     1.609
M. chain angle B values: refined atoms          929     2.792     2.404
M. chain angle B values: others                 930     2.791     2.404
S. chain bond B values: refined atoms           811     3.243     2.024
S. chain bond B values: others                  810     3.238     2.023
S. chain angle B values: refined atoms         1177     4.933     2.864
S. chain angle B values: others                1178     4.931     2.863
Long range B values: refined atoms             1842     7.716    22.068
Long range B values: others                    1756     7.444    20.674
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0454, B  =    0.0032
Partial structure    1: scale =     0.3921, B  =   38.5688
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.055    4255 100.00   410.0   419.8  0.17  0.18     202   402.5   410.0  0.21  0.21
 0.165    7230  99.97   230.9   211.6  0.18  0.16     410   243.5   219.7  0.22  0.20
 0.274    9230 100.00   128.4   118.0  0.20  0.18     500   126.3   117.5  0.25  0.22
 0.384   10862 100.00    51.8    64.3  0.40  0.35     542    52.0    65.3  0.42  0.37
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0553   3161   0.919   1094   0.817   4255   0.893  0.948  0.9637  0.9716  0.9055  0.9362
  0.1648   6129   0.878   1101   0.784   7230   0.863  1.053  0.9480  0.9573  0.8873  0.9340
  0.2743   8131   0.853   1099   0.763   9230   0.843  1.027  0.9415  0.9534  0.8922  0.9332
  0.3838   9762   0.661   1107   0.594  10869   0.654  0.624  0.8305  0.8365  0.7546  0.7959
 $$
Resolution limits                    =     41.964     1.510
Number of used reflections           =      31584
Percentage observed                  =    99.9910
Percentage of free reflections       =     4.9791
Overall R factor                     =     0.2051
Free R factor                        =     0.2421
Average Fourier shell correlation    =     0.9165
AverageFree Fourier shell correlation=     0.9094
Overall weighted R factor            =     0.1746
Free weighted R factor               =     0.2098
Overall weighted R2 factor           =     0.2040
Free weighted R2 factor              =     0.2460
Average correlation coefficient      =     0.8866
Overall correlation coefficient      =     0.9594
Free correlation coefficient         =     0.9387
Cruickshanks DPI for coordinate error=     0.0867
DPI based on free R factor           =     0.0897
Overall figure of merit              =     0.7894
ML based su of positional parameters =     0.0635
ML based su of thermal parameters    =     1.8227
-----------------------------------------------------------------------------
  Time in seconds: CPU =        25.87
             Elapsed =         128.00

    ****           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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2054   0.2429   0.750      153963.    8264.9   0.0132  0.991   1.857  1.080   0.091
       1   0.2058   0.2418   0.781      152831.    8226.4   0.0120  0.900   1.785  1.037   0.087
       2   0.2052   0.2420   0.788      152638.    8221.3   0.0130  0.976   1.824  1.061   0.089
       3   0.2051   0.2421   0.789      152600.    8220.5   0.0131  0.984   1.840  1.071   0.090
       4   0.2051   0.2421   0.789      152595.    8220.8   0.0131  0.987   1.848  1.075   0.090
       5   0.2051   0.2421   0.789      152594.    8220.8   0.0131  0.987   1.849  1.076   0.090
       6   0.2051   0.2421   0.789      152595.    8220.9   0.0131  0.988   1.850  1.076   0.090
       7   0.2051   0.2421   0.789      152594.    8221.0   0.0131  0.988   1.850  1.076   0.090
       8   0.2051   0.2421   0.789      152594.    8220.9   0.0131  0.988   1.851  1.077   0.090
       9   0.2051   0.2421   0.789      152594.    8220.9   0.0131  0.988   1.851  1.077   0.090
      10   0.2051   0.2421   0.789      152594.    8221.0   0.0131  0.988   1.852  1.077   0.090
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2054   0.2051
             R free    0.2429   0.2421
     Rms BondLength    0.0132   0.0131
      Rms BondAngle    1.8571   1.8516
     Rms ChirVolume    0.0905   0.0904
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      57.9s System:    0.2s Elapsed:     0:58