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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: 02:03:52 


 Please reference: Collaborative Computational Project, Number 4. 2011.
 "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242.
 as well as any specific reference in the program write-up.


 $TEXT:Reference1: $$ Primary reference $$ 
   "Overview of refinement procedures within REFMAC5: utilizing data from different sources"
   O.Kovalevskiy, R.A.Nicholls, F.Long, G.N.Murshudov,(2018) 
   Acta Crystallogr. D74, 492-505

 $$
 $SUMMARY :Reference1:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference1: $$ Primary reference for EM $$ 
   "Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM
   R.A. Nicholls, M. Tykac, O.Kovalevskiy, G.N.Murshudov,(2018) 
   Acta Crystallogr. D74, 215-227

 $$
 $SUMMARY :Reference2:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference1: $$ Secondary reference $$ 
   "REFMAC5 for the refinement of macromolecular crystal structures:"
   G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011) 
   Acta Crystallogr. D67, 355-367

 $$
 $SUMMARY :Reference3:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference2: $$ Secondary reference $$ 
   "Refinement of Macromolecular Structures by the  Maximum-Likelihood Method:"
   G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
   Acta Crystallogr. D53, 240-255
   EU  Validation contract: BIO2CT-92-0524

 $$
 $SUMMARY :Reference4:  $$ Refmac: $$
 :TEXT:Reference2: $$

  Data line--- make     check NONE
  Data line--- refi     type REST reso 41.96 1.50     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- bins 4
  Data line--- ncyc 10
  Data line--- monitor MEDIum
  Data line--- free 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_1-51A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-50A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_step0-01A_R00_1-50A.mtz

Cell from mtz :    57.632    57.632   122.391    90.000    90.000    90.000
Space group from mtz: number -   96; name - P 43 21 2

  Refinement type                        : Restrained

    ****                           Makecif parameters                           ****

Dictionary files for restraints : /protein2/ccp4/ccp4-7.0/ccp4-7.0/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /protein2/ccp4/ccp4-7.0/ccp4-7.0/lib/data/monomers/ener_lib.cif
    Program will rely on residue and atom names. No checking
    If this option is used then monomers should be checked carefully before using
    Hydrogens will be restored in their riding positions
    Links between monomers will be checked. Only those links present in the coordinate file will be used
    Standard sugar links will be analysed and used
    For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
    Symmetry related links will be analysed and used
    Cis peptides will be found and used automatically


  Residual                               : Rice Maximum Likelihood for Fs

    ****                    Least-square scaling parameters                     ****

Overall scale
Overall B value
Overall anisotropic B with tr(B) = 0.0
Constant bulk solvent in non protein region
Probe radii for non-ions     1.200
Probe radii for ions         0.800
Shrinkage of the mask  by    0.800


    ****                 Map sharpening parameters and methods                  ****

No map sharpening will be performed

  Method of minimisation                 : Sparse Matrix
  Experimental sigmas used for weighting
  Number of Bins and width:     4       0.1111
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.5000
  Estimated number of reflections :      43652
  Free R exclusion - flag equals:     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  1.5000

  Damping factors:     1.0000  1.0000  1.0000


    ****                    Geometry restraints and weights                     ****


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

 Planar groups (all and main chain)
          WEIGHT= 1.00 1.00

 Chiral centers
          Weight= 1.00

 NON-BONDED CONTACTS
          Overall weight                          =  1.00
          Sigma for simple VDW                    =  0.20
          Sigma for VDW trhough torsion angle     =  0.20
          Sigma for HBOND                         =  0.20
          Sigma for metal-ion                     =  0.20
          Sigma for DUMMY and other atom          =  0.30
          Distance for donor-accepetor = vdw1+vdw2+(-0.30)
          Distance for acceptor - H    = vdw1+     ( 0.10)
          VDW distance through torsion = vdw1+vdw2+(-0.30)
          Distance for DUMMY-others    = vdw1+vdw2+(-0.70)

 TORSION ANGLES
          Weight= 1.00

 THERMAL FACTORS
          Weight= 1.00
     Main chain bond (1-2 neighbour)          1.5A**2
     Main chain angle (1-3 neighbour)         2.0A**2
     Side chain bond                          3.0A**2
     Side chain angle                         4.5A**2

 RESTRAINTS AGAINST EXCESSIVE SHIFTS
     Positional parameters                   0.00A
     Thermal parameters                      0.00A
     Occupancy parameters                    0.00

 RADIUS OF CONFIDENCE
     Positional parameters 0.00A
     Thermal parameters    0.00A**2
     Occupancy parameters  0.00

Monitoring style is "MEDIUM". Complete information will be printed out in the
first and last cycle. In all other cycles minimum information will be printed out
Sigma cutoffs for printing out outliers
If deviation of restraint parameter > alpha*sigma then information will be printed out
Distance outliers      10.000
Angle outliers         10.000
Torsion outliers       10.000
Chiral volume outliers 10.000
Plane outliers         10.000
Non-bonding outliers   10.000
B value  outliers      10.000
Rigid bond outliers    10.000
Sphericity outliers    10.000
---------------------------------------------------------------

 Input file :CDO_step0-01A_R00_1-51A.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=   2.055 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=   1.828 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=   2.218 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=   2.411 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=   2.385 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=   2.105 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       1689
Number of   all  reflections      33910
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          33910

   Current auto weighting coefficient =    6.2496691    

 mode : HKRF


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



     CGMAT cycle number =      1

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.892 id.= 3.000 dev= -2.11 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Weight matrix   0.27294940    
 Actual weight    6.2496691      is applied to the X-ray term
Norm of X_ray positional gradient                36.3
Norm of Geom. positional gradient                82.6
Norm of X_ray B-factor gradient                  95.4
Norm of Geom. B-factor gradient                  104.
Product of X_ray and Geom posit. gradients     -0.146E+08
 Cosine of angle between them                      -0.502
Product of X_ray and Geom B-fact gradients     -0.287E+08
 Cosine of angle between them                      -0.893


Residuals: XRAY=     0.9784E+06 GEOM=     0.1328E+05 TOTAL=     0.9917E+06
 function value    991655.56    

-------------------------------------------------------------------------------
             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     1.852     1.644
Bond angles  : others                          3238     2.366     1.580
Torsion angles, period  1. refined              185     6.750     5.000
Torsion angles, period  2. refined               90    34.675    22.778
Torsion angles, period  3. refined              268    13.297    15.000
Torsion angles, period  4. refined                9    12.403    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.016     0.020
VDW repulsions: refined_atoms                   303     0.245     0.200
VDW repulsions.others                          1338     0.220     0.200
VDW; torsion: refined_atoms                     729     0.174     0.200
VDW; torsion.others                             724     0.081     0.200
HBOND: refined_atoms                            208     0.200     0.200
HBOND.others                                      1     0.074     0.200
VDW repulsions: symmetry: refined_atoms           8     0.202     0.200
VDW repulsions: symmetry: others                 23     0.200     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     1.797     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             1843     7.714    22.073
Long range B values: others                    1757     7.443    20.682
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    0.1065
Partial structure    1: scale =     0.3923, B  =   38.4771
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    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4341 100.00   406.3   416.0  0.17  0.18     206   398.6   404.9  0.21  0.21
 0.167    7383  99.97   227.5   207.8  0.18  0.16     415   239.4   216.5  0.22  0.20
 0.278    9395 100.00   124.0   114.1  0.21  0.18     515   123.2   114.5  0.25  0.22
 0.389   11089 100.00    50.2    62.4  0.40  0.36     552    50.4    63.7  0.43  0.39
$$

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

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3228   0.902   1113   0.793   4341   0.874  0.946  0.9588  0.9675  0.9042  0.9361
  0.1670   6271   0.866   1112   0.765   7383   0.851  1.057  0.9453  0.9546  0.8887  0.9338
  0.2780   8277   0.832   1118   0.747   9395   0.822  1.019  0.9361  0.9464  0.8942  0.9315
  0.3890   9980   0.544   1120   0.475  11100   0.537  0.557  0.7595  0.7687  0.7420  0.7836
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32219
Percentage observed                  =    99.9912
Percentage of free reflections       =     4.9811
Overall R factor                     =     0.2067
Free R factor                        =     0.2442
Average Fourier shell correlation    =     0.8899
AverageFree Fourier shell correlation=     0.8833
Overall weighted R factor            =     0.1756
Free weighted R factor               =     0.2111
Overall weighted R2 factor           =     0.2049
Free weighted R2 factor              =     0.2472
Average correlation coefficient      =     0.8817
Overall correlation coefficient      =     0.9594
Free correlation coefficient         =     0.9386
Cruickshanks DPI for coordinate error=     0.0857
DPI based on free R factor           =     0.0889
Overall figure of merit              =     0.7374
ML based su of positional parameters =     0.0733
ML based su of thermal parameters    =     2.1373
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    156548.27       13280.711       991655.56      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.35173157    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    979309.50    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =   -0.0634
Partial structure    1: scale =     0.3918, B  =   38.4513
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                     =     0.2073
Free R factor                        =     0.2430
Average Fourier shell correlation    =     0.9062
AverageFree Fourier shell correlation=     0.9006
Average correlation coefficient      =     0.8801
Overall figure of merit              =     0.7701
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    155377.70       8250.2275       979309.50       991655.56    


     CGMAT cycle number =      3

 Weight matrix   0.36176932    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    978394.25    

-------------------------------------------------------------------------------
             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 =     0.0455, B  =   -0.0141
Partial structure    1: scale =     0.3917, B  =   38.3178
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                     =     0.2067
Free R factor                        =     0.2431
Average Fourier shell correlation    =     0.9101
AverageFree Fourier shell correlation=     0.9040
Average correlation coefficient      =     0.8814
Overall figure of merit              =     0.7774
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    155165.84       8659.0430       978394.25       979309.50    


     CGMAT cycle number =      4

 Weight matrix   0.36481842    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    978159.56    

-------------------------------------------------------------------------------
             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 =     0.0455, B  =   -0.0067
Partial structure    1: scale =     0.3922, B  =   38.3385
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                     =     0.2065
Free R factor                        =     0.2434
Average Fourier shell correlation    =     0.9112
AverageFree Fourier shell correlation=     0.9049
Average correlation coefficient      =     0.8820
Overall figure of merit              =     0.7798
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    155113.75       8749.9492       978159.56       978394.25    


     CGMAT cycle number =      5

 Weight matrix   0.36493674    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    978096.38    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0455, B  =   -0.0004
Partial structure    1: scale =     0.3922, B  =   38.3411
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                     =     0.2065
Free R factor                        =     0.2434
Average Fourier shell correlation    =     0.9115
AverageFree Fourier shell correlation=     0.9051
Average correlation coefficient      =     0.8822
Overall figure of merit              =     0.7803
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    155097.13       8790.6924       978096.38       978159.56    


     CGMAT cycle number =      6

 Weight matrix   0.36499825    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    978101.56    

-------------------------------------------------------------------------------
             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 =     0.0455, B  =   -0.0000
Partial structure    1: scale =     0.3922, B  =   38.3103
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                     =     0.2065
Free R factor                        =     0.2435
Average Fourier shell correlation    =     0.9115
AverageFree Fourier shell correlation=     0.9051
Average correlation coefficient      =     0.8824
Overall figure of merit              =     0.7804
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    155095.97       8803.6650       978109.38       978096.38    

 fvalues    155095.97       8803.6650       978098.69       978102.19    
 fvalues    155095.97       8803.6650       978098.69       978102.19    


     CGMAT cycle number =      7

 Weight matrix   0.36493209    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    978100.94    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0455, B  =   -0.0000
Partial structure    1: scale =     0.3922, B  =   38.2976
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                     =     0.2065
Free R factor                        =     0.2435
Average Fourier shell correlation    =     0.9115
AverageFree Fourier shell correlation=     0.9050
Average correlation coefficient      =     0.8824
Overall figure of merit              =     0.7803
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    155095.77       8803.7520       978100.94       978102.19    


     CGMAT cycle number =      8

 Weight matrix   0.36460057    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    978152.50    

-------------------------------------------------------------------------------
             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 =     0.0455, B  =   -0.0012
Partial structure    1: scale =     0.3922, B  =   38.3065
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                     =     0.2065
Free R factor                        =     0.2435
Average Fourier shell correlation    =     0.9115
AverageFree Fourier shell correlation=     0.9050
Average correlation coefficient      =     0.8823
Overall figure of merit              =     0.7803
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    155105.05       8800.6426       978156.44       978100.94    

 fvalues    155105.05       8800.6426       978154.94       978155.81    
 fvalues    155105.05       8800.6426       978154.94       978155.81    


     CGMAT cycle number =      9

 Weight matrix   0.36448526    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    978154.94    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0455, B  =   -0.0000
Partial structure    1: scale =     0.3922, B  =   38.3064
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                     =     0.2065
Free R factor                        =     0.2435
Average Fourier shell correlation    =     0.9115
AverageFree Fourier shell correlation=     0.9050
Average correlation coefficient      =     0.8823
Overall figure of merit              =     0.7803
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    155105.11       8799.3037       978154.94       978155.81    


     CGMAT cycle number =     10

    ****                              VDW outliers                              ****

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

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

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Weight matrix   0.36448357    
 Actual weight    6.2496691      is applied to the X-ray term
Norm of X_ray positional gradient                43.8
Norm of Geom. positional gradient                43.8
Norm of X_ray B-factor gradient                  109.
Norm of Geom. B-factor gradient                  109.
Product of X_ray and Geom posit. gradients     -0.186E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.384E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.9694E+06 GEOM=      8798.     TOTAL=     0.9782E+06
 function value    978158.75    

-------------------------------------------------------------------------------
             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     1.856     1.644
Bond angles  : others                          3238     1.516     1.580
Torsion angles, period  1. refined              185     6.757     5.000
Torsion angles, period  2. refined               90    34.689    22.778
Torsion angles, period  3. refined              268    13.312    15.000
Torsion angles, period  4. refined                9    12.421    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                   303     0.245     0.200
VDW repulsions.others                          1374     0.193     0.200
VDW; torsion: refined_atoms                     729     0.174     0.200
VDW; torsion.others                             774     0.085     0.200
HBOND: refined_atoms                            207     0.200     0.200
HBOND.others                                      1     0.022     0.200
VDW repulsions: symmetry: refined_atoms           8     0.203     0.200
VDW repulsions: symmetry: others                 24     0.184     0.200
HBOND: symmetry: refined_atoms                   22     0.165     0.200
M. chain bond B values: refined atoms           746     1.816     1.618
M. chain bond B values: others                  746     1.811     1.618
M. chain angle B values: refined atoms          929     2.802     2.418
M. chain angle B values: others                 930     2.801     2.418
S. chain bond B values: refined atoms           811     3.246     2.034
S. chain bond B values: others                  810     3.241     2.033
S. chain angle B values: refined atoms         1177     4.942     2.879
S. chain angle B values: others                1178     4.939     2.878
Long range B values: refined atoms             1842     7.858    22.210
Long range B values: others                    1757     7.596    20.834
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0455, B  =   -0.0002
Partial structure    1: scale =     0.3921, B  =   38.3018
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10.  v. resln :N:1,6,7,11,12:
:Cycle   10.  and  v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4341 100.00   407.0   416.5  0.17  0.18     206   399.3   405.5  0.21  0.21
 0.167    7383  99.97   227.9   208.1  0.18  0.16     415   239.8   216.7  0.22  0.20
 0.278    9395 100.00   124.2   114.4  0.21  0.18     515   123.4   114.7  0.25  0.22
 0.389   11089 100.00    50.3    62.4  0.40  0.35     552    50.5    63.8  0.43  0.39
$$

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

 $TABLE: Cycle   10. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3228   0.919   1113   0.818   4341   0.893  0.948  0.9634  0.9715  0.9047  0.9363
  0.1670   6271   0.877   1112   0.776   7383   0.862  1.057  0.9477  0.9569  0.8892  0.9333
  0.2780   8277   0.851   1118   0.768   9395   0.842  1.023  0.9427  0.9529  0.8951  0.9320
  0.3890   9980   0.637   1120   0.571  11100   0.630  0.604  0.8160  0.8228  0.7417  0.7852
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32219
Percentage observed                  =    99.9912
Percentage of free reflections       =     4.9811
Overall R factor                     =     0.2065
Free R factor                        =     0.2435
Average Fourier shell correlation    =     0.9115
AverageFree Fourier shell correlation=     0.9050
Overall weighted R factor            =     0.1756
Free weighted R factor               =     0.2104
Overall weighted R2 factor           =     0.2049
Free weighted R2 factor              =     0.2461
Average correlation coefficient      =     0.8823
Overall correlation coefficient      =     0.9594
Free correlation coefficient         =     0.9389
Cruickshanks DPI for coordinate error=     0.0856
DPI based on free R factor           =     0.0887
Overall figure of merit              =     0.7803
ML based su of positional parameters =     0.0634
ML based su of thermal parameters    =     1.8162
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    155106.14       8798.3799       978162.50       978154.94    

 fvalues    155106.14       8798.3799       978158.19       978160.44    
 fvalues    155106.14       8798.3799       978158.19       978160.44    

    ****                              VDW outliers                              ****

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

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

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

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_step0-01A_R00_1-50A.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     1.857     1.644
Bond angles  : others                          3238     1.516     1.580
Torsion angles, period  1. refined              185     6.757     5.000
Torsion angles, period  2. refined               90    34.688    22.778
Torsion angles, period  3. refined              268    13.313    15.000
Torsion angles, period  4. refined                9    12.419    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                   303     0.245     0.200
VDW repulsions.others                          1369     0.193     0.200
VDW; torsion: refined_atoms                     729     0.174     0.200
VDW; torsion.others                             777     0.085     0.200
HBOND: refined_atoms                            207     0.200     0.200
HBOND.others                                      1     0.022     0.200
VDW repulsions: symmetry: refined_atoms           8     0.203     0.200
VDW repulsions: symmetry: others                 24     0.184     0.200
HBOND: symmetry: refined_atoms                   22     0.165     0.200
M. chain bond B values: refined atoms           746     1.816     1.618
M. chain bond B values: others                  746     1.811     1.618
M. chain angle B values: refined atoms          929     2.802     2.418
M. chain angle B values: others                 930     2.801     2.418
S. chain bond B values: refined atoms           811     3.246     2.034
S. chain bond B values: others                  810     3.241     2.033
S. chain angle B values: refined atoms         1177     4.942     2.879
S. chain angle B values: others                1178     4.939     2.878
Long range B values: refined atoms             1842     7.858    22.210
Long range B values: others                    1757     7.596    20.834
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0455, B  =   -0.0000
Partial structure    1: scale =     0.3921, B  =   38.3005
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4341 100.00   407.0   416.5  0.17  0.18     206   399.3   405.5  0.21  0.21
 0.167    7383  99.97   227.9   208.1  0.18  0.16     415   239.8   216.7  0.22  0.20
 0.278    9395 100.00   124.2   114.4  0.21  0.18     515   123.4   114.7  0.25  0.22
 0.389   11089 100.00    50.3    62.4  0.40  0.35     552    50.5    63.8  0.43  0.39
$$

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

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3228   0.919   1113   0.818   4341   0.893  0.948  0.9634  0.9716  0.9047  0.9363
  0.1670   6271   0.877   1112   0.776   7383   0.862  1.057  0.9477  0.9569  0.8892  0.9333
  0.2780   8277   0.852   1118   0.768   9395   0.842  1.023  0.9427  0.9529  0.8951  0.9320
  0.3890   9980   0.637   1120   0.571  11100   0.630  0.604  0.8160  0.8228  0.7417  0.7852
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32219
Percentage observed                  =    99.9912
Percentage of free reflections       =     4.9811
Overall R factor                     =     0.2065
Free R factor                        =     0.2435
Average Fourier shell correlation    =     0.9115
AverageFree Fourier shell correlation=     0.9050
Overall weighted R factor            =     0.1756
Free weighted R factor               =     0.2104
Overall weighted R2 factor           =     0.2049
Free weighted R2 factor              =     0.2462
Average correlation coefficient      =     0.8823
Overall correlation coefficient      =     0.9594
Free correlation coefficient         =     0.9389
Cruickshanks DPI for coordinate error=     0.0856
DPI based on free R factor           =     0.0887
Overall figure of merit              =     0.7803
ML based su of positional parameters =     0.0634
ML based su of thermal parameters    =     1.8162
-----------------------------------------------------------------------------
  Time in seconds: CPU =        26.07
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2067   0.2442   0.737      156548.    8399.1   0.0132  0.989   1.852  1.077   0.090
       1   0.2073   0.2430   0.770      155378.    8361.8   0.0119  0.896   1.781  1.035   0.087
       2   0.2067   0.2431   0.777      155166.    8356.3   0.0130  0.979   1.825  1.062   0.090
       3   0.2065   0.2434   0.780      155114.    8354.9   0.0131  0.987   1.841  1.072   0.091
       4   0.2065   0.2434   0.780      155097.    8354.7   0.0132  0.992   1.849  1.076   0.091
       5   0.2065   0.2435   0.780      155096.    8355.1   0.0132  0.993   1.853  1.079   0.091
       6   0.2065   0.2435   0.780      155096.    8355.1   0.0132  0.993   1.855  1.079   0.091
       7   0.2065   0.2435   0.780      155105.    8355.8   0.0132  0.993   1.856  1.080   0.091
       8   0.2065   0.2435   0.780      155105.    8355.8   0.0132  0.993   1.856  1.080   0.091
       9   0.2065   0.2435   0.780      155106.    8355.9   0.0132  0.993   1.856  1.080   0.091
      10   0.2065   0.2435   0.780      155106.    8355.9   0.0132  0.993   1.857  1.080   0.091
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2067   0.2065
             R free    0.2442   0.2435
     Rms BondLength    0.0132   0.0132
      Rms BondAngle    1.8522   1.8565
     Rms ChirVolume    0.0903   0.0911
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      57.8s System:    0.2s Elapsed:     0:58