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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
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 User: maly  Run date: 27/ 5/2020 Run time: 00:09:54 


 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 1.54     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_1-55A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-54A.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_1-54A.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       0.1054
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.5400
  Estimated number of reflections :      40432
  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  1.5400

  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_1-55A.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=   2.192 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=   1.827 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=   2.217 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=   2.405 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=   2.389 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=   2.119 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       1574
Number of   all  reflections      31395
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          31395

   Current auto weighting coefficient =    6.3496833    

 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        :   128  128  280
 Maximuum H,K,L                 :    38   38   80
 Minimum acceptable grid spacing:    85   85  180
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  280
 Maximuum H,K,L                 :    38   38   80
 Minimum acceptable grid spacing:    85   85  180
 Weight matrix   0.27985665    
 Actual weight    6.3496833      is applied to the X-ray term
Norm of X_ray positional gradient                36.6
Norm of Geom. positional gradient                82.7
Norm of X_ray B-factor gradient                  99.5
Norm of Geom. B-factor gradient                  109.
Product of X_ray and Geom posit. gradients     -0.145E+08
 Cosine of angle between them                      -0.495
Product of X_ray and Geom B-fact gradients     -0.306E+08
 Cosine of angle between them                      -0.875


Residuals: XRAY=     0.9351E+06 GEOM=     0.1345E+05 TOTAL=     0.9486E+06
 function value    948589.69    

-------------------------------------------------------------------------------
             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     1.865     1.644
Bond angles  : others                          3238     2.368     1.580
Torsion angles, period  1. refined              185     6.749     5.000
Torsion angles, period  2. refined               90    34.694    22.778
Torsion angles, period  3. refined              268    13.292    15.000
Torsion angles, period  4. refined                9    12.499    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                   306     0.245     0.200
VDW repulsions.others                          1339     0.220     0.200
VDW; torsion: refined_atoms                     730     0.174     0.200
VDW; torsion.others                             731     0.081     0.200
HBOND: refined_atoms                            213     0.200     0.200
HBOND.others                                      1     0.053     0.200
VDW repulsions: symmetry: refined_atoms           8     0.204     0.200
VDW repulsions: symmetry: others                 22     0.207     0.200
HBOND: symmetry: refined_atoms                   22     0.177     0.200
M. chain bond B values: refined atoms           746     1.778     1.562
M. chain bond B values: others                  746     1.773     1.562
M. chain angle B values: refined atoms          929     2.757     2.333
M. chain angle B values: others                 930     2.757     2.333
S. chain bond B values: refined atoms           811     3.214     1.971
S. chain bond B values: others                  810     3.209     1.970
S. chain angle B values: refined atoms         1177     4.877     2.787
S. chain angle B values: others                1178     4.874     2.787
Long range B values: refined atoms             1851     7.728    21.594
Long range B values: others                    1763     7.434    20.185
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0451, B  =    0.1246
Partial structure    1: scale =     0.3878, B  =   40.5523
Overall anisotropic scale factors
   B11 =  -0.19 B22 =  -0.19 B33 =   0.38 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.053    4022 100.00   418.6   428.2  0.17  0.17     190   413.5   419.8  0.21  0.21
 0.158    6845  99.97   239.4   221.4  0.18  0.16     386   250.4   229.0  0.22  0.20
 0.264    8702 100.00   141.0   128.4  0.20  0.18     471   140.6   129.0  0.24  0.21
 0.369   10241 100.00    57.1    70.4  0.37  0.31     526    57.2    71.3  0.41  0.35
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0532   2972   0.906   1050   0.797   4022   0.877  0.947  0.9593  0.9683  0.9012  0.9364
  0.1585   5785   0.867   1060   0.772   6845   0.852  1.040  0.9452  0.9544  0.8874  0.9338
  0.2637   7643   0.846   1059   0.748   8702   0.834  1.038  0.9401  0.9506  0.8934  0.9349
  0.3690   9185   0.586   1065   0.511  10250   0.578  0.614  0.8039  0.8156  0.7633  0.8255
 $$
Resolution limits                    =     41.964     1.540
Number of used reflections           =      29819
Percentage observed                  =    99.9904
Percentage of free reflections       =     5.0139
Overall R factor                     =     0.2012
Free R factor                        =     0.2408
Average Fourier shell correlation    =     0.9074
AverageFree Fourier shell correlation=     0.8981
Overall weighted R factor            =     0.1727
Free weighted R factor               =     0.2102
Overall weighted R2 factor           =     0.2028
Free weighted R2 factor              =     0.2468
Average correlation coefficient      =     0.8973
Overall correlation coefficient      =     0.9589
Free correlation coefficient         =     0.9369
Cruickshanks DPI for coordinate error=     0.0901
DPI based on free R factor           =     0.0936
Overall figure of merit              =     0.7560
ML based su of positional parameters =     0.0730
ML based su of thermal parameters    =     2.1503
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    147273.56       13449.195       948589.69      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.36508566    
 Actual weight    6.3496833      is applied to the X-ray term


 function value    935483.63    

-------------------------------------------------------------------------------
             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 =     0.0450, B  =   -0.0656
Partial structure    1: scale =     0.3876, B  =   40.4280
Overall anisotropic scale factors
   B11 =  -0.19 B22 =  -0.19 B33 =   0.38 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2016
Free R factor                        =     0.2399
Average Fourier shell correlation    =     0.9240
AverageFree Fourier shell correlation=     0.9158
Average correlation coefficient      =     0.8956
Overall figure of merit              =     0.7967
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    146010.16       8365.3828       935483.63       948589.69    


     CGMAT cycle number =      3

 Weight matrix   0.37754229    
 Actual weight    6.3496833      is applied to the X-ray term


 function value    934243.75    

-------------------------------------------------------------------------------
             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 =     0.0450, B  =   -0.0093
Partial structure    1: scale =     0.3878, B  =   40.5630
Overall anisotropic scale factors
   B11 =  -0.19 B22 =  -0.19 B33 =   0.38 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2010
Free R factor                        =     0.2400
Average Fourier shell correlation    =     0.9279
AverageFree Fourier shell correlation=     0.9192
Average correlation coefficient      =     0.8968
Overall figure of merit              =     0.8070
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    145750.45       8774.5869       934243.75       935483.63    


     CGMAT cycle number =      4

 Weight matrix   0.38128632    
 Actual weight    6.3496833      is applied to the X-ray term


 function value    933884.81    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0450, B  =   -0.0003
Partial structure    1: scale =     0.3881, B  =   40.5554
Overall anisotropic scale factors
   B11 =  -0.19 B22 =  -0.19 B33 =   0.38 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2009
Free R factor                        =     0.2401
Average Fourier shell correlation    =     0.9292
AverageFree Fourier shell correlation=     0.9201
Average correlation coefficient      =     0.8973
Overall figure of merit              =     0.8108
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    145678.95       8869.6230       933884.81       934243.75    


     CGMAT cycle number =      5

 Weight matrix   0.38205478    
 Actual weight    6.3496833      is applied to the X-ray term


 function value    933752.50    

-------------------------------------------------------------------------------
             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 =     0.0450, B  =    0.0026
Partial structure    1: scale =     0.3882, B  =   40.5569
Overall anisotropic scale factors
   B11 =  -0.19 B22 =  -0.19 B33 =   0.38 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2009
Free R factor                        =     0.2402
Average Fourier shell correlation    =     0.9295
AverageFree Fourier shell correlation=     0.9204
Average correlation coefficient      =     0.8976
Overall figure of merit              =     0.8120
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    145651.73       8910.1191       933752.50       933884.81    


     CGMAT cycle number =      6

 Weight matrix   0.38187853    
 Actual weight    6.3496833      is applied to the X-ray term


 function value    933758.94    

-------------------------------------------------------------------------------
             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 =     0.0450, B  =    0.0089
Partial structure    1: scale =     0.3884, B  =   40.5038
Overall anisotropic scale factors
   B11 =  -0.19 B22 =  -0.19 B33 =   0.38 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2010
Free R factor                        =     0.2402
Average Fourier shell correlation    =     0.9296
AverageFree Fourier shell correlation=     0.9204
Average correlation coefficient      =     0.8977
Overall figure of merit              =     0.8120
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    145650.77       8924.8564       933761.00       933752.50    
 fvalues    145650.77       8924.8564       933761.00       933761.13    


     CGMAT cycle number =      7

 Weight matrix   0.38223207    
 Actual weight    6.3496833      is applied to the X-ray term


 function value    933747.50    

-------------------------------------------------------------------------------
             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 =     0.0450, B  =    0.0012
Partial structure    1: scale =     0.3884, B  =   40.5017
Overall anisotropic scale factors
   B11 =  -0.19 B22 =  -0.19 B33 =   0.38 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2010
Free R factor                        =     0.2403
Average Fourier shell correlation    =     0.9296
AverageFree Fourier shell correlation=     0.9203
Average correlation coefficient      =     0.8977
Overall figure of merit              =     0.8120
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    145648.53       8925.4375       933747.50       933761.13    


     CGMAT cycle number =      8

 Weight matrix   0.38120136    
 Actual weight    6.3496833      is applied to the X-ray term


 function value    933784.69    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0450, B  =    0.0124
Partial structure    1: scale =     0.3885, B  =   40.4855
Overall anisotropic scale factors
   B11 =  -0.19 B22 =  -0.19 B33 =   0.38 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2010
Free R factor                        =     0.2403
Average Fourier shell correlation    =     0.9295
AverageFree Fourier shell correlation=     0.9203
Average correlation coefficient      =     0.8976
Overall figure of merit              =     0.8118
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    145651.50       8928.1855       933762.50       933747.50    
 fvalues    145651.50       8928.1855       933762.50       933769.06    


     CGMAT cycle number =      9

 Weight matrix   0.38097125    
 Actual weight    6.3496833      is applied to the X-ray term


 function value    933783.44    

-------------------------------------------------------------------------------
             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 =     0.0450, B  =    0.0122
Partial structure    1: scale =     0.3885, B  =   40.4873
Overall anisotropic scale factors
   B11 =  -0.19 B22 =  -0.19 B33 =   0.38 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2010
Free R factor                        =     0.2402
Average Fourier shell correlation    =     0.9295
AverageFree Fourier shell correlation=     0.9203
Average correlation coefficient      =     0.8977
Overall figure of merit              =     0.8118
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    145655.25       8917.2422       933780.81       933769.06    
 fvalues    145655.25       8917.2422       933780.81       933781.94    


     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        :   128  128  280
 Maximuum H,K,L                 :    38   38   80
 Minimum acceptable grid spacing:    85   85  180
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  280
 Maximuum H,K,L                 :    38   38   80
 Minimum acceptable grid spacing:    85   85  180
 Weight matrix   0.38090271    
 Actual weight    6.3496833      is applied to the X-ray term
Norm of X_ray positional gradient                44.0
Norm of Geom. positional gradient                44.0
Norm of X_ray B-factor gradient                  114.
Norm of Geom. B-factor gradient                  113.
Product of X_ray and Geom posit. gradients     -0.187E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.416E+08
 Cosine of angle between them                      -0.999


Residuals: XRAY=     0.9249E+06 GEOM=      8918.     TOTAL=     0.9338E+06
 function value    933787.69    

-------------------------------------------------------------------------------
             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     1.869     1.644
Bond angles  : others                          3238     1.521     1.580
Torsion angles, period  1. refined              185     6.751     5.000
Torsion angles, period  2. refined               90    34.740    22.778
Torsion angles, period  3. refined              268    13.307    15.000
Torsion angles, period  4. refined                9    12.457    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                   304     0.245     0.200
VDW repulsions.others                          1372     0.192     0.200
VDW; torsion: refined_atoms                     731     0.174     0.200
VDW; torsion.others                             790     0.085     0.200
HBOND: refined_atoms                            211     0.201     0.200
HBOND.others                                      1     0.020     0.200
VDW repulsions: symmetry: refined_atoms           8     0.205     0.200
VDW repulsions: symmetry: others                 26     0.177     0.200
HBOND: symmetry: refined_atoms                   22     0.172     0.200
M. chain bond B values: refined atoms           746     1.786     1.573
M. chain bond B values: others                  746     1.782     1.573
M. chain angle B values: refined atoms          929     2.764     2.350
M. chain angle B values: others                 930     2.763     2.350
S. chain bond B values: refined atoms           811     3.219     1.982
S. chain bond B values: others                  810     3.215     1.981
S. chain angle B values: refined atoms         1177     4.887     2.803
S. chain angle B values: others                1178     4.885     2.803
Long range B values: refined atoms             1848     7.856    21.755
Long range B values: others                    1760     7.573    20.327
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0450, B  =    0.0104
Partial structure    1: scale =     0.3884, B  =   40.5317
Overall anisotropic scale factors
   B11 =  -0.19 B22 =  -0.19 B33 =   0.38 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.053    4022 100.00   419.1   428.6  0.17  0.17     190   414.0   420.2  0.21  0.21
 0.158    6845  99.97   239.7   221.6  0.18  0.16     386   250.7   229.1  0.22  0.20
 0.264    8702 100.00   141.1   128.8  0.20  0.17     471   140.8   129.1  0.24  0.21
 0.369   10241 100.00    57.2    70.5  0.37  0.31     526    57.3    71.4  0.41  0.35
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0532   2972   0.922   1050   0.820   4022   0.895  0.950  0.9634  0.9719  0.9017  0.9364
  0.1585   5785   0.875   1060   0.781   6845   0.861  1.040  0.9472  0.9563  0.8887  0.9338
  0.2637   7643   0.861   1059   0.765   8702   0.849  1.039  0.9453  0.9555  0.8939  0.9349
  0.3690   9185   0.723   1065   0.646  10250   0.715  0.681  0.8626  0.8728  0.7629  0.8267
 $$
Resolution limits                    =     41.964     1.540
Number of used reflections           =      29819
Percentage observed                  =    99.9904
Percentage of free reflections       =     5.0139
Overall R factor                     =     0.2010
Free R factor                        =     0.2402
Average Fourier shell correlation    =     0.9295
AverageFree Fourier shell correlation=     0.9202
Overall weighted R factor            =     0.1726
Free weighted R factor               =     0.2097
Overall weighted R2 factor           =     0.2028
Free weighted R2 factor              =     0.2458
Average correlation coefficient      =     0.8977
Overall correlation coefficient      =     0.9590
Free correlation coefficient         =     0.9372
Cruickshanks DPI for coordinate error=     0.0900
DPI based on free R factor           =     0.0934
Overall figure of merit              =     0.8118
ML based su of positional parameters =     0.0625
ML based su of thermal parameters    =     1.7972
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02

 fvalues    145653.47       8917.9980       933771.38       933781.94    

    ****                              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_1-54A.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     1.870     1.644
Bond angles  : others                          3238     1.521     1.580
Torsion angles, period  1. refined              185     6.750     5.000
Torsion angles, period  2. refined               90    34.740    22.778
Torsion angles, period  3. refined              268    13.310    15.000
Torsion angles, period  4. refined                9    12.451    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                   304     0.245     0.200
VDW repulsions.others                          1368     0.193     0.200
VDW; torsion: refined_atoms                     731     0.174     0.200
VDW; torsion.others                             797     0.085     0.200
HBOND: refined_atoms                            212     0.201     0.200
HBOND.others                                      1     0.021     0.200
VDW repulsions: symmetry: refined_atoms           8     0.205     0.200
VDW repulsions: symmetry: others                 26     0.177     0.200
HBOND: symmetry: refined_atoms                   22     0.173     0.200
M. chain bond B values: refined atoms           746     1.786     1.573
M. chain bond B values: others                  746     1.782     1.573
M. chain angle B values: refined atoms          929     2.764     2.350
M. chain angle B values: others                 930     2.763     2.349
S. chain bond B values: refined atoms           811     3.220     1.982
S. chain bond B values: others                  810     3.215     1.981
S. chain angle B values: refined atoms         1177     4.888     2.803
S. chain angle B values: others                1178     4.886     2.803
Long range B values: refined atoms             1849     7.861    21.757
Long range B values: others                    1760     7.577    20.327
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0450, B  =    0.0088
Partial structure    1: scale =     0.3884, B  =   40.5259
Overall anisotropic scale factors
   B11 =  -0.19 B22 =  -0.19 B33 =   0.38 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.053    4022 100.00   419.1   428.7  0.17  0.17     190   414.0   420.1  0.21  0.21
 0.158    6845  99.97   239.7   221.7  0.18  0.16     386   250.7   229.1  0.22  0.20
 0.264    8702 100.00   141.1   128.8  0.20  0.17     471   140.8   129.1  0.24  0.21
 0.369   10241 100.00    57.2    70.5  0.37  0.31     526    57.3    71.4  0.41  0.35
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0532   2972   0.922   1050   0.820   4022   0.895  0.950  0.9634  0.9720  0.9017  0.9364
  0.1585   5785   0.875   1060   0.781   6845   0.861  1.040  0.9472  0.9563  0.8887  0.9338
  0.2637   7643   0.861   1059   0.765   8702   0.849  1.039  0.9453  0.9555  0.8938  0.9348
  0.3690   9185   0.723   1065   0.647  10250   0.715  0.681  0.8626  0.8729  0.7629  0.8267
 $$
Resolution limits                    =     41.964     1.540
Number of used reflections           =      29819
Percentage observed                  =    99.9904
Percentage of free reflections       =     5.0139
Overall R factor                     =     0.2010
Free R factor                        =     0.2402
Average Fourier shell correlation    =     0.9295
AverageFree Fourier shell correlation=     0.9203
Overall weighted R factor            =     0.1725
Free weighted R factor               =     0.2096
Overall weighted R2 factor           =     0.2027
Free weighted R2 factor              =     0.2456
Average correlation coefficient      =     0.8977
Overall correlation coefficient      =     0.9590
Free correlation coefficient         =     0.9372
Cruickshanks DPI for coordinate error=     0.0900
DPI based on free R factor           =     0.0934
Overall figure of merit              =     0.8118
ML based su of positional parameters =     0.0625
ML based su of thermal parameters    =     1.7972
-----------------------------------------------------------------------------
  Time in seconds: CPU =        21.57
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2012   0.2408   0.756      147274.    7954.5   0.0132  0.994   1.865  1.084   0.091
       1   0.2016   0.2399   0.797      146010.    7911.8   0.0120  0.901   1.793  1.042   0.087
       2   0.2010   0.2400   0.807      145750.    7903.2   0.0131  0.982   1.835  1.068   0.090
       3   0.2009   0.2401   0.811      145679.    7900.8   0.0132  0.991   1.852  1.078   0.091
       4   0.2009   0.2402   0.812      145652.    7900.0   0.0132  0.995   1.860  1.082   0.091
       5   0.2010   0.2402   0.812      145650.    7900.1   0.0133  0.997   1.864  1.085   0.091
       6   0.2010   0.2403   0.812      145649.    7900.5   0.0133  0.997   1.866  1.086   0.091
       7   0.2010   0.2403   0.812      145654.    7900.8   0.0133  0.998   1.868  1.087   0.091
       8   0.2010   0.2402   0.812      145655.    7900.6   0.0133  0.997   1.869  1.087   0.091
       9   0.2010   0.2402   0.812      145656.    7900.8   0.0133  0.997   1.869  1.087   0.091
      10   0.2010   0.2402   0.812      145655.    7900.7   0.0133  0.997   1.870  1.088   0.091
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2012   0.2010
             R free    0.2408   0.2402
     Rms BondLength    0.0132   0.0133
      Rms BondAngle    1.8647   1.8696
     Rms ChirVolume    0.0910   0.0912
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      53.3s System:    0.2s Elapsed:     0:54