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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 26/ 5/2020 Run time: 13:59:57 


 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 1.88     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_1-89A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-88A.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_1-88A.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       0.0707
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.8800
  Estimated number of reflections :      22199
  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  1.8800

  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_1-89A.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=   2.007 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=   2.206 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=   1.872 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=   2.378 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=   2.434 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=   2.126 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        897
Number of   all  reflections      17532
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          17532

   Current auto weighting coefficient =    7.1996050    

 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.= 0.935 id.= 3.000 dev= -2.06 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        :   112  112  240
 Maximuum H,K,L                 :    31   31   66
 Minimum acceptable grid spacing:    73   73  155
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    31   31   66
 Minimum acceptable grid spacing:    73   73  155
 Weight matrix   0.22234966    
 Actual weight    7.1996050      is applied to the X-ray term
Norm of X_ray positional gradient                31.8
Norm of Geom. positional gradient                77.8
Norm of X_ray B-factor gradient                  107.
Norm of Geom. B-factor gradient                  108.
Product of X_ray and Geom posit. gradients     -0.927E+07
 Cosine of angle between them                      -0.387
Product of X_ray and Geom B-fact gradients     -0.348E+08
 Cosine of angle between them                      -0.933


Residuals: XRAY=     0.6507E+06 GEOM=     0.1273E+05 TOTAL=     0.6634E+06
 function value    663439.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.035     0.017
Bond angles  : refined atoms                   2106     1.721     1.644
Bond angles  : others                          3238     2.346     1.580
Torsion angles, period  1. refined              185     6.989     5.000
Torsion angles, period  2. refined               90    36.821    22.778
Torsion angles, period  3. refined              268    13.865    15.000
Torsion angles, period  4. refined                9    11.144    15.000
Chiral centres: refined atoms                   196     0.084     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.016     0.020
VDW repulsions: refined_atoms                   297     0.243     0.200
VDW repulsions.others                          1333     0.219     0.200
VDW; torsion: refined_atoms                     714     0.171     0.200
VDW; torsion.others                             713     0.079     0.200
HBOND: refined_atoms                            226     0.211     0.200
VDW repulsions: symmetry: refined_atoms           6     0.259     0.200
VDW repulsions: symmetry: others                 26     0.191     0.200
HBOND: symmetry: refined_atoms                   21     0.209     0.200
M. chain bond B values: refined atoms           746     1.551     1.225
M. chain bond B values: others                  746     1.550     1.225
M. chain angle B values: refined atoms          929     2.498     1.823
M. chain angle B values: others                 930     2.497     1.823
S. chain bond B values: refined atoms           812     2.502     1.558
S. chain bond B values: others                  811     2.499     1.558
S. chain angle B values: refined atoms         1177     3.925     2.193
S. chain angle B values: others                1178     3.923     2.192
Long range B values: refined atoms             1847     6.579    16.973
Long range B values: others                    1750     6.284    15.596
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =   -0.0314
Partial structure    1: scale =     0.3761, B  =   46.6696
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.036    2287 100.00   479.5   484.5  0.16  0.17     103   474.9   481.6  0.20  0.22
 0.106    3835 100.00   377.4   360.9  0.16  0.15     197   381.9   357.1  0.21  0.20
 0.177    4830  99.96   243.9   237.6  0.16  0.13     282   257.1   245.3  0.22  0.19
 0.248    5672 100.00   180.2   181.8  0.17  0.13     314   182.2   184.8  0.23  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0359   1583   0.911    704   0.807   2287   0.879  0.960  0.9607  0.9684  0.9105  0.9406
  0.1065   3126   0.882    709   0.775   3835   0.863  0.996  0.9473  0.9627  0.8815  0.9455
  0.1770   4120   0.868    710   0.766   4830   0.853  0.985  0.9450  0.9573  0.8850  0.9388
  0.2476   4972   0.852    709   0.738   5681   0.837  0.941  0.9366  0.9523  0.8639  0.9352
 $$
Resolution limits                    =     41.964     1.880
Number of used reflections           =      16633
Percentage observed                  =    99.9829
Percentage of free reflections       =     5.1169
Overall R factor                     =     0.1614
Free R factor                        =     0.2169
Average Fourier shell correlation    =     0.9584
AverageFree Fourier shell correlation=     0.9444
Overall weighted R factor            =     0.1504
Free weighted R factor               =     0.2005
Overall weighted R2 factor           =     0.1829
Free weighted R2 factor              =     0.2421
Average correlation coefficient      =     0.9394
Overall correlation coefficient      =     0.9555
Free correlation coefficient         =     0.9142
Cruickshanks DPI for coordinate error=     0.1373
DPI based on free R factor           =     0.1379
Overall figure of merit              =     0.8534
ML based su of positional parameters =     0.0872
ML based su of thermal parameters    =     2.8847
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    90381.813       12725.906       663439.25      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.23320614    
 Actual weight    7.1996050      is applied to the X-ray term


 function value    657264.44    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =   -0.0921
Partial structure    1: scale =     0.3763, B  =   46.6556
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1615
Free R factor                        =     0.2160
Average Fourier shell correlation    =     0.9598
AverageFree Fourier shell correlation=     0.9460
Average correlation coefficient      =     0.9397
Overall figure of merit              =     0.8584
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    90155.719       8178.8760       657264.44       663439.25    


     CGMAT cycle number =      3

 Weight matrix   0.23352672    
 Actual weight    7.1996050      is applied to the X-ray term


 function value    657154.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =   -0.0783
Partial structure    1: scale =     0.3764, B  =   46.6724
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1612
Free R factor                        =     0.2160
Average Fourier shell correlation    =     0.9599
AverageFree Fourier shell correlation=     0.9461
Average correlation coefficient      =     0.9399
Overall figure of merit              =     0.8586
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    90129.617       8256.6436       657154.25       657264.44    


     CGMAT cycle number =      4

 Weight matrix   0.23382470    
 Actual weight    7.1996050      is applied to the X-ray term


 function value    657067.88    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =   -0.0748
Partial structure    1: scale =     0.3767, B  =   46.3071
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1612
Free R factor                        =     0.2159
Average Fourier shell correlation    =     0.9599
AverageFree Fourier shell correlation=     0.9462
Average correlation coefficient      =     0.9400
Overall figure of merit              =     0.8587
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    90116.133       8267.3184       657067.88       657154.25    


     CGMAT cycle number =      5

 Weight matrix   0.23383744    
 Actual weight    7.1996050      is applied to the X-ray term


 function value    657026.44    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =   -0.0756
Partial structure    1: scale =     0.3767, B  =   46.3532
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1611
Free R factor                        =     0.2161
Average Fourier shell correlation    =     0.9599
AverageFree Fourier shell correlation=     0.9462
Average correlation coefficient      =     0.9400
Overall figure of merit              =     0.8587
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    90110.203       8268.5586       657026.44       657067.88    


     CGMAT cycle number =      6

 Weight matrix   0.23396431    
 Actual weight    7.1996050      is applied to the X-ray term


 function value    656998.63    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =   -0.0816
Partial structure    1: scale =     0.3766, B  =   46.3692
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1611
Free R factor                        =     0.2161
Average Fourier shell correlation    =     0.9599
AverageFree Fourier shell correlation=     0.9462
Average correlation coefficient      =     0.9400
Overall figure of merit              =     0.8587
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    90106.977       8263.9990       656998.63       657026.44    


     CGMAT cycle number =      7

 Weight matrix   0.23423159    
 Actual weight    7.1996050      is applied to the X-ray term


 function value    656957.06    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =   -0.0860
Partial structure    1: scale =     0.3762, B  =   46.5698
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1612
Free R factor                        =     0.2159
Average Fourier shell correlation    =     0.9600
AverageFree Fourier shell correlation=     0.9463
Average correlation coefficient      =     0.9400
Overall figure of merit              =     0.8588
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    90101.984       8258.3467       656957.06       656998.63    


     CGMAT cycle number =      8

 Weight matrix   0.23424509    
 Actual weight    7.1996050      is applied to the X-ray term


 function value    656952.31    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =   -0.0898
Partial structure    1: scale =     0.3760, B  =   46.4664
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1612
Free R factor                        =     0.2158
Average Fourier shell correlation    =     0.9600
AverageFree Fourier shell correlation=     0.9463
Average correlation coefficient      =     0.9400
Overall figure of merit              =     0.8589
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    90100.914       8261.2832       656952.31       656957.06    


     CGMAT cycle number =      9

 Weight matrix   0.23419045    
 Actual weight    7.1996050      is applied to the X-ray term


 function value    656953.50    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =   -0.0782
Partial structure    1: scale =     0.3760, B  =   46.4058
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1612
Free R factor                        =     0.2158
Average Fourier shell correlation    =     0.9600
AverageFree Fourier shell correlation=     0.9463
Average correlation coefficient      =     0.9400
Overall figure of merit              =     0.8589
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02

 fvalues    90101.422       8256.1289       656950.75       656952.31    


     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.= 0.959 id.= 3.000 dev= -2.04 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        :   112  112  240
 Maximuum H,K,L                 :    31   31   66
 Minimum acceptable grid spacing:    73   73  155
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    31   31   66
 Minimum acceptable grid spacing:    73   73  155
 Weight matrix   0.23388700    
 Actual weight    7.1996050      is applied to the X-ray term
Norm of X_ray positional gradient                32.3
Norm of Geom. positional gradient                32.3
Norm of X_ray B-factor gradient                  109.
Norm of Geom. B-factor gradient                  112.
Product of X_ray and Geom posit. gradients     -0.101E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.391E+08
 Cosine of angle between them                      -0.994


Residuals: XRAY=     0.6487E+06 GEOM=      8256.     TOTAL=     0.6570E+06
 function value    656980.56    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.734     1.644
Bond angles  : others                          3238     1.440     1.580
Torsion angles, period  1. refined              185     6.972     5.000
Torsion angles, period  2. refined               90    36.532    22.778
Torsion angles, period  3. refined              268    13.600    15.000
Torsion angles, period  4. refined                9    11.165    15.000
Chiral centres: refined atoms                   196     0.084     0.200
Planar groups: refined atoms                   1743     0.009     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   300     0.241     0.200
VDW repulsions.others                          1384     0.189     0.200
VDW; torsion: refined_atoms                     715     0.171     0.200
VDW; torsion.others                             795     0.082     0.200
HBOND: refined_atoms                            227     0.209     0.200
VDW repulsions: symmetry: refined_atoms           7     0.239     0.200
VDW repulsions: symmetry: others                 24     0.190     0.200
HBOND: symmetry: refined_atoms                   21     0.208     0.200
HBOND: symmetry: others                           1     0.004     0.200
M. chain bond B values: refined atoms           746     1.561     1.233
M. chain bond B values: others                  746     1.560     1.233
M. chain angle B values: refined atoms          929     2.508     1.835
M. chain angle B values: others                 930     2.507     1.834
S. chain bond B values: refined atoms           812     2.525     1.571
S. chain bond B values: others                  811     2.523     1.570
S. chain angle B values: refined atoms         1177     3.966     2.210
S. chain angle B values: others                1178     3.965     2.209
Long range B values: refined atoms             1854     6.611    17.049
Long range B values: others                    1759     6.333    15.703
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =   -0.0712
Partial structure    1: scale =     0.3760, B  =   46.3891
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.036    2287 100.00   479.8   484.8  0.16  0.17     103   475.2   483.2  0.20  0.22
 0.106    3835 100.00   377.6   360.6  0.16  0.15     197   382.1   357.1  0.21  0.20
 0.177    4830  99.96   244.0   237.4  0.16  0.13     282   257.2   244.5  0.22  0.19
 0.248    5672 100.00   180.3   181.9  0.17  0.13     314   182.3   184.9  0.23  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0359   1583   0.923    704   0.818   2287   0.890  0.960  0.9634  0.9709  0.9104  0.9407
  0.1065   3126   0.885    709   0.779   3835   0.865  0.996  0.9488  0.9634  0.8838  0.9449
  0.1770   4120   0.869    710   0.767   4830   0.854  0.985  0.9456  0.9578  0.8861  0.9389
  0.2476   4972   0.860    709   0.746   5681   0.846  0.941  0.9397  0.9550  0.8677  0.9373
 $$
Resolution limits                    =     41.964     1.880
Number of used reflections           =      16633
Percentage observed                  =    99.9829
Percentage of free reflections       =     5.1169
Overall R factor                     =     0.1612
Free R factor                        =     0.2157
Average Fourier shell correlation    =     0.9599
AverageFree Fourier shell correlation=     0.9463
Overall weighted R factor            =     0.1504
Free weighted R factor               =     0.1992
Overall weighted R2 factor           =     0.1833
Free weighted R2 factor              =     0.2402
Average correlation coefficient      =     0.9400
Overall correlation coefficient      =     0.9554
Free correlation coefficient         =     0.9153
Cruickshanks DPI for coordinate error=     0.1371
DPI based on free R factor           =     0.1371
Overall figure of merit              =     0.8588
ML based su of positional parameters =     0.0850
ML based su of thermal parameters    =     2.8077
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    90103.055       8255.8525       656945.56       656950.75    
 fvalues    90103.055       8255.8525       656945.56       656962.25    

    ****                              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.= 0.959 id.= 3.000 dev= -2.04 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_1-88A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.734     1.644
Bond angles  : others                          3238     1.440     1.580
Torsion angles, period  1. refined              185     6.972     5.000
Torsion angles, period  2. refined               90    36.498    22.778
Torsion angles, period  3. refined              268    13.577    15.000
Torsion angles, period  4. refined                9    11.159    15.000
Chiral centres: refined atoms                   196     0.084     0.200
Planar groups: refined atoms                   1743     0.009     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   300     0.241     0.200
VDW repulsions.others                          1380     0.189     0.200
VDW; torsion: refined_atoms                     715     0.171     0.200
VDW; torsion.others                             796     0.082     0.200
HBOND: refined_atoms                            227     0.209     0.200
VDW repulsions: symmetry: refined_atoms           7     0.240     0.200
VDW repulsions: symmetry: others                 24     0.190     0.200
HBOND: symmetry: refined_atoms                   21     0.208     0.200
HBOND: symmetry: others                           1     0.004     0.200
M. chain bond B values: refined atoms           746     1.561     1.233
M. chain bond B values: others                  746     1.560     1.233
M. chain angle B values: refined atoms          929     2.508     1.835
M. chain angle B values: others                 930     2.507     1.834
S. chain bond B values: refined atoms           812     2.524     1.571
S. chain bond B values: others                  811     2.522     1.570
S. chain angle B values: refined atoms         1177     3.965     2.210
S. chain angle B values: others                1178     3.963     2.209
Long range B values: refined atoms             1854     6.609    17.036
Long range B values: others                    1760     6.336    15.716
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =   -0.0771
Partial structure    1: scale =     0.3762, B  =   46.4633
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.036    2287 100.00   479.7   484.8  0.16  0.17     103   475.1   483.3  0.20  0.22
 0.106    3835 100.00   377.5   360.6  0.16  0.15     197   382.0   357.1  0.21  0.20
 0.177    4830  99.96   244.0   237.5  0.16  0.13     282   257.2   244.6  0.22  0.19
 0.248    5672 100.00   180.3   182.0  0.17  0.13     314   182.3   185.0  0.23  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0359   1583   0.923    704   0.819   2287   0.891  0.960  0.9635  0.9709  0.9105  0.9406
  0.1065   3126   0.885    709   0.779   3835   0.865  0.996  0.9488  0.9634  0.8838  0.9448
  0.1770   4120   0.869    710   0.767   4830   0.854  0.985  0.9457  0.9578  0.8862  0.9389
  0.2476   4972   0.860    709   0.747   5681   0.846  0.941  0.9397  0.9551  0.8678  0.9373
 $$
Resolution limits                    =     41.964     1.880
Number of used reflections           =      16633
Percentage observed                  =    99.9829
Percentage of free reflections       =     5.1169
Overall R factor                     =     0.1612
Free R factor                        =     0.2156
Average Fourier shell correlation    =     0.9600
AverageFree Fourier shell correlation=     0.9463
Overall weighted R factor            =     0.1504
Free weighted R factor               =     0.1991
Overall weighted R2 factor           =     0.1833
Free weighted R2 factor              =     0.2401
Average correlation coefficient      =     0.9400
Overall correlation coefficient      =     0.9554
Free correlation coefficient         =     0.9153
Cruickshanks DPI for coordinate error=     0.1371
DPI based on free R factor           =     0.1371
Overall figure of merit              =     0.8589
ML based su of positional parameters =     0.0850
ML based su of thermal parameters    =     2.8077
-----------------------------------------------------------------------------
  Time in seconds: CPU =        14.13
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1614   0.2169   0.853       90382.    5046.2   0.0112  0.835   1.721  1.001   0.084
       1   0.1615   0.2160   0.858       90156.    5042.0   0.0110  0.817   1.702  0.990   0.084
       2   0.1612   0.2160   0.859       90130.    5041.6   0.0113  0.841   1.719  1.000   0.084
       3   0.1612   0.2159   0.859       90116.    5040.8   0.0114  0.843   1.724  1.002   0.084
       4   0.1611   0.2161   0.859       90110.    5040.7   0.0114  0.844   1.726  1.004   0.084
       5   0.1611   0.2161   0.859       90107.    5040.5   0.0114  0.845   1.728  1.004   0.084
       6   0.1612   0.2159   0.859       90102.    5040.2   0.0114  0.845   1.729  1.005   0.084
       7   0.1612   0.2158   0.859       90101.    5040.1   0.0114  0.846   1.731  1.006   0.084
       8   0.1612   0.2158   0.859       90102.    5040.1   0.0114  0.847   1.733  1.006   0.084
       9   0.1612   0.2157   0.859       90106.    5040.1   0.0114  0.847   1.734  1.007   0.084
      10   0.1612   0.2156   0.859       90099.    5039.8   0.0114  0.847   1.734  1.007   0.084
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1614   0.1612
             R free    0.2169   0.2156
     Rms BondLength    0.0112   0.0114
      Rms BondAngle    1.7205   1.7339
     Rms ChirVolume    0.0842   0.0839
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      46.2s System:    0.1s Elapsed:     0:47