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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: 14:43:42 


 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 1.90     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 10
  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_complete_R10_2-00A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R10_1-90A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R10_1-90A.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       0.0693
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.9000
  Estimated number of reflections :      21862
  Free R exclusion - flag equals:    10
  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  1.9000

  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_complete_R10_2-00A.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=   2.013 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=   2.245 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=   1.829 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=   2.206 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=   2.376 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=   2.461 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=   1.949 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:26-MAY-20
  --------------------------------
  ATTENTION: atom:OXT  THR               171  AAA  is missing in the structure
  ATTENTION: atom:OXT  PRO               190  AAA  is missing in the structure
  Number of chains                  :       4
  Total number of monomers          :     502
  Number of atoms                   :    3948
  Number of missing atoms           :       0
  Number of rebuilt atoms           :    1482
  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:      2950         0      2950
               Angles:      5345         0      5345
              Chirals:       196         0       196
               Planes:       451         0       451
             Torsions:      1553         0      1553
            Intervals:         0         0         0
--------------------------------------------------------------------------------


  Number of harmonic restraints       =            0
  Number of atoms in special position =            0
 -----------------------------------------------------


    ****                           Info from mtz file                           ****

FreeR flag                           10
Number of "free" reflections        863
Number of   all  reflections      16986
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          16986

   Current auto weighting coefficient =    7.2495699    

 mode : HKRF


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



     CGMAT cycle number =      1

    ****                         Bond distance outliers                         ****

Bond distance deviations from the ideal >10.000Sigma will be monitored

A    125 LEU C   . - A    126 ARG N   . mod.= 1.520 id.= 1.337 dev= -0.183 sig.= 0.011

    ****                Large deviation of atoms from planarity                 ****

Deviations from the planarity >10.000Sigma will be monitored
Atom: A     10 ARG C     deviation=  -0.21 sigma.=   0.02

    ****                              VDW outliers                              ****

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

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

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    31   31   65
 Minimum acceptable grid spacing:    73   73  154
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    31   31   65
 Minimum acceptable grid spacing:    73   73  154
 Weight matrix   0.25862175    
 Actual weight    7.2495699      is applied to the X-ray term
Norm of X_ray positional gradient                50.9
Norm of Geom. positional gradient                87.0
Norm of X_ray B-factor gradient                  163.
Norm of Geom. B-factor gradient                 0.208E+05
Product of X_ray and Geom posit. gradients     -0.667E+07
 Cosine of angle between them                      -0.156
Product of X_ray and Geom B-fact gradients     -0.397E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.6380E+06 GEOM=     0.2582E+05 TOTAL=     0.6638E+06
 function value    663821.81    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.833     1.644
Bond angles  : others                          3242     2.354     1.582
Torsion angles, period  1. refined              184     7.311     5.000
Torsion angles, period  2. refined               90    36.928    22.778
Torsion angles, period  3. refined              268    14.456    15.000
Torsion angles, period  4. refined                9    10.063    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.012     0.020
Planar groups: others                           331     0.017     0.020
VDW repulsions: refined_atoms                   323     0.258     0.200
VDW repulsions.others                          1338     0.233     0.200
VDW; torsion: refined_atoms                     705     0.170     0.200
VDW; torsion.others                             692     0.081     0.200
HBOND: refined_atoms                            237     0.217     0.200
HBOND.others                                      3     0.030     0.200
Metal-ion: refined_atoms                          1     0.011     0.200
VDW repulsions: symmetry: refined_atoms          10     0.235     0.200
VDW repulsions: symmetry: others                 29     0.176     0.200
HBOND: symmetry: refined_atoms                   16     0.258     0.200
HBOND: symmetry: others                           1     0.134     0.200
M. chain bond B values: refined atoms           745     1.509     1.172
M. chain bond B values: others                  745     1.508     1.172
M. chain angle B values: refined atoms          926     2.442     1.740
M. chain angle B values: others                 927     2.441     1.740
S. chain bond B values: refined atoms           811     2.374     1.489
S. chain bond B values: others                  810     2.370     1.488
S. chain angle B values: refined atoms         1177     3.734     2.095
S. chain angle B values: others                1178     3.733     2.095
Long range B values: refined atoms             1874     6.560    16.497
Long range B values: others                    1778     6.251    15.223
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =    0.3443
Partial structure    1: scale =     0.3742, B  =   48.2364
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2195 100.00   482.5   486.5  0.16  0.18     116   460.8   463.3  0.21  0.22
 0.104    3701 100.00   386.9   370.6  0.16  0.15     223   381.0   360.3  0.21  0.19
 0.173    4734  99.96   248.3   243.1  0.15  0.13     208   253.0   243.2  0.21  0.17
 0.242    5488 100.00   189.1   189.8  0.19  0.15     316   182.9   187.1  0.22  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1510   0.907    685   0.802   2195   0.875  0.960  0.9560  0.9675  0.8949  0.9385
  0.1042   3003   0.898    698   0.789   3701   0.877  1.002  0.9529  0.9659  0.8994  0.9460
  0.1733   4031   0.883    703   0.787   4734   0.869  0.985  0.9530  0.9640  0.9064  0.9460
  0.2425   4791   0.878    700   0.772   5491   0.865  0.955  0.9406  0.9527  0.8718  0.9159
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16121
Percentage observed                  =    99.9823
Percentage of free reflections       =     5.0813
Overall R factor                     =     0.1631
Free R factor                        =     0.2111
Average Fourier shell correlation    =     0.9611
AverageFree Fourier shell correlation=     0.9488
Overall weighted R factor            =     0.1511
Free weighted R factor               =     0.1964
Overall weighted R2 factor           =     0.1849
Free weighted R2 factor              =     0.2368
Average correlation coefficient      =     0.9347
Overall correlation coefficient      =     0.9537
Free correlation coefficient         =     0.9201
Cruickshanks DPI for coordinate error=     0.1442
DPI based on free R factor           =     0.1377
Overall figure of merit              =     0.8702
ML based su of positional parameters =     0.0812
ML based su of thermal parameters    =     2.6917
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    88004.789       25824.930       663821.81      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.28437248    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    644110.81    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.1170
Partial structure    1: scale =     0.3744, B  =   48.3654
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1606
Free R factor                        =     0.2076
Average Fourier shell correlation    =     0.9639
AverageFree Fourier shell correlation=     0.9517
Average correlation coefficient      =     0.9392
Overall figure of merit              =     0.8767
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    87356.953       10810.473       644110.81       663821.81    


     CGMAT cycle number =      3

 Weight matrix   0.28931898    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    641306.44    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.1145
Partial structure    1: scale =     0.3750, B  =   46.9121
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1593
Free R factor                        =     0.2059
Average Fourier shell correlation    =     0.9646
AverageFree Fourier shell correlation=     0.9524
Average correlation coefficient      =     0.9408
Overall figure of merit              =     0.8778
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    87128.391       9663.0498       641306.44       644110.81    


     CGMAT cycle number =      4

 Weight matrix   0.29090169    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    640303.94    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.0987
Partial structure    1: scale =     0.3748, B  =   47.1717
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1590
Free R factor                        =     0.2057
Average Fourier shell correlation    =     0.9648
AverageFree Fourier shell correlation=     0.9526
Average correlation coefficient      =     0.9413
Overall figure of merit              =     0.8781
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    87041.523       9290.2910       640303.94       641306.44    


     CGMAT cycle number =      5

 Weight matrix   0.29133955    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    639944.31    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.1017
Partial structure    1: scale =     0.3754, B  =   47.3790
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1588
Free R factor                        =     0.2059
Average Fourier shell correlation    =     0.9649
AverageFree Fourier shell correlation=     0.9526
Average correlation coefficient      =     0.9415
Overall figure of merit              =     0.8781
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    87000.852       9225.5410       639944.31       640303.94    


     CGMAT cycle number =      6

 Weight matrix   0.29151395    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    639777.88    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.1005
Partial structure    1: scale =     0.3757, B  =   47.2516
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1586
Free R factor                        =     0.2057
Average Fourier shell correlation    =     0.9649
AverageFree Fourier shell correlation=     0.9526
Average correlation coefficient      =     0.9417
Overall figure of merit              =     0.8781
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    86976.375       9236.5586       639777.88       639944.31    


     CGMAT cycle number =      7

 Weight matrix   0.29135919    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    639713.50    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.1049
Partial structure    1: scale =     0.3758, B  =   47.0795
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                     =     0.1585
Free R factor                        =     0.2058
Average Fourier shell correlation    =     0.9649
AverageFree Fourier shell correlation=     0.9525
Average correlation coefficient      =     0.9418
Overall figure of merit              =     0.8781
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    86966.930       9240.6904       639713.50       639777.88    


     CGMAT cycle number =      8

 Weight matrix   0.29096645    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    639680.94    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.1051
Partial structure    1: scale =     0.3757, B  =   47.1353
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                     =     0.1585
Free R factor                        =     0.2062
Average Fourier shell correlation    =     0.9649
AverageFree Fourier shell correlation=     0.9525
Average correlation coefficient      =     0.9419
Overall figure of merit              =     0.8779
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    86962.656       9239.0820       639680.94       639713.50    


     CGMAT cycle number =      9

 Weight matrix   0.29076442    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    639647.06    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.0970
Partial structure    1: scale =     0.3757, B  =   47.2562
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                     =     0.1585
Free R factor                        =     0.2064
Average Fourier shell correlation    =     0.9649
AverageFree Fourier shell correlation=     0.9524
Average correlation coefficient      =     0.9419
Overall figure of merit              =     0.8779
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    86958.766       9233.4180       639647.06       639680.94    


     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.= 0.923 id.= 3.000 dev= -2.08 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   65
 Minimum acceptable grid spacing:    73   73  154
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    31   31   65
 Minimum acceptable grid spacing:    73   73  154
 Weight matrix   0.29086715    
 Actual weight    7.2495699      is applied to the X-ray term
Norm of X_ray positional gradient                38.2
Norm of Geom. positional gradient                38.2
Norm of X_ray B-factor gradient                  125.
Norm of Geom. B-factor gradient                  130.
Product of X_ray and Geom posit. gradients     -0.141E+08
 Cosine of angle between them                      -0.998
Product of X_ray and Geom B-fact gradients     -0.518E+08
 Cosine of angle between them                      -0.985


Residuals: XRAY=     0.6303E+06 GEOM=      9232.     TOTAL=     0.6396E+06
 function value    639581.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.817     1.644
Bond angles  : others                          3242     1.455     1.582
Torsion angles, period  1. refined              184     6.913     5.000
Torsion angles, period  2. refined               90    36.900    22.778
Torsion angles, period  3. refined              268    13.973    15.000
Torsion angles, period  4. refined                9    10.205    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   315     0.264     0.200
VDW repulsions.others                          1357     0.207     0.200
VDW; torsion: refined_atoms                     711     0.171     0.200
VDW; torsion.others                             779     0.084     0.200
HBOND: refined_atoms                            240     0.205     0.200
HBOND.others                                      2     0.029     0.200
VDW repulsions: symmetry: refined_atoms          10     0.238     0.200
VDW repulsions: symmetry: others                 27     0.200     0.200
HBOND: symmetry: refined_atoms                   24     0.208     0.200
HBOND: symmetry: others                           1     0.123     0.200
M. chain bond B values: refined atoms           745     1.605     1.202
M. chain bond B values: others                  745     1.604     1.202
M. chain angle B values: refined atoms          926     2.534     1.784
M. chain angle B values: others                 927     2.532     1.783
S. chain bond B values: refined atoms           812     2.716     1.552
S. chain bond B values: others                  811     2.712     1.552
S. chain angle B values: refined atoms         1177     4.183     2.180
S. chain angle B values: others                1178     4.181     2.179
Long range B values: refined atoms             1874     6.874    17.133
Long range B values: others                    1775     6.575    15.737
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.0942
Partial structure    1: scale =     0.3758, B  =   47.3180
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2195 100.00   482.1   487.3  0.16  0.18     116   460.4   461.7  0.20  0.21
 0.104    3701 100.00   386.5   369.2  0.16  0.15     223   380.6   357.6  0.21  0.19
 0.173    4734  99.96   248.0   243.0  0.15  0.13     208   252.8   243.7  0.20  0.17
 0.242    5488 100.00   189.0   189.9  0.16  0.13     316   182.7   187.2  0.22  0.17
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1510   0.916    685   0.810   2195   0.883  0.960  0.9587  0.9689  0.8981  0.9375
  0.1042   3003   0.901    698   0.790   3701   0.880  1.002  0.9539  0.9663  0.9014  0.9442
  0.1733   4031   0.890    703   0.793   4734   0.876  0.985  0.9562  0.9653  0.9107  0.9439
  0.2425   4791   0.890    700   0.784   5491   0.877  0.959  0.9466  0.9621  0.8806  0.9404
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16121
Percentage observed                  =    99.9823
Percentage of free reflections       =     5.0813
Overall R factor                     =     0.1585
Free R factor                        =     0.2065
Average Fourier shell correlation    =     0.9649
AverageFree Fourier shell correlation=     0.9524
Overall weighted R factor            =     0.1498
Free weighted R factor               =     0.1922
Overall weighted R2 factor           =     0.1861
Free weighted R2 factor              =     0.2335
Average correlation coefficient      =     0.9419
Overall correlation coefficient      =     0.9548
Free correlation coefficient         =     0.9226
Cruickshanks DPI for coordinate error=     0.1401
DPI based on free R factor           =     0.1348
Overall figure of merit              =     0.8779
ML based su of positional parameters =     0.0765
ML based su of thermal parameters    =     2.5159
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    86949.852       9232.2500       639581.25       639647.06    

    ****                              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.= 0.925 id.= 3.000 dev= -2.08 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_complete_R10_1-90A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.818     1.644
Bond angles  : others                          3242     1.455     1.582
Torsion angles, period  1. refined              184     6.908     5.000
Torsion angles, period  2. refined               90    36.888    22.778
Torsion angles, period  3. refined              268    13.962    15.000
Torsion angles, period  4. refined                9    10.222    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   314     0.264     0.200
VDW repulsions.others                          1354     0.207     0.200
VDW; torsion: refined_atoms                     711     0.171     0.200
VDW; torsion.others                             781     0.084     0.200
HBOND: refined_atoms                            239     0.206     0.200
HBOND.others                                      2     0.033     0.200
VDW repulsions: symmetry: refined_atoms          10     0.238     0.200
VDW repulsions: symmetry: others                 27     0.200     0.200
HBOND: symmetry: refined_atoms                   24     0.208     0.200
HBOND: symmetry: others                           1     0.123     0.200
M. chain bond B values: refined atoms           745     1.607     1.202
M. chain bond B values: others                  745     1.606     1.202
M. chain angle B values: refined atoms          926     2.537     1.785
M. chain angle B values: others                 927     2.536     1.784
S. chain bond B values: refined atoms           812     2.717     1.553
S. chain bond B values: others                  811     2.714     1.553
S. chain angle B values: refined atoms         1177     4.183     2.181
S. chain angle B values: others                1178     4.181     2.180
Long range B values: refined atoms             1872     6.857    17.140
Long range B values: others                    1774     6.557    15.764
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.1019
Partial structure    1: scale =     0.3758, B  =   47.1852
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2195 100.00   482.0   487.2  0.16  0.18     116   460.4   461.9  0.20  0.22
 0.104    3701 100.00   386.5   369.2  0.16  0.15     223   380.6   357.7  0.21  0.19
 0.173    4734  99.96   248.0   243.0  0.15  0.13     208   252.8   243.6  0.20  0.17
 0.242    5488 100.00   189.0   189.9  0.16  0.13     316   182.7   187.2  0.22  0.17
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1510   0.916    685   0.810   2195   0.883  0.960  0.9587  0.9690  0.8978  0.9376
  0.1042   3003   0.901    698   0.790   3701   0.880  1.002  0.9539  0.9663  0.9013  0.9441
  0.1733   4031   0.890    703   0.793   4734   0.876  0.985  0.9562  0.9652  0.9106  0.9439
  0.2425   4791   0.890    700   0.784   5491   0.877  0.959  0.9467  0.9622  0.8806  0.9406
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16121
Percentage observed                  =    99.9823
Percentage of free reflections       =     5.0813
Overall R factor                     =     0.1584
Free R factor                        =     0.2066
Average Fourier shell correlation    =     0.9649
AverageFree Fourier shell correlation=     0.9524
Overall weighted R factor            =     0.1497
Free weighted R factor               =     0.1923
Overall weighted R2 factor           =     0.1861
Free weighted R2 factor              =     0.2337
Average correlation coefficient      =     0.9420
Overall correlation coefficient      =     0.9548
Free correlation coefficient         =     0.9225
Cruickshanks DPI for coordinate error=     0.1401
DPI based on free R factor           =     0.1348
Overall figure of merit              =     0.8779
ML based su of positional parameters =     0.0765
ML based su of thermal parameters    =     2.5159
-----------------------------------------------------------------------------
  Time in seconds: CPU =        12.40
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1631   0.2111   0.870       88005.    4832.7   0.0133  1.020   1.833  1.064   0.087
       1   0.1606   0.2076   0.877       87357.    4817.9   0.0121  0.883   1.775  1.027   0.088
       2   0.1593   0.2059   0.878       87128.    4812.0   0.0126  0.924   1.796  1.040   0.089
       3   0.1590   0.2057   0.878       87042.    4810.2   0.0126  0.927   1.805  1.046   0.089
       4   0.1588   0.2059   0.878       87001.    4810.4   0.0126  0.927   1.811  1.049   0.088
       5   0.1586   0.2057   0.878       86976.    4810.5   0.0125  0.926   1.814  1.051   0.088
       6   0.1585   0.2058   0.878       86967.    4811.0   0.0125  0.925   1.815  1.052   0.088
       7   0.1585   0.2062   0.878       86963.    4811.8   0.0125  0.923   1.816  1.053   0.088
       8   0.1585   0.2064   0.878       86959.    4812.1   0.0125  0.922   1.816  1.053   0.088
       9   0.1585   0.2065   0.878       86950.    4811.9   0.0125  0.922   1.817  1.054   0.087
      10   0.1584   0.2066   0.878       86944.    4812.0   0.0125  0.921   1.818  1.054   0.087
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1631   0.1584
             R free    0.2111   0.2066
     Rms BondLength    0.0133   0.0125
      Rms BondAngle    1.8333   1.8178
     Rms ChirVolume    0.0868   0.0874
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      44.4s System:    0.1s Elapsed:     0:45