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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: 14:36:25 


 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 7
  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_R07_2-00A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R07_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_R07_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:     7
  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_R07_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=   2.229 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=   1.859 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=   2.203 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=   2.446 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=   2.004 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                            7
Number of "free" reflections        845
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     10 ARG C   . - A     11 THR N   . mod.= 1.458 id.= 1.337 dev= -0.121 sig.= 0.011
A    125 LEU C   . - A    126 ARG N   . mod.= 1.560 id.= 1.337 dev= -0.223 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.= 0.927 id.= 3.000 dev= -2.07 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   0.23744687    
 Actual weight    7.2495699      is applied to the X-ray term
Norm of X_ray positional gradient                41.5
Norm of Geom. positional gradient                88.2
Norm of X_ray B-factor gradient                  138.
Norm of Geom. B-factor gradient                 0.225E+05
Product of X_ray and Geom posit. gradients     -0.731E+07
 Cosine of angle between them                      -0.206
Product of X_ray and Geom B-fact gradients     -0.375E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.6371E+06 GEOM=     0.2695E+05 TOTAL=     0.6640E+06
 function value    664023.94    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.014     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.838     1.644
Bond angles  : others                          3242     2.356     1.582
Torsion angles, period  1. refined              184     7.294     5.000
Torsion angles, period  2. refined               90    37.260    22.778
Torsion angles, period  3. refined              268    14.684    15.000
Torsion angles, period  4. refined                9    10.724    15.000
Chiral centres: refined atoms                   196     0.084     0.200
Planar groups: refined atoms                   1736     0.012     0.020
Planar groups: others                           331     0.015     0.020
VDW repulsions: refined_atoms                   316     0.257     0.200
VDW repulsions.others                          1335     0.230     0.200
VDW; torsion: refined_atoms                     708     0.171     0.200
VDW; torsion.others                             706     0.081     0.200
HBOND: refined_atoms                            236     0.210     0.200
HBOND.others                                      4     0.070     0.200
VDW repulsions: symmetry: refined_atoms           9     0.245     0.200
VDW repulsions: symmetry: others                 29     0.183     0.200
HBOND: symmetry: refined_atoms                   18     0.244     0.200
HBOND: symmetry: others                           1     0.109     0.200
M. chain bond B values: refined atoms           745     1.563     1.184
M. chain bond B values: others                  745     1.562     1.184
M. chain angle B values: refined atoms          926     2.548     1.756
M. chain angle B values: others                 927     2.547     1.756
S. chain bond B values: refined atoms           812     2.517     1.517
S. chain bond B values: others                  811     2.513     1.517
S. chain angle B values: refined atoms         1177     3.978     2.131
S. chain angle B values: others                1178     3.977     2.131
Long range B values: refined atoms             1871     6.967    16.606
Long range B values: others                    1772     6.619    15.233
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =    0.3864
Partial structure    1: scale =     0.3740, B  =   48.8922
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2198 100.00   481.0   486.7  0.16  0.17     113   448.2   457.5  0.20  0.21
 0.104    3738 100.00   387.1   370.1  0.15  0.14     186   341.9   336.8  0.21  0.20
 0.173    4687  99.96   247.2   241.5  0.16  0.13     255   251.5   253.1  0.22  0.18
 0.242    5513 100.00   187.7   189.1  0.19  0.15     291   193.6   191.2  0.22  0.17
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1530   0.930    668   0.834   2198   0.900  0.956  0.9666  0.9735  0.9211  0.9436
  0.1042   3038   0.908    700   0.808   3738   0.889  1.005  0.9504  0.9692  0.8958  0.9487
  0.1733   4001   0.875    686   0.773   4687   0.860  0.982  0.9487  0.9608  0.8794  0.9426
  0.2425   4802   0.859    714   0.744   5516   0.844  0.944  0.9392  0.9471  0.8858  0.9128
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16139
Percentage observed                  =    99.9823
Percentage of free reflections       =     4.9753
Overall R factor                     =     0.1621
Free R factor                        =     0.2130
Average Fourier shell correlation    =     0.9598
AverageFree Fourier shell correlation=     0.9482
Overall weighted R factor            =     0.1482
Free weighted R factor               =     0.1947
Overall weighted R2 factor           =     0.1789
Free weighted R2 factor              =     0.2294
Average correlation coefficient      =     0.9339
Overall correlation coefficient      =     0.9551
Free correlation coefficient         =     0.9197
Cruickshanks DPI for coordinate error=     0.1431
DPI based on free R factor           =     0.1389
Overall figure of merit              =     0.8669
ML based su of positional parameters =     0.0847
ML based su of thermal parameters    =     2.8881
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    87878.156       26945.109       664023.94      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.25366959    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    644795.69    

-------------------------------------------------------------------------------
             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 =     0.0403, B  =   -0.1229
Partial structure    1: scale =     0.3743, B  =   48.5772
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1599
Free R factor                        =     0.2103
Average Fourier shell correlation    =     0.9623
AverageFree Fourier shell correlation=     0.9509
Average correlation coefficient      =     0.9377
Overall figure of merit              =     0.8722
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    87470.242       10674.081       644795.69       664023.94    


     CGMAT cycle number =      3

 Weight matrix   0.25703895    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    642641.81    

-------------------------------------------------------------------------------
             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 =     0.0403, B  =   -0.0669
Partial structure    1: scale =     0.3743, B  =   46.7487
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                     =     0.1586
Free R factor                        =     0.2086
Average Fourier shell correlation    =     0.9630
AverageFree Fourier shell correlation=     0.9516
Average correlation coefficient      =     0.9392
Overall figure of merit              =     0.8731
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    87342.258       9447.9844       642641.81       644795.69    


     CGMAT cycle number =      4

 Weight matrix   0.25850919    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    641882.19    

-------------------------------------------------------------------------------
             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 =     0.0403, B  =   -0.0591
Partial structure    1: scale =     0.3748, B  =   47.1766
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                     =     0.1582
Free R factor                        =     0.2077
Average Fourier shell correlation    =     0.9633
AverageFree Fourier shell correlation=     0.9519
Average correlation coefficient      =     0.9398
Overall figure of merit              =     0.8736
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    87293.109       9044.6582       641882.19       642641.81    


     CGMAT cycle number =      5

 Weight matrix   0.25925806    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    641550.19    

-------------------------------------------------------------------------------
             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 =     0.0403, B  =   -0.0516
Partial structure    1: scale =     0.3749, B  =   47.2326
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                     =     0.1579
Free R factor                        =     0.2070
Average Fourier shell correlation    =     0.9634
AverageFree Fourier shell correlation=     0.9521
Average correlation coefficient      =     0.9401
Overall figure of merit              =     0.8738
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    87256.320       8979.3701       641550.19       641882.19    


     CGMAT cycle number =      6

 Weight matrix   0.25940648    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    641425.94    

-------------------------------------------------------------------------------
             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 =     0.0403, B  =   -0.0515
Partial structure    1: scale =     0.3753, B  =   47.3387
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                     =     0.1578
Free R factor                        =     0.2070
Average Fourier shell correlation    =     0.9635
AverageFree Fourier shell correlation=     0.9521
Average correlation coefficient      =     0.9404
Overall figure of merit              =     0.8739
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    87237.250       8993.4043       641425.94       641550.19    


     CGMAT cycle number =      7

 Weight matrix   0.25916958    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    641400.69    

-------------------------------------------------------------------------------
             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 =     0.0403, B  =   -0.0548
Partial structure    1: scale =     0.3755, B  =   47.4681
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                     =     0.1577
Free R factor                        =     0.2069
Average Fourier shell correlation    =     0.9635
AverageFree Fourier shell correlation=     0.9521
Average correlation coefficient      =     0.9405
Overall figure of merit              =     0.8739
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    87232.656       9001.4141       641400.69       641425.94    


     CGMAT cycle number =      8

 Weight matrix   0.25873896    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    641421.31    

-------------------------------------------------------------------------------
             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 =     0.0403, B  =   -0.0544
Partial structure    1: scale =     0.3751, B  =   47.3465
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                     =     0.1576
Free R factor                        =     0.2070
Average Fourier shell correlation    =     0.9635
AverageFree Fourier shell correlation=     0.9520
Average correlation coefficient      =     0.9406
Overall figure of merit              =     0.8737
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    87233.875       9011.5342       641381.69       641400.69    
 fvalues    87233.875       9011.5342       641381.69       641419.63    


     CGMAT cycle number =      9

 Weight matrix   0.25830692    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    641413.38    

-------------------------------------------------------------------------------
             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 =     0.0403, B  =   -0.0529
Partial structure    1: scale =     0.3751, B  =   47.4221
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                     =     0.1576
Free R factor                        =     0.2069
Average Fourier shell correlation    =     0.9635
AverageFree Fourier shell correlation=     0.9520
Average correlation coefficient      =     0.9407
Overall figure of merit              =     0.8736
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    87234.852       8998.2490       641413.38       641419.63    


     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.= 0.936 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   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   0.25804755    
 Actual weight    7.2495699      is applied to the X-ray term
Norm of X_ray positional gradient                35.2
Norm of Geom. positional gradient                35.2
Norm of X_ray B-factor gradient                  115.
Norm of Geom. B-factor gradient                  118.
Product of X_ray and Geom posit. gradients     -0.120E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.438E+08
 Cosine of angle between them                      -0.996


Residuals: XRAY=     0.6324E+06 GEOM=      8996.     TOTAL=     0.6414E+06
 function value    641363.06    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2103     1.792     1.644
Bond angles  : others                          3242     1.455     1.582
Torsion angles, period  1. refined              184     7.010     5.000
Torsion angles, period  2. refined               90    37.291    22.778
Torsion angles, period  3. refined              268    14.236    15.000
Torsion angles, period  4. refined                9    10.929    15.000
Chiral centres: refined atoms                   196     0.085     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   300     0.267     0.200
VDW repulsions.others                          1353     0.205     0.200
VDW; torsion: refined_atoms                     710     0.173     0.200
VDW; torsion.others                             785     0.083     0.200
HBOND: refined_atoms                            232     0.209     0.200
HBOND.others                                      2     0.081     0.200
Metal-ion: refined_atoms                          1     0.003     0.200
VDW repulsions: symmetry: refined_atoms          11     0.218     0.200
VDW repulsions: symmetry: others                 26     0.205     0.200
HBOND: symmetry: refined_atoms                   21     0.227     0.200
HBOND: symmetry: others                           1     0.089     0.200
M. chain bond B values: refined atoms           745     1.589     1.212
M. chain bond B values: others                  745     1.588     1.212
M. chain angle B values: refined atoms          926     2.564     1.799
M. chain angle B values: others                 927     2.562     1.799
S. chain bond B values: refined atoms           812     2.753     1.573
S. chain bond B values: others                  811     2.750     1.572
S. chain angle B values: refined atoms         1177     4.297     2.205
S. chain angle B values: others                1178     4.295     2.204
Long range B values: refined atoms             1850     7.058    17.078
Long range B values: others                    1751     6.718    15.609
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =   -0.0512
Partial structure    1: scale =     0.3750, B  =   47.4258
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.53 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2198 100.00   481.2   487.7  0.16  0.17     113   448.4   457.4  0.19  0.20
 0.104    3738 100.00   387.2   369.5  0.15  0.14     186   342.1   336.0  0.21  0.20
 0.173    4687  99.96   247.3   241.5  0.15  0.13     255   251.6   253.5  0.21  0.17
 0.242    5513 100.00   187.8   189.4  0.17  0.14     291   193.7   191.6  0.21  0.16
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1530   0.937    668   0.844   2198   0.909  0.955  0.9690  0.9751  0.9225  0.9436
  0.1042   3038   0.909    700   0.815   3738   0.892  1.005  0.9512  0.9698  0.8955  0.9480
  0.1733   4001   0.885    686   0.785   4687   0.870  0.982  0.9534  0.9637  0.8885  0.9434
  0.2425   4802   0.865    714   0.750   5516   0.850  0.944  0.9447  0.9544  0.8961  0.9325
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16139
Percentage observed                  =    99.9823
Percentage of free reflections       =     4.9753
Overall R factor                     =     0.1575
Free R factor                        =     0.2068
Average Fourier shell correlation    =     0.9635
AverageFree Fourier shell correlation=     0.9520
Overall weighted R factor            =     0.1464
Free weighted R factor               =     0.1896
Overall weighted R2 factor           =     0.1790
Free weighted R2 factor              =     0.2272
Average correlation coefficient      =     0.9408
Overall correlation coefficient      =     0.9567
Free correlation coefficient         =     0.9227
Cruickshanks DPI for coordinate error=     0.1391
DPI based on free R factor           =     0.1348
Overall figure of merit              =     0.8735
ML based su of positional parameters =     0.0812
ML based su of thermal parameters    =     2.7650
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    87228.219       8995.9834       641363.06       641413.38    

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.935 id.= 3.000 dev= -2.07 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_R07_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     1.791     1.644
Bond angles  : others                          3242     1.455     1.582
Torsion angles, period  1. refined              184     7.006     5.000
Torsion angles, period  2. refined               90    37.304    22.778
Torsion angles, period  3. refined              268    14.203    15.000
Torsion angles, period  4. refined                9    10.972    15.000
Chiral centres: refined atoms                   196     0.085     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   302     0.266     0.200
VDW repulsions.others                          1359     0.204     0.200
VDW; torsion: refined_atoms                     711     0.173     0.200
VDW; torsion.others                             786     0.083     0.200
HBOND: refined_atoms                            233     0.209     0.200
HBOND.others                                      2     0.082     0.200
Metal-ion: refined_atoms                          1     0.003     0.200
VDW repulsions: symmetry: refined_atoms          11     0.218     0.200
VDW repulsions: symmetry: others                 26     0.205     0.200
HBOND: symmetry: refined_atoms                   21     0.228     0.200
HBOND: symmetry: others                           1     0.088     0.200
M. chain bond B values: refined atoms           745     1.587     1.212
M. chain bond B values: others                  745     1.586     1.212
M. chain angle B values: refined atoms          926     2.560     1.800
M. chain angle B values: others                 927     2.559     1.799
S. chain bond B values: refined atoms           812     2.754     1.573
S. chain bond B values: others                  811     2.752     1.573
S. chain angle B values: refined atoms         1177     4.298     2.205
S. chain angle B values: others                1178     4.296     2.205
Long range B values: refined atoms             1854     7.106    17.138
Long range B values: others                    1754     6.760    15.654
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =   -0.0480
Partial structure    1: scale =     0.3748, B  =   47.3606
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.53 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2198 100.00   481.2   487.8  0.15  0.17     113   448.4   457.5  0.19  0.20
 0.104    3738 100.00   387.2   369.4  0.15  0.14     186   342.1   336.1  0.21  0.20
 0.173    4687  99.96   247.3   241.4  0.15  0.13     255   251.6   253.4  0.21  0.17
 0.242    5513 100.00   187.8   189.3  0.17  0.14     291   193.7   191.5  0.21  0.17
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1530   0.937    668   0.844   2198   0.909  0.955  0.9689  0.9752  0.9222  0.9437
  0.1042   3038   0.909    700   0.814   3738   0.891  1.005  0.9510  0.9697  0.8951  0.9479
  0.1733   4001   0.885    686   0.785   4687   0.870  0.982  0.9533  0.9637  0.8885  0.9434
  0.2425   4802   0.864    714   0.750   5516   0.850  0.944  0.9446  0.9543  0.8960  0.9326
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16139
Percentage observed                  =    99.9823
Percentage of free reflections       =     4.9753
Overall R factor                     =     0.1575
Free R factor                        =     0.2070
Average Fourier shell correlation    =     0.9634
AverageFree Fourier shell correlation=     0.9519
Overall weighted R factor            =     0.1464
Free weighted R factor               =     0.1900
Overall weighted R2 factor           =     0.1789
Free weighted R2 factor              =     0.2278
Average correlation coefficient      =     0.9408
Overall correlation coefficient      =     0.9567
Free correlation coefficient         =     0.9225
Cruickshanks DPI for coordinate error=     0.1390
DPI based on free R factor           =     0.1350
Overall figure of merit              =     0.8733
ML based su of positional parameters =     0.0812
ML based su of thermal parameters    =     2.7650
-----------------------------------------------------------------------------
  Time in seconds: CPU =        15.00
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1621   0.2130   0.867       87878.    4746.4   0.0138  1.076   1.838  1.067   0.084
       1   0.1599   0.2103   0.872       87470.    4733.2   0.0119  0.874   1.763  1.016   0.085
       2   0.1586   0.2086   0.873       87342.    4728.3   0.0123  0.905   1.775  1.023   0.086
       3   0.1582   0.2077   0.874       87293.    4726.0   0.0124  0.913   1.782  1.027   0.086
       4   0.1579   0.2070   0.874       87256.    4724.6   0.0124  0.918   1.786  1.030   0.086
       5   0.1578   0.2070   0.874       87237.    4724.6   0.0125  0.920   1.789  1.032   0.086
       6   0.1577   0.2069   0.874       87233.    4724.0   0.0125  0.921   1.791  1.033   0.085
       7   0.1576   0.2070   0.874       87234.    4724.9   0.0125  0.921   1.792  1.034   0.085
       8   0.1576   0.2069   0.874       87235.    4725.1   0.0125  0.920   1.792  1.033   0.085
       9   0.1575   0.2068   0.874       87228.    4725.4   0.0125  0.920   1.792  1.033   0.085
      10   0.1575   0.2070   0.873       87231.    4726.5   0.0125  0.920   1.791  1.033   0.085
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1621   0.1575
             R free    0.2130   0.2070
     Rms BondLength    0.0138   0.0125
      Rms BondAngle    1.8379   1.7911
     Rms ChirVolume    0.0836   0.0849
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      47.0s System:    0.1s Elapsed:     0:48