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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
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 User: maly  Run date: 26/ 5/2020 Run time: 15:32:25 


 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 1.80     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 8
  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_R08_1-90A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R08_1-80A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R08_1-80A.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       0.0772
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.8000
  Estimated number of reflections :      25918
  Free R exclusion - flag equals:     8
  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  1.8000

  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_R08_1-90A.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=   2.025 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=   2.200 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=   2.185 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=   2.375 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=   2.411 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=   2.079 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  PRO               190  AAA  is missing in the structure
  Number of chains                  :       4
  Total number of monomers          :     502
  Number of atoms                   :    3945
  Number of missing atoms           :       1
  Number of rebuilt atoms           :    1480
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0

_ccp4_form_factor.scat_method    'Sum of Gaussians'
_ccp4_form_factor.scat_data_source  X-ray


 loop_
     _atom_type_symbol
     _atom_type_scat_Cromer_Mann_a1
     _atom_type_scat_Cromer_Mann_b1
     _atom_type_scat_Cromer_Mann_a2
     _atom_type_scat_Cromer_Mann_b2
     _atom_type_scat_Cromer_Mann_a3
     _atom_type_scat_Cromer_Mann_b3
     _atom_type_scat_Cromer_Mann_a4
     _atom_type_scat_Cromer_Mann_b4
     _atom_type_scat_Cromer_Mann_c


  N     12.2220   0.0057   3.1346   9.8933   2.0141  28.9975   1.1672   0.5826 -11.5379
  H      0.4930  10.5109   0.3229  26.1257   0.1402   3.1424   0.0408  57.7997   0.0030
  C      2.3103  20.8439   1.0201  10.2075   1.5888   0.5687   0.8651  51.6512   0.2156
  O      3.0487  13.2771   2.2870   5.7011   1.5464   0.3239   0.8671  32.9089   0.2508
  S      6.9054   1.4679   5.2035  22.2151   1.4379   0.2536   1.5863  56.1720   1.0490
  FE    11.7738   4.7611   7.3600   0.3072   3.5235  15.3535   2.3054  76.8805   1.2805


 Number of distances         :           0
 Number of angles            :           0
 Number of torsions          :           0
 Number of planes            :           0
 Number of chirals           :           0
 Number of intervals         :           0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
                        Standard  External       All
                Bonds:      2949         0      2949
               Angles:      5344         0      5344
              Chirals:       196         0       196
               Planes:       453         0       453
             Torsions:      1556         0      1556
            Intervals:         0         0         0
--------------------------------------------------------------------------------


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


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

FreeR flag                            8
Number of "free" reflections        999
Number of   all  reflections      19877
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          19877

   Current auto weighting coefficient =    6.9995613    

 mode : HKRF


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



     CGMAT cycle number =      1

    ****                         Bond distance outliers                         ****

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

A    171 THR C   . - A    172 GLY N   . mod.= 1.736 id.= 1.337 dev= -0.399 sig.= 0.011

    ****                              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.= 0.924 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        :   120  120  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Weight matrix   0.28412473    
 Actual weight    6.9995613      is applied to the X-ray term
Norm of X_ray positional gradient                43.1
Norm of Geom. positional gradient                93.5
Norm of X_ray B-factor gradient                  139.
Norm of Geom. B-factor gradient                  118.
Product of X_ray and Geom posit. gradients     -0.103E+08
 Cosine of angle between them                      -0.265
Product of X_ray and Geom B-fact gradients     -0.408E+08
 Cosine of angle between them                      -0.775


Residuals: XRAY=     0.7045E+06 GEOM=     0.1419E+05 TOTAL=     0.7187E+06
 function value    718715.94    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.016     0.013
Bond distances: others                         1391     0.035     0.017
Bond angles  : refined atoms                   2106     1.836     1.644
Bond angles  : others                          3238     2.362     1.580
Torsion angles, period  1. refined              185     7.101     5.000
Torsion angles, period  2. refined               90    36.829    22.778
Torsion angles, period  3. refined              268    14.016    15.000
Torsion angles, period  4. refined                9    11.218    15.000
Chiral centres: refined atoms                   196     0.086     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.017     0.020
VDW repulsions: refined_atoms                   301     0.244     0.200
VDW repulsions.others                          1312     0.222     0.200
VDW; torsion: refined_atoms                     717     0.171     0.200
VDW; torsion.others                             704     0.081     0.200
HBOND: refined_atoms                            232     0.202     0.200
HBOND.others                                      1     0.048     0.200
VDW repulsions: symmetry: refined_atoms           9     0.253     0.200
VDW repulsions: symmetry: others                 27     0.182     0.200
HBOND: symmetry: refined_atoms                   22     0.185     0.200
M. chain bond B values: refined atoms           746     1.624     1.216
M. chain bond B values: others                  746     1.623     1.216
M. chain angle B values: refined atoms          929     2.590     1.808
M. chain angle B values: others                 930     2.589     1.808
S. chain bond B values: refined atoms           812     2.739     1.573
S. chain bond B values: others                  811     2.735     1.573
S. chain angle B values: refined atoms         1177     4.278     2.206
S. chain angle B values: others                1178     4.276     2.205
Long range B values: refined atoms             1857     6.999    17.117
Long range B values: others                    1757     6.680    15.694
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =    0.8281
Partial structure    1: scale =     0.3776, B  =   46.0791
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2556 100.00   473.0   482.2  0.16  0.17     137   470.4   465.8  0.19  0.21
 0.116    4358 100.00   341.5   326.8  0.16  0.15     221   343.5   334.1  0.21  0.19
 0.193    5506  99.97   226.2   215.1  0.16  0.13     302   224.7   215.2  0.21  0.18
 0.270    6448 100.00   148.0   155.0  0.21  0.16     339   146.0   151.7  0.24  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1795   0.925    761   0.832   2556   0.897  0.951  0.9644  0.9719  0.9190  0.9421
  0.1161   3575   0.889    783   0.784   4358   0.870  0.997  0.9543  0.9650  0.9065  0.9453
  0.1931   4721   0.879    785   0.762   5506   0.862  1.013  0.9457  0.9610  0.8785  0.9423
  0.2701   5675   0.839    781   0.755   6456   0.829  0.901  0.9323  0.9445  0.8719  0.9072
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18876
Percentage observed                  =    99.9849
Percentage of free reflections       =     5.0264
Overall R factor                     =     0.1689
Free R factor                        =     0.2105
Average Fourier shell correlation    =     0.9577
AverageFree Fourier shell correlation=     0.9456
Overall weighted R factor            =     0.1523
Free weighted R factor               =     0.1920
Overall weighted R2 factor           =     0.1839
Free weighted R2 factor              =     0.2285
Average correlation coefficient      =     0.9310
Overall correlation coefficient      =     0.9562
Free correlation coefficient         =     0.9317
Cruickshanks DPI for coordinate error=     0.1234
DPI based on free R factor           =     0.1202
Overall figure of merit              =     0.8575
ML based su of positional parameters =     0.0761
ML based su of thermal parameters    =     2.4430
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    100653.30       14186.990       718715.94      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.30258894    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    710288.94    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0803
Partial structure    1: scale =     0.3784, B  =   46.1865
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1676
Free R factor                        =     0.2089
Average Fourier shell correlation    =     0.9601
AverageFree Fourier shell correlation=     0.9482
Average correlation coefficient      =     0.9340
Overall figure of merit              =     0.8641
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    100258.41       8523.9951       710288.94       718715.94    


     CGMAT cycle number =      3

 Weight matrix   0.30776212    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    709454.50    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0608
Partial structure    1: scale =     0.3786, B  =   46.2086
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1666
Free R factor                        =     0.2084
Average Fourier shell correlation    =     0.9608
AverageFree Fourier shell correlation=     0.9489
Average correlation coefficient      =     0.9355
Overall figure of merit              =     0.8656
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    100092.92       8847.9609       709454.50       710288.94    


     CGMAT cycle number =      4

 Weight matrix   0.30960238    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    709201.13    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0441
Partial structure    1: scale =     0.3782, B  =   46.2991
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1663
Free R factor                        =     0.2085
Average Fourier shell correlation    =     0.9611
AverageFree Fourier shell correlation=     0.9492
Average correlation coefficient      =     0.9360
Overall figure of merit              =     0.8660
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    100036.82       8987.2578       709201.13       709454.50    


     CGMAT cycle number =      5

 Weight matrix   0.31076181    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    709043.75    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0528
Partial structure    1: scale =     0.3781, B  =   46.2507
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1662
Free R factor                        =     0.2085
Average Fourier shell correlation    =     0.9612
AverageFree Fourier shell correlation=     0.9493
Average correlation coefficient      =     0.9363
Overall figure of merit              =     0.8662
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    100007.78       9033.1514       709043.75       709201.13    


     CGMAT cycle number =      6

 Weight matrix   0.31150639    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    708924.06    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0459
Partial structure    1: scale =     0.3779, B  =   46.3038
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1661
Free R factor                        =     0.2089
Average Fourier shell correlation    =     0.9613
AverageFree Fourier shell correlation=     0.9494
Average correlation coefficient      =     0.9365
Overall figure of merit              =     0.8664
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    99985.656       9068.2998       708924.06       709043.75    


     CGMAT cycle number =      7

 Weight matrix   0.31185919    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    708861.50    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0441
Partial structure    1: scale =     0.3779, B  =   46.3843
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1661
Free R factor                        =     0.2091
Average Fourier shell correlation    =     0.9614
AverageFree Fourier shell correlation=     0.9495
Average correlation coefficient      =     0.9366
Overall figure of merit              =     0.8665
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    99975.680       9075.6016       708861.50       708924.06    


     CGMAT cycle number =      8

 Weight matrix   0.31219611    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    708827.88    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0393
Partial structure    1: scale =     0.3779, B  =   46.3610
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1662
Free R factor                        =     0.2090
Average Fourier shell correlation    =     0.9614
AverageFree Fourier shell correlation=     0.9496
Average correlation coefficient      =     0.9367
Overall figure of merit              =     0.8666
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    99970.000       9081.7500       708827.88       708861.50    


     CGMAT cycle number =      9

 Weight matrix   0.31190449    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    708843.63    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0362
Partial structure    1: scale =     0.3778, B  =   46.3658
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1662
Free R factor                        =     0.2094
Average Fourier shell correlation    =     0.9614
AverageFree Fourier shell correlation=     0.9495
Average correlation coefficient      =     0.9367
Overall figure of merit              =     0.8666
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    99973.695       9079.9961       708817.63       708827.88    
 fvalues    99973.695       9079.9961       708817.63       708852.00    


     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.= 0.929 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        :   120  120  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Weight matrix   0.31201681    
 Actual weight    6.9995613      is applied to the X-ray term
Norm of X_ray positional gradient                38.7
Norm of Geom. positional gradient                38.6
Norm of X_ray B-factor gradient                  125.
Norm of Geom. B-factor gradient                  127.
Product of X_ray and Geom posit. gradients     -0.144E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.508E+08
 Cosine of angle between them                      -0.997


Residuals: XRAY=     0.6997E+06 GEOM=      9079.     TOTAL=     0.7088E+06
 function value    708813.06    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.818     1.644
Bond angles  : others                          3238     1.479     1.580
Torsion angles, period  1. refined              185     7.031     5.000
Torsion angles, period  2. refined               90    36.587    22.778
Torsion angles, period  3. refined              268    13.957    15.000
Torsion angles, period  4. refined                9    11.755    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1743     0.009     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   295     0.245     0.200
VDW repulsions.others                          1344     0.194     0.200
VDW; torsion: refined_atoms                     720     0.171     0.200
VDW; torsion.others                             796     0.084     0.200
HBOND: refined_atoms                            219     0.198     0.200
HBOND.others                                      1     0.035     0.200
VDW repulsions: symmetry: refined_atoms          10     0.211     0.200
VDW repulsions: symmetry: others                 24     0.183     0.200
HBOND: symmetry: refined_atoms                   25     0.173     0.200
M. chain bond B values: refined atoms           746     1.675     1.291
M. chain bond B values: others                  746     1.673     1.291
M. chain angle B values: refined atoms          929     2.626     1.923
M. chain angle B values: others                 930     2.625     1.923
S. chain bond B values: refined atoms           811     2.933     1.674
S. chain bond B values: others                  810     2.929     1.673
S. chain angle B values: refined atoms         1177     4.556     2.347
S. chain angle B values: others                1178     4.554     2.346
Long range B values: refined atoms             1839     6.990    17.869
Long range B values: others                    1748     6.721    16.538
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0363
Partial structure    1: scale =     0.3776, B  =   46.2514
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2556 100.00   473.1   482.7  0.16  0.17     137   470.5   468.9  0.20  0.21
 0.116    4358 100.00   341.6   326.0  0.16  0.15     221   343.6   332.4  0.20  0.19
 0.193    5506  99.97   226.3   214.8  0.16  0.14     302   224.8   214.4  0.21  0.18
 0.270    6448 100.00   148.0   154.6  0.19  0.15     339   146.0   151.4  0.23  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1795   0.932    761   0.840   2556   0.904  0.951  0.9659  0.9734  0.9172  0.9415
  0.1161   3575   0.892    783   0.789   4358   0.874  0.997  0.9562  0.9659  0.9125  0.9455
  0.1931   4721   0.883    785   0.768   5506   0.866  1.013  0.9474  0.9613  0.8809  0.9400
  0.2701   5675   0.857    781   0.777   6456   0.847  0.908  0.9405  0.9539  0.8819  0.9263
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18876
Percentage observed                  =    99.9849
Percentage of free reflections       =     5.0264
Overall R factor                     =     0.1661
Free R factor                        =     0.2095
Average Fourier shell correlation    =     0.9615
AverageFree Fourier shell correlation=     0.9496
Overall weighted R factor            =     0.1520
Free weighted R factor               =     0.1930
Overall weighted R2 factor           =     0.1846
Free weighted R2 factor              =     0.2303
Average correlation coefficient      =     0.9368
Overall correlation coefficient      =     0.9570
Free correlation coefficient         =     0.9333
Cruickshanks DPI for coordinate error=     0.1214
DPI based on free R factor           =     0.1196
Overall figure of merit              =     0.8666
ML based su of positional parameters =     0.0725
ML based su of thermal parameters    =     2.3121
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    99968.344       9078.5068       708813.06       708852.00    

    ****                              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.= 0.929 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_R08_1-80A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.818     1.644
Bond angles  : others                          3238     1.479     1.580
Torsion angles, period  1. refined              185     7.024     5.000
Torsion angles, period  2. refined               90    36.567    22.778
Torsion angles, period  3. refined              268    13.968    15.000
Torsion angles, period  4. refined                9    11.728    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1743     0.009     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   295     0.245     0.200
VDW repulsions.others                          1343     0.194     0.200
VDW; torsion: refined_atoms                     720     0.171     0.200
VDW; torsion.others                             798     0.084     0.200
HBOND: refined_atoms                            219     0.198     0.200
HBOND.others                                      1     0.036     0.200
VDW repulsions: symmetry: refined_atoms          10     0.210     0.200
VDW repulsions: symmetry: others                 24     0.185     0.200
HBOND: symmetry: refined_atoms                   25     0.174     0.200
M. chain bond B values: refined atoms           746     1.676     1.291
M. chain bond B values: others                  746     1.674     1.292
M. chain angle B values: refined atoms          929     2.627     1.923
M. chain angle B values: others                 930     2.625     1.923
S. chain bond B values: refined atoms           811     2.933     1.674
S. chain bond B values: others                  810     2.928     1.673
S. chain angle B values: refined atoms         1177     4.554     2.347
S. chain angle B values: others                1178     4.552     2.346
Long range B values: refined atoms             1839     6.994    17.895
Long range B values: others                    1748     6.727    16.567
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0352
Partial structure    1: scale =     0.3775, B  =   46.0640
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2556 100.00   473.1   482.6  0.16  0.17     137   470.4   469.3  0.20  0.21
 0.116    4358 100.00   341.5   326.0  0.16  0.15     221   343.6   332.4  0.20  0.19
 0.193    5506  99.97   226.2   214.8  0.16  0.14     302   224.7   214.5  0.21  0.18
 0.270    6448 100.00   148.0   154.6  0.19  0.15     339   146.0   151.4  0.23  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1795   0.932    761   0.841   2556   0.905  0.951  0.9661  0.9734  0.9176  0.9415
  0.1161   3575   0.892    783   0.789   4358   0.874  0.997  0.9562  0.9659  0.9125  0.9455
  0.1931   4721   0.882    785   0.768   5506   0.866  1.013  0.9473  0.9613  0.8805  0.9400
  0.2701   5675   0.857    781   0.777   6456   0.847  0.908  0.9406  0.9540  0.8821  0.9265
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18876
Percentage observed                  =    99.9849
Percentage of free reflections       =     5.0264
Overall R factor                     =     0.1662
Free R factor                        =     0.2095
Average Fourier shell correlation    =     0.9615
AverageFree Fourier shell correlation=     0.9496
Overall weighted R factor            =     0.1520
Free weighted R factor               =     0.1930
Overall weighted R2 factor           =     0.1846
Free weighted R2 factor              =     0.2302
Average correlation coefficient      =     0.9369
Overall correlation coefficient      =     0.9570
Free correlation coefficient         =     0.9334
Cruickshanks DPI for coordinate error=     0.1214
DPI based on free R factor           =     0.1197
Overall figure of merit              =     0.8666
ML based su of positional parameters =     0.0725
ML based su of thermal parameters    =     2.3121
-----------------------------------------------------------------------------
  Time in seconds: CPU =        15.08
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1689   0.2105   0.857      100653.    5481.5   0.0160  1.295   1.836  1.057   0.086
       1   0.1676   0.2089   0.864      100258.    5468.0   0.0123  0.908   1.789  1.029   0.086
       2   0.1666   0.2084   0.866      100093.    5462.0   0.0127  0.935   1.801  1.036   0.087
       3   0.1663   0.2085   0.866      100037.    5459.5   0.0128  0.942   1.809  1.040   0.087
       4   0.1662   0.2085   0.866      100008.    5458.5   0.0128  0.945   1.813  1.042   0.088
       5   0.1661   0.2089   0.866       99986.    5458.0   0.0128  0.946   1.815  1.043   0.088
       6   0.1661   0.2091   0.867       99976.    5457.6   0.0128  0.946   1.817  1.044   0.088
       7   0.1662   0.2090   0.867       99970.    5457.5   0.0128  0.946   1.818  1.044   0.088
       8   0.1662   0.2094   0.867       99973.    5458.3   0.0128  0.946   1.818  1.045   0.088
       9   0.1661   0.2095   0.867       99968.    5458.3   0.0128  0.946   1.818  1.045   0.088
      10   0.1662   0.2095   0.867       99964.    5458.3   0.0128  0.946   1.818  1.045   0.088
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1689   0.1662
             R free    0.2105   0.2095
     Rms BondLength    0.0160   0.0128
      Rms BondAngle    1.8358   1.8183
     Rms ChirVolume    0.0858   0.0880
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      47.0s System:    0.1s Elapsed:     0:47