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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: 16:02:32 


 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 18
  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_R18_1-90A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R18_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_R18_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:    18
  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_R18_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=   2.016 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=   2.196 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=   1.850 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=   2.192 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=   2.354 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=   2.409 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=   2.107 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                           18
Number of "free" reflections       1013
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

    ****                              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.= 0.919 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   0.25758603    
 Actual weight    6.9995613      is applied to the X-ray term
Norm of X_ray positional gradient                38.2
Norm of Geom. positional gradient                78.1
Norm of X_ray B-factor gradient                  127.
Norm of Geom. B-factor gradient                 0.221E+05
Product of X_ray and Geom posit. gradients     -0.978E+07
 Cosine of angle between them                      -0.339
Product of X_ray and Geom B-fact gradients     -0.404E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.7063E+06 GEOM=     0.2634E+05 TOTAL=     0.7327E+06
 function value    732670.38    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.751     1.644
Bond angles  : others                          3242     2.334     1.582
Torsion angles, period  1. refined              184     6.983     5.000
Torsion angles, period  2. refined               90    36.725    22.778
Torsion angles, period  3. refined              268    14.170    15.000
Torsion angles, period  4. refined                9    11.358    15.000
Chiral centres: refined atoms                   196     0.084     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.017     0.020
VDW repulsions: refined_atoms                   309     0.262     0.200
VDW repulsions.others                          1338     0.229     0.200
VDW; torsion: refined_atoms                     716     0.171     0.200
VDW; torsion.others                             713     0.079     0.200
HBOND: refined_atoms                            242     0.205     0.200
HBOND.others                                      1     0.060     0.200
VDW repulsions: symmetry: refined_atoms          11     0.225     0.200
VDW repulsions: symmetry: others                 30     0.170     0.200
HBOND: symmetry: refined_atoms                   21     0.247     0.200
HBOND: symmetry: others                           1     0.097     0.200
M. chain bond B values: refined atoms           745     1.563     1.212
M. chain bond B values: others                  745     1.562     1.213
M. chain angle B values: refined atoms          926     2.519     1.800
M. chain angle B values: others                 927     2.517     1.799
S. chain bond B values: refined atoms           811     2.621     1.565
S. chain bond B values: others                  810     2.618     1.565
S. chain angle B values: refined atoms         1177     4.135     2.196
S. chain angle B values: others                1178     4.133     2.196
Long range B values: refined atoms             1873     7.139    17.366
Long range B values: others                    1770     6.804    15.879
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0414, B  =    0.8949
Partial structure    1: scale =     0.3845, B  =   50.0539
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.51 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2548 100.00   470.0   477.9  0.15  0.16     145   506.3   521.5  0.18  0.19
 0.116    4337 100.00   340.2   325.8  0.16  0.15     242   354.2   343.3  0.22  0.20
 0.193    5522  99.97   226.1   215.2  0.16  0.13     286   216.9   210.0  0.23  0.19
 0.270    6448 100.00   147.2   154.0  0.21  0.16     339   154.3   161.3  0.24  0.19
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1796   0.916    752   0.816   2548   0.887  0.947  0.9674  0.9710  0.9168  0.9423
  0.1161   3567   0.872    770   0.765   4337   0.853  0.990  0.9503  0.9590  0.9054  0.9427
  0.1931   4754   0.878    768   0.764   5522   0.862  1.011  0.9439  0.9603  0.8929  0.9417
  0.2701   5671   0.819    784   0.741   6455   0.810  0.894  0.9322  0.9402  0.8681  0.9068
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18862
Percentage observed                  =    99.9849
Percentage of free reflections       =     5.0969
Overall R factor                     =     0.1694
Free R factor                        =     0.2137
Average Fourier shell correlation    =     0.9546
AverageFree Fourier shell correlation=     0.9449
Overall weighted R factor            =     0.1528
Free weighted R factor               =     0.1954
Overall weighted R2 factor           =     0.1838
Free weighted R2 factor              =     0.2347
Average correlation coefficient      =     0.9301
Overall correlation coefficient      =     0.9555
Free correlation coefficient         =     0.9339
Cruickshanks DPI for coordinate error=     0.1239
DPI based on free R factor           =     0.1221
Overall figure of merit              =     0.8454
ML based su of positional parameters =     0.0799
ML based su of thermal parameters    =     2.5650
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    100911.16       26336.484       732670.38      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.27998561    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    712928.38    

-------------------------------------------------------------------------------
             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 =     0.0414, B  =   -0.0792
Partial structure    1: scale =     0.3850, B  =   49.5694
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                     =     0.1685
Free R factor                        =     0.2127
Average Fourier shell correlation    =     0.9576
AverageFree Fourier shell correlation=     0.9477
Average correlation coefficient      =     0.9327
Overall figure of merit              =     0.8555
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    100448.51       9832.8438       712928.38       732670.38    


     CGMAT cycle number =      3

 Weight matrix   0.28533000    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    710843.88    

-------------------------------------------------------------------------------
             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 =     0.0414, B  =   -0.0577
Partial structure    1: scale =     0.3854, B  =   47.0723
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                     =     0.1672
Free R factor                        =     0.2118
Average Fourier shell correlation    =     0.9586
AverageFree Fourier shell correlation=     0.9486
Average correlation coefficient      =     0.9344
Overall figure of merit              =     0.8574
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    100265.43       9029.8672       710843.88       712928.38    


     CGMAT cycle number =      4

 Weight matrix   0.28753516    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    710031.69    

-------------------------------------------------------------------------------
             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 =     0.0414, B  =   -0.0316
Partial structure    1: scale =     0.3853, B  =   46.8459
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                     =     0.1668
Free R factor                        =     0.2114
Average Fourier shell correlation    =     0.9590
AverageFree Fourier shell correlation=     0.9490
Average correlation coefficient      =     0.9351
Overall figure of merit              =     0.8582
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    100180.41       8812.8164       710031.69       710843.88    


     CGMAT cycle number =      5

 Weight matrix   0.28907064    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    709745.38    

-------------------------------------------------------------------------------
             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 =     0.0414, B  =   -0.0319
Partial structure    1: scale =     0.3852, B  =   46.8988
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                     =     0.1667
Free R factor                        =     0.2111
Average Fourier shell correlation    =     0.9592
AverageFree Fourier shell correlation=     0.9493
Average correlation coefficient      =     0.9354
Overall figure of merit              =     0.8587
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    100140.23       8807.6797       709745.38       710031.69    


     CGMAT cycle number =      6

 Weight matrix   0.29066855    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    709615.13    

-------------------------------------------------------------------------------
             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 =     0.0414, B  =   -0.0253
Partial structure    1: scale =     0.3851, B  =   46.8997
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                        =     0.2110
Average Fourier shell correlation    =     0.9594
AverageFree Fourier shell correlation=     0.9495
Average correlation coefficient      =     0.9356
Overall figure of merit              =     0.8593
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    100116.80       8841.4150       709615.13       709745.38    


     CGMAT cycle number =      7

 Weight matrix   0.29209933    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    709437.00    

-------------------------------------------------------------------------------
             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 =     0.0414, B  =   -0.0421
Partial structure    1: scale =     0.3850, B  =   46.7826
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                     =     0.1665
Free R factor                        =     0.2110
Average Fourier shell correlation    =     0.9595
AverageFree Fourier shell correlation=     0.9497
Average correlation coefficient      =     0.9358
Overall figure of merit              =     0.8599
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    100090.27       8849.0430       709437.00       709615.13    


     CGMAT cycle number =      8

 Weight matrix   0.29265776    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    709347.63    

-------------------------------------------------------------------------------
             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 =     0.0414, B  =   -0.0349
Partial structure    1: scale =     0.3850, B  =   46.7850
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                     =     0.1665
Free R factor                        =     0.2110
Average Fourier shell correlation    =     0.9596
AverageFree Fourier shell correlation=     0.9498
Average correlation coefficient      =     0.9359
Overall figure of merit              =     0.8601
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    100074.09       8872.8604       709347.63       709437.00    


     CGMAT cycle number =      9

 Weight matrix   0.29310638    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    709296.13    

-------------------------------------------------------------------------------
             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 =     0.0414, B  =   -0.0305
Partial structure    1: scale =     0.3849, B  =   46.7303
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                     =     0.1665
Free R factor                        =     0.2110
Average Fourier shell correlation    =     0.9597
AverageFree Fourier shell correlation=     0.9499
Average correlation coefficient      =     0.9360
Overall figure of merit              =     0.8604
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    100066.53       8874.2959       709296.13       709347.63    


     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.= 0.930 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   0.29352653    
 Actual weight    6.9995613      is applied to the X-ray term
Norm of X_ray positional gradient                36.5
Norm of Geom. positional gradient                36.4
Norm of X_ray B-factor gradient                  119.
Norm of Geom. B-factor gradient                  120.
Product of X_ray and Geom posit. gradients     -0.129E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.460E+08
 Cosine of angle between them                      -0.998


Residuals: XRAY=     0.7004E+06 GEOM=      8885.     TOTAL=     0.7093E+06
 function value    709267.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.781     1.644
Bond angles  : others                          3242     1.471     1.582
Torsion angles, period  1. refined              184     7.041     5.000
Torsion angles, period  2. refined               90    36.619    22.778
Torsion angles, period  3. refined              268    14.044    15.000
Torsion angles, period  4. refined                9    11.782    15.000
Chiral centres: refined atoms                   196     0.086     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   311     0.262     0.200
VDW repulsions.others                          1360     0.202     0.200
VDW; torsion: refined_atoms                     722     0.171     0.200
VDW; torsion.others                             793     0.083     0.200
HBOND: refined_atoms                            236     0.200     0.200
HBOND.others                                      2     0.069     0.200
VDW repulsions: symmetry: refined_atoms          11     0.203     0.200
VDW repulsions: symmetry: others                 26     0.168     0.200
HBOND: symmetry: refined_atoms                   23     0.226     0.200
HBOND: symmetry: others                           1     0.047     0.200
M. chain bond B values: refined atoms           745     1.611     1.292
M. chain bond B values: others                  745     1.609     1.292
M. chain angle B values: refined atoms          926     2.551     1.919
M. chain angle B values: others                 927     2.550     1.919
S. chain bond B values: refined atoms           811     2.808     1.668
S. chain bond B values: others                  810     2.805     1.668
S. chain angle B values: refined atoms         1177     4.419     2.343
S. chain angle B values: others                1178     4.417     2.342
Long range B values: refined atoms             1873     7.094    18.250
Long range B values: others                    1773     6.783    16.803
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0340
Partial structure    1: scale =     0.3847, B  =   46.6586
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2548 100.00   470.5   478.7  0.16  0.17     145   506.7   521.3  0.18  0.20
 0.116    4337 100.00   340.5   325.4  0.16  0.15     242   354.6   342.3  0.21  0.20
 0.193    5522  99.97   226.3   215.2  0.16  0.14     286   217.1   208.9  0.23  0.18
 0.270    6448 100.00   147.4   153.8  0.19  0.15     339   154.5   161.5  0.23  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1796   0.932    752   0.837   2548   0.904  0.949  0.9689  0.9737  0.9139  0.9414
  0.1161   3567   0.880    770   0.774   4337   0.861  0.990  0.9535  0.9610  0.9105  0.9429
  0.1931   4754   0.882    768   0.769   5522   0.867  1.011  0.9462  0.9611  0.8966  0.9400
  0.2701   5671   0.847    784   0.770   6455   0.837  0.905  0.9425  0.9521  0.8803  0.9260
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18862
Percentage observed                  =    99.9849
Percentage of free reflections       =     5.0969
Overall R factor                     =     0.1664
Free R factor                        =     0.2110
Average Fourier shell correlation    =     0.9597
AverageFree Fourier shell correlation=     0.9500
Overall weighted R factor            =     0.1522
Free weighted R factor               =     0.1941
Overall weighted R2 factor           =     0.1846
Free weighted R2 factor              =     0.2350
Average correlation coefficient      =     0.9360
Overall correlation coefficient      =     0.9563
Free correlation coefficient         =     0.9353
Cruickshanks DPI for coordinate error=     0.1217
DPI based on free R factor           =     0.1206
Overall figure of merit              =     0.8605
ML based su of positional parameters =     0.0748
ML based su of thermal parameters    =     2.3859
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    100060.89       8884.9414       709267.25       709296.13    

    ****                              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.= 0.930 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_R18_1-80A.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     1.782     1.644
Bond angles  : others                          3242     1.472     1.582
Torsion angles, period  1. refined              184     7.040     5.000
Torsion angles, period  2. refined               90    36.604    22.778
Torsion angles, period  3. refined              268    14.059    15.000
Torsion angles, period  4. refined                9    11.790    15.000
Chiral centres: refined atoms                   196     0.086     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   310     0.262     0.200
VDW repulsions.others                          1358     0.202     0.200
VDW; torsion: refined_atoms                     722     0.171     0.200
VDW; torsion.others                             794     0.083     0.200
HBOND: refined_atoms                            236     0.200     0.200
HBOND.others                                      2     0.072     0.200
VDW repulsions: symmetry: refined_atoms          11     0.202     0.200
VDW repulsions: symmetry: others                 26     0.169     0.200
HBOND: symmetry: refined_atoms                   23     0.226     0.200
HBOND: symmetry: others                           1     0.044     0.200
M. chain bond B values: refined atoms           745     1.611     1.291
M. chain bond B values: others                  745     1.610     1.291
M. chain angle B values: refined atoms          926     2.551     1.919
M. chain angle B values: others                 927     2.550     1.918
S. chain bond B values: refined atoms           811     2.811     1.668
S. chain bond B values: others                  810     2.807     1.668
S. chain angle B values: refined atoms         1177     4.422     2.342
S. chain angle B values: others                1178     4.420     2.342
Long range B values: refined atoms             1872     7.099    18.239
Long range B values: others                    1772     6.788    16.791
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0279
Partial structure    1: scale =     0.3846, B  =   46.6708
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2548 100.00   470.5   478.7  0.16  0.17     145   506.8   521.3  0.18  0.20
 0.116    4337 100.00   340.5   325.4  0.16  0.15     242   354.6   342.3  0.21  0.20
 0.193    5522  99.97   226.4   215.2  0.16  0.14     286   217.1   208.9  0.23  0.18
 0.270    6448 100.00   147.4   153.8  0.19  0.15     339   154.5   161.5  0.23  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1796   0.932    752   0.838   2548   0.904  0.949  0.9690  0.9737  0.9140  0.9414
  0.1161   3567   0.880    770   0.774   4337   0.861  0.990  0.9536  0.9611  0.9106  0.9429
  0.1931   4754   0.882    768   0.769   5522   0.867  1.011  0.9462  0.9610  0.8967  0.9399
  0.2701   5671   0.847    784   0.770   6455   0.838  0.905  0.9426  0.9522  0.8805  0.9262
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18862
Percentage observed                  =    99.9849
Percentage of free reflections       =     5.0969
Overall R factor                     =     0.1664
Free R factor                        =     0.2111
Average Fourier shell correlation    =     0.9597
AverageFree Fourier shell correlation=     0.9500
Overall weighted R factor            =     0.1522
Free weighted R factor               =     0.1943
Overall weighted R2 factor           =     0.1846
Free weighted R2 factor              =     0.2350
Average correlation coefficient      =     0.9361
Overall correlation coefficient      =     0.9564
Free correlation coefficient         =     0.9354
Cruickshanks DPI for coordinate error=     0.1217
DPI based on free R factor           =     0.1206
Overall figure of merit              =     0.8606
ML based su of positional parameters =     0.0748
ML based su of thermal parameters    =     2.3859
-----------------------------------------------------------------------------
  Time in seconds: CPU =        14.56
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1694   0.2137   0.845      100911.    5628.5   0.0118  0.872   1.751  1.015   0.084
       1   0.1685   0.2127   0.855      100449.    5617.5   0.0116  0.850   1.730  1.001   0.085
       2   0.1672   0.2118   0.857      100265.    5611.6   0.0121  0.890   1.750  1.013   0.086
       3   0.1668   0.2114   0.858      100180.    5608.0   0.0122  0.897   1.761  1.020   0.086
       4   0.1667   0.2111   0.859      100140.    5605.9   0.0122  0.901   1.767  1.023   0.086
       5   0.1666   0.2110   0.859      100117.    5604.5   0.0122  0.904   1.772  1.026   0.086
       6   0.1665   0.2110   0.860      100090.    5603.4   0.0123  0.905   1.775  1.027   0.086
       7   0.1665   0.2110   0.860      100074.    5602.9   0.0123  0.907   1.778  1.029   0.086
       8   0.1665   0.2110   0.860      100067.    5602.3   0.0123  0.908   1.779  1.029   0.086
       9   0.1664   0.2110   0.860      100061.    5602.2   0.0123  0.909   1.781  1.030   0.086
      10   0.1664   0.2111   0.861      100056.    5601.8   0.0123  0.910   1.782  1.031   0.086
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1694   0.1664
             R free    0.2137   0.2111
     Rms BondLength    0.0118   0.0123
      Rms BondAngle    1.7512   1.7823
     Rms ChirVolume    0.0839   0.0862
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      46.6s System:    0.1s Elapsed:     0:47