###############################################################
 ###############################################################
 ###############################################################
 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 26/ 5/2020 Run time: 15:11:15 


 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 1
  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_R01_1-90A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R01_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_R01_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:     1
  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_R01_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=   2.224 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=   1.842 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=   2.184 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=   2.391 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=   2.426 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=   2.099 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                            1
Number of "free" reflections        993
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.= 0.909 id.= 3.000 dev= -2.09 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   0.27379760    
 Actual weight    6.9995613      is applied to the X-ray term
Norm of X_ray positional gradient                40.7
Norm of Geom. positional gradient                78.8
Norm of X_ray B-factor gradient                  132.
Norm of Geom. B-factor gradient                 0.225E+05
Product of X_ray and Geom posit. gradients     -0.107E+08
 Cosine of angle between them                      -0.343
Product of X_ray and Geom B-fact gradients     -0.416E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.7055E+06 GEOM=     0.2669E+05 TOTAL=     0.7322E+06
 function value    732181.13    

-------------------------------------------------------------------------------
             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     1.781     1.644
Bond angles  : others                          3242     2.340     1.582
Torsion angles, period  1. refined              184     6.949     5.000
Torsion angles, period  2. refined               90    36.760    22.778
Torsion angles, period  3. refined              268    13.858    15.000
Torsion angles, period  4. refined                9    10.863    15.000
Chiral centres: refined atoms                   196     0.086     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.016     0.020
VDW repulsions: refined_atoms                   299     0.271     0.200
VDW repulsions.others                          1334     0.231     0.200
VDW; torsion: refined_atoms                     712     0.170     0.200
VDW; torsion.others                             702     0.080     0.200
HBOND: refined_atoms                            230     0.206     0.200
HBOND.others                                      1     0.034     0.200
VDW repulsions: symmetry: refined_atoms           7     0.268     0.200
VDW repulsions: symmetry: others                 24     0.211     0.200
HBOND: symmetry: refined_atoms                   19     0.214     0.200
HBOND: symmetry: others                           1     0.080     0.200
M. chain bond B values: refined atoms           745     1.599     1.214
M. chain bond B values: others                  745     1.598     1.214
M. chain angle B values: refined atoms          926     2.523     1.802
M. chain angle B values: others                 927     2.522     1.801
S. chain bond B values: refined atoms           812     2.654     1.564
S. chain bond B values: others                  811     2.651     1.564
S. chain angle B values: refined atoms         1177     4.179     2.197
S. chain angle B values: others                1178     4.177     2.196
Long range B values: refined atoms             1847     6.803    17.049
Long range B values: others                    1749     6.508    15.637
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =    0.8479
Partial structure    1: scale =     0.3780, B  =   49.4567
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2559 100.00   472.6   481.4  0.16  0.17     134   471.0   479.5  0.19  0.20
 0.116    4331 100.00   341.1   326.7  0.16  0.14     248   344.8   340.0  0.20  0.18
 0.193    5518  99.97   225.6   214.9  0.16  0.14     290   232.2   222.6  0.23  0.19
 0.270    6466 100.00   147.5   154.1  0.21  0.16     321   152.8   163.7  0.23  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1803   0.916    756   0.805   2559   0.883  0.953  0.9581  0.9697  0.8954  0.9410
  0.1161   3574   0.894    757   0.796   4331   0.877  0.999  0.9577  0.9672  0.9036  0.9490
  0.1931   4735   0.868    783   0.748   5518   0.851  1.006  0.9435  0.9562  0.8835  0.9376
  0.2701   5687   0.832    787   0.748   6474   0.822  0.896  0.9433  0.9439  0.9071  0.9088
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18882
Percentage observed                  =    99.9849
Percentage of free reflections       =     4.9962
Overall R factor                     =     0.1688
Free R factor                        =     0.2114
Average Fourier shell correlation    =     0.9563
AverageFree Fourier shell correlation=     0.9489
Overall weighted R factor            =     0.1528
Free weighted R factor               =     0.1884
Overall weighted R2 factor           =     0.1857
Free weighted R2 factor              =     0.2153
Average correlation coefficient      =     0.9308
Overall correlation coefficient      =     0.9564
Free correlation coefficient         =     0.9253
Cruickshanks DPI for coordinate error=     0.1233
DPI based on free R factor           =     0.1207
Overall figure of merit              =     0.8514
ML based su of positional parameters =     0.0775
ML based su of thermal parameters    =     2.5000
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    100790.09       26694.746       732181.13      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.29489887    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    712595.81    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0257
Partial structure    1: scale =     0.3782, B  =   48.7650
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                     =     0.1679
Free R factor                        =     0.2099
Average Fourier shell correlation    =     0.9591
AverageFree Fourier shell correlation=     0.9513
Average correlation coefficient      =     0.9333
Overall figure of merit              =     0.8601
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    100357.33       10138.535       712595.81       732181.13    


     CGMAT cycle number =      3

 Weight matrix   0.29875112    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    710494.63    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0039
Partial structure    1: scale =     0.3782, B  =   46.2398
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                        =     0.2090
Average Fourier shell correlation    =     0.9598
AverageFree Fourier shell correlation=     0.9518
Average correlation coefficient      =     0.9349
Overall figure of merit              =     0.8616
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    100183.14       9256.5342       710494.63       712595.81    


     CGMAT cycle number =      4

 Weight matrix   0.30017263    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    709787.50    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0031
Partial structure    1: scale =     0.3786, B  =   46.3042
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                        =     0.2084
Average Fourier shell correlation    =     0.9601
AverageFree Fourier shell correlation=     0.9521
Average correlation coefficient      =     0.9354
Overall figure of merit              =     0.8622
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    100118.00       9005.4531       709787.50       710494.63    


     CGMAT cycle number =      5

 Weight matrix   0.30049083    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    709579.06    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =    0.0028
Partial structure    1: scale =     0.3788, B  =   46.3847
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                     =     0.1664
Free R factor                        =     0.2082
Average Fourier shell correlation    =     0.9602
AverageFree Fourier shell correlation=     0.9522
Average correlation coefficient      =     0.9357
Overall figure of merit              =     0.8624
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    100089.70       8995.1250       709579.06       709787.50    


     CGMAT cycle number =      6

 Weight matrix   0.30051416    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    709473.69    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =    0.0075
Partial structure    1: scale =     0.3791, B  =   46.3991
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1663
Free R factor                        =     0.2082
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9522
Average correlation coefficient      =     0.9358
Overall figure of merit              =     0.8625
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    100072.27       9011.6680       709473.69       709579.06    


     CGMAT cycle number =      7

 Weight matrix   0.30041590    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    709413.63    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0414, B  =    0.0060
Partial structure    1: scale =     0.3791, B  =   46.4446
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1662
Free R factor                        =     0.2081
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9522
Average correlation coefficient      =     0.9359
Overall figure of merit              =     0.8625
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    100063.05       9016.1172       709413.63       709473.69    


     CGMAT cycle number =      8

 Weight matrix   0.30014437    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    709396.94    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0414, B  =    0.0059
Partial structure    1: scale =     0.3791, B  =   46.4393
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1662
Free R factor                        =     0.2082
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9522
Average correlation coefficient      =     0.9359
Overall figure of merit              =     0.8625
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    100060.42       9017.9023       709396.94       709413.63    


     CGMAT cycle number =      9

 Weight matrix   0.29955912    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    709417.69    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0414, B  =    0.0062
Partial structure    1: scale =     0.3792, B  =   46.4862
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1663
Free R factor                        =     0.2084
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9521
Average correlation coefficient      =     0.9360
Overall figure of merit              =     0.8624
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    100065.05       9006.1709       709426.13       709396.94    

 fvalues    100065.05       9006.1709       709413.44       709417.63    
 fvalues    100065.05       9006.1709       709413.44       709417.63    


     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.= 0.922 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   0.29950139    
 Actual weight    6.9995613      is applied to the X-ray term
Norm of X_ray positional gradient                37.8
Norm of Geom. positional gradient                37.8
Norm of X_ray B-factor gradient                  121.
Norm of Geom. B-factor gradient                  121.
Product of X_ray and Geom posit. gradients     -0.138E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.474E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.7004E+06 GEOM=      9004.     TOTAL=     0.7094E+06
 function value    709426.44    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.806     1.644
Bond angles  : others                          3242     1.465     1.582
Torsion angles, period  1. refined              184     6.932     5.000
Torsion angles, period  2. refined               90    36.479    22.778
Torsion angles, period  3. refined              268    13.764    15.000
Torsion angles, period  4. refined                9    11.446    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                   299     0.272     0.200
VDW repulsions.others                          1344     0.205     0.200
VDW; torsion: refined_atoms                     719     0.171     0.200
VDW; torsion.others                             786     0.084     0.200
HBOND: refined_atoms                            221     0.203     0.200
HBOND.others                                      1     0.098     0.200
VDW repulsions: symmetry: refined_atoms           7     0.240     0.200
VDW repulsions: symmetry: others                 22     0.188     0.200
HBOND: symmetry: refined_atoms                   24     0.193     0.200
HBOND: symmetry: others                           1     0.050     0.200
M. chain bond B values: refined atoms           745     1.661     1.292
M. chain bond B values: others                  745     1.659     1.292
M. chain angle B values: refined atoms          926     2.583     1.919
M. chain angle B values: others                 927     2.582     1.919
S. chain bond B values: refined atoms           811     2.845     1.669
S. chain bond B values: others                  810     2.841     1.668
S. chain angle B values: refined atoms         1177     4.474     2.342
S. chain angle B values: others                1178     4.472     2.341
Long range B values: refined atoms             1842     6.876    17.971
Long range B values: others                    1747     6.616    16.538
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0414, B  =    0.0017
Partial structure    1: scale =     0.3793, B  =   46.5116
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2559 100.00   472.4   481.7  0.16  0.17     134   470.8   479.7  0.19  0.19
 0.116    4331 100.00   341.0   325.7  0.16  0.14     248   344.7   338.0  0.20  0.18
 0.193    5518  99.97   225.5   214.3  0.16  0.14     290   232.1   222.4  0.23  0.19
 0.270    6466 100.00   147.5   154.0  0.19  0.15     321   152.7   163.7  0.23  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1803   0.930    756   0.825   2559   0.899  0.953  0.9616  0.9728  0.8977  0.9412
  0.1161   3574   0.899    757   0.800   4331   0.882  0.999  0.9590  0.9681  0.9052  0.9486
  0.1931   4735   0.873    783   0.751   5518   0.855  1.006  0.9454  0.9571  0.8857  0.9360
  0.2701   5687   0.851    787   0.770   6474   0.841  0.902  0.9488  0.9527  0.9099  0.9254
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18882
Percentage observed                  =    99.9849
Percentage of free reflections       =     4.9962
Overall R factor                     =     0.1663
Free R factor                        =     0.2086
Average Fourier shell correlation    =     0.9602
AverageFree Fourier shell correlation=     0.9521
Overall weighted R factor            =     0.1523
Free weighted R factor               =     0.1847
Overall weighted R2 factor           =     0.1861
Free weighted R2 factor              =     0.2129
Average correlation coefficient      =     0.9360
Overall correlation coefficient      =     0.9572
Free correlation coefficient         =     0.9266
Cruickshanks DPI for coordinate error=     0.1214
DPI based on free R factor           =     0.1191
Overall figure of merit              =     0.8624
ML based su of positional parameters =     0.0740
ML based su of thermal parameters    =     2.3798
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    100066.99       9003.6504       709424.50       709417.63    
 fvalues    100066.99       9003.6504       709424.50       709428.69    

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.923 id.= 3.000 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 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_R01_1-80A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.806     1.644
Bond angles  : others                          3242     1.465     1.582
Torsion angles, period  1. refined              184     6.931     5.000
Torsion angles, period  2. refined               90    36.467    22.778
Torsion angles, period  3. refined              268    13.775    15.000
Torsion angles, period  4. refined                9    11.464    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                   299     0.272     0.200
VDW repulsions.others                          1343     0.205     0.200
VDW; torsion: refined_atoms                     719     0.171     0.200
VDW; torsion.others                             789     0.084     0.200
HBOND: refined_atoms                            222     0.202     0.200
HBOND.others                                      1     0.101     0.200
VDW repulsions: symmetry: refined_atoms           7     0.239     0.200
VDW repulsions: symmetry: others                 23     0.184     0.200
HBOND: symmetry: refined_atoms                   24     0.193     0.200
HBOND: symmetry: others                           1     0.050     0.200
M. chain bond B values: refined atoms           745     1.660     1.292
M. chain bond B values: others                  745     1.658     1.292
M. chain angle B values: refined atoms          926     2.582     1.919
M. chain angle B values: others                 927     2.581     1.919
S. chain bond B values: refined atoms           811     2.844     1.669
S. chain bond B values: others                  810     2.841     1.668
S. chain angle B values: refined atoms         1177     4.473     2.342
S. chain angle B values: others                1178     4.471     2.342
Long range B values: refined atoms             1843     6.878    17.976
Long range B values: others                    1748     6.617    16.544
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0414, B  =    0.0053
Partial structure    1: scale =     0.3794, B  =   46.5597
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2559 100.00   472.4   481.7  0.16  0.17     134   470.8   479.6  0.19  0.19
 0.116    4331 100.00   341.0   325.7  0.16  0.14     248   344.7   338.0  0.20  0.18
 0.193    5518  99.97   225.5   214.3  0.17  0.14     290   232.1   222.4  0.23  0.19
 0.270    6466 100.00   147.5   154.0  0.19  0.15     321   152.7   163.6  0.23  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1803   0.930    756   0.825   2559   0.899  0.953  0.9615  0.9728  0.8973  0.9411
  0.1161   3574   0.899    757   0.800   4331   0.882  0.999  0.9590  0.9680  0.9051  0.9486
  0.1931   4735   0.873    783   0.752   5518   0.855  1.006  0.9453  0.9570  0.8857  0.9359
  0.2701   5687   0.850    787   0.770   6474   0.841  0.902  0.9487  0.9527  0.9099  0.9255
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18882
Percentage observed                  =    99.9849
Percentage of free reflections       =     4.9962
Overall R factor                     =     0.1662
Free R factor                        =     0.2086
Average Fourier shell correlation    =     0.9602
AverageFree Fourier shell correlation=     0.9520
Overall weighted R factor            =     0.1523
Free weighted R factor               =     0.1848
Overall weighted R2 factor           =     0.1861
Free weighted R2 factor              =     0.2130
Average correlation coefficient      =     0.9360
Overall correlation coefficient      =     0.9572
Free correlation coefficient         =     0.9265
Cruickshanks DPI for coordinate error=     0.1214
DPI based on free R factor           =     0.1191
Overall figure of merit              =     0.8623
ML based su of positional parameters =     0.0740
ML based su of thermal parameters    =     2.3798
-----------------------------------------------------------------------------
  Time in seconds: CPU =        16.01
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1688   0.2114   0.851      100790.    5503.6   0.0123  0.894   1.781  1.027   0.086
       1   0.1679   0.2099   0.860      100357.    5494.5   0.0122  0.889   1.766  1.018   0.086
       2   0.1668   0.2090   0.862      100183.    5488.9   0.0127  0.924   1.787  1.030   0.087
       3   0.1665   0.2084   0.862      100118.    5485.8   0.0127  0.931   1.797  1.036   0.087
       4   0.1664   0.2082   0.862      100090.    5484.6   0.0128  0.934   1.802  1.038   0.087
       5   0.1663   0.2082   0.862      100072.    5483.9   0.0127  0.934   1.804  1.040   0.087
       6   0.1662   0.2081   0.863      100063.    5483.8   0.0127  0.935   1.806  1.040   0.086
       7   0.1662   0.2082   0.863      100060.    5483.8   0.0127  0.934   1.806  1.040   0.086
       8   0.1663   0.2084   0.862      100065.    5484.5   0.0127  0.934   1.807  1.041   0.086
       9   0.1663   0.2086   0.862      100067.    5484.8   0.0127  0.934   1.806  1.041   0.086
      10   0.1662   0.2086   0.862      100070.    5485.1   0.0127  0.934   1.806  1.041   0.086
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1688   0.1662
             R free    0.2114   0.2086
     Rms BondLength    0.0123   0.0127
      Rms BondAngle    1.7805   1.8062
     Rms ChirVolume    0.0855   0.0861
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      48.0s System:    0.1s Elapsed:     0:48