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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
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 User: maly  Run date: 26/ 5/2020 Run time: 17:41:48 


 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 1.60     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 5
  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_R05_1-70A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R05_1-60A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R05_1-60A.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       0.0977
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.6000
  Estimated number of reflections :      36894
  Free R exclusion - flag equals:     5
  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  1.6000

  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_R05_1-70A.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=   2.050 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=   2.202 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=   1.838 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=   2.227 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=   2.370 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=   2.393 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=   2.070 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                            5
Number of "free" reflections       1362
Number of   all  reflections      28041
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          28041

   Current auto weighting coefficient =    6.4996524    

 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.= 0.905 id.= 3.000 dev= -2.10 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        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Weight matrix   0.28195441    
 Actual weight    6.4996524      is applied to the X-ray term
Norm of X_ray positional gradient                38.8
Norm of Geom. positional gradient                79.0
Norm of X_ray B-factor gradient                  114.
Norm of Geom. B-factor gradient                 0.219E+05
Product of X_ray and Geom posit. gradients     -0.127E+08
 Cosine of angle between them                      -0.428
Product of X_ray and Geom B-fact gradients     -0.368E+08
 Cosine of angle between them                      -0.005


Residuals: XRAY=     0.8764E+06 GEOM=     0.2624E+05 TOTAL=     0.9026E+06
 function value    902605.75    

-------------------------------------------------------------------------------
             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     1.770     1.644
Bond angles  : others                          3242     2.340     1.582
Torsion angles, period  1. refined              184     6.996     5.000
Torsion angles, period  2. refined               90    36.500    22.778
Torsion angles, period  3. refined              268    14.005    15.000
Torsion angles, period  4. refined                9    13.218    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.014     0.020
VDW repulsions: refined_atoms                   308     0.266     0.200
VDW repulsions.others                          1350     0.229     0.200
VDW; torsion: refined_atoms                     723     0.173     0.200
VDW; torsion.others                             715     0.081     0.200
HBOND: refined_atoms                            216     0.199     0.200
HBOND.others                                      2     0.052     0.200
VDW repulsions: symmetry: refined_atoms           8     0.200     0.200
VDW repulsions: symmetry: others                 26     0.166     0.200
HBOND: symmetry: refined_atoms                   22     0.205     0.200
M. chain bond B values: refined atoms           745     1.626     1.390
M. chain bond B values: others                  745     1.623     1.391
M. chain angle B values: refined atoms          926     2.608     2.070
M. chain angle B values: others                 927     2.607     2.070
S. chain bond B values: refined atoms           811     2.936     1.786
S. chain bond B values: others                  810     2.930     1.785
S. chain angle B values: refined atoms         1177     4.600     2.513
S. chain angle B values: others                1178     4.598     2.513
Long range B values: refined atoms             1849     7.009    19.568
Long range B values: others                    1760     6.734    18.195
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =    1.2361
Partial structure    1: scale =     0.3869, B  =   48.2464
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3587 100.00   434.8   444.3  0.16  0.17     195   393.7   410.0  0.21  0.21
 0.147    6130  99.97   259.3   243.7  0.17  0.15     314   251.5   239.6  0.22  0.19
 0.244    7830 100.00   167.4   151.4  0.19  0.17     388   167.9   150.7  0.23  0.21
 0.342    9127 100.00    71.6    85.8  0.33  0.26     463    67.9    83.9  0.37  0.31
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2622   0.920    965   0.827   3587   0.895  0.948  0.9622  0.9720  0.9240  0.9367
  0.1468   5141   0.874    989   0.778   6130   0.859  1.020  0.9450  0.9593  0.8917  0.9392
  0.2444   6828   0.860   1002   0.748   7830   0.845  1.052  0.9408  0.9522  0.8871  0.9340
  0.3419   8148   0.662    983   0.582   9131   0.654  0.700  0.8417  0.8649  0.8207  0.8571
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26677
Percentage observed                  =    99.9893
Percentage of free reflections       =     4.8541
Overall R factor                     =     0.1936
Free R factor                        =     0.2374
Average Fourier shell correlation    =     0.9266
AverageFree Fourier shell correlation=     0.9111
Overall weighted R factor            =     0.1675
Free weighted R factor               =     0.2066
Overall weighted R2 factor           =     0.1977
Free weighted R2 factor              =     0.2366
Average correlation coefficient      =     0.9093
Overall correlation coefficient      =     0.9579
Free correlation coefficient         =     0.9374
Cruickshanks DPI for coordinate error=     0.0970
DPI based on free R factor           =     0.1013
Overall figure of merit              =     0.7895
ML based su of positional parameters =     0.0736
ML based su of thermal parameters    =     2.2256
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    134833.33       26236.018       902605.75      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.37586570    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    877525.06    

-------------------------------------------------------------------------------
             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 =     0.0441, B  =   -0.0498
Partial structure    1: scale =     0.3871, B  =   47.8330
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1931
Free R factor                        =     0.2373
Average Fourier shell correlation    =     0.9418
AverageFree Fourier shell correlation=     0.9283
Average correlation coefficient      =     0.9101
Overall figure of merit              =     0.8324
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    133520.30       9689.5693       877525.06       902605.75    


     CGMAT cycle number =      3

 Weight matrix   0.39267603    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    874786.94    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0157
Partial structure    1: scale =     0.3867, B  =   43.8254
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1921
Free R factor                        =     0.2366
Average Fourier shell correlation    =     0.9447
AverageFree Fourier shell correlation=     0.9308
Average correlation coefficient      =     0.9130
Overall figure of merit              =     0.8404
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    133163.27       9271.9912       874786.94       877525.06    


     CGMAT cycle number =      4

 Weight matrix   0.39563772    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    874006.06    

-------------------------------------------------------------------------------
             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 =     0.0441, B  =   -0.0040
Partial structure    1: scale =     0.3868, B  =   43.6521
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1919
Free R factor                        =     0.2360
Average Fourier shell correlation    =     0.9453
AverageFree Fourier shell correlation=     0.9312
Average correlation coefficient      =     0.9141
Overall figure of merit              =     0.8418
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    133056.97       9182.0293       874006.06       874786.94    


     CGMAT cycle number =      5

 Weight matrix   0.36068413    
 Actual weight    5.9087749      is applied to the X-ray term


 function value    795201.06    

-------------------------------------------------------------------------------
             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 =     0.0441, B  =    0.0010
Partial structure    1: scale =     0.3868, B  =   43.6629
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1919
Free R factor                        =     0.2357
Average Fourier shell correlation    =     0.9455
AverageFree Fourier shell correlation=     0.9313
Average correlation coefficient      =     0.9145
Overall figure of merit              =     0.8420
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    133016.83       9234.5615       795201.06       874006.06    


     CGMAT cycle number =      6

 Weight matrix   0.32764980    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    723639.81    

-------------------------------------------------------------------------------
             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 =     0.0442, B  =    0.0088
Partial structure    1: scale =     0.3868, B  =   43.6226
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1923
Free R factor                        =     0.2355
Average Fourier shell correlation    =     0.9454
AverageFree Fourier shell correlation=     0.9313
Average correlation coefficient      =     0.9143
Overall figure of merit              =     0.8421
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    133043.09       8983.7441       723639.81       795201.06    


     CGMAT cycle number =      7

 Weight matrix   0.32752880    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    723587.00    

-------------------------------------------------------------------------------
             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 =     0.0442, B  =    0.0002
Partial structure    1: scale =     0.3868, B  =   43.6125
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1928
Free R factor                        =     0.2354
Average Fourier shell correlation    =     0.9452
AverageFree Fourier shell correlation=     0.9312
Average correlation coefficient      =     0.9139
Overall figure of merit              =     0.8421
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    133095.39       8650.0225       723587.00       723639.81    


     CGMAT cycle number =      8

 Weight matrix   0.32670620    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    723664.75    

-------------------------------------------------------------------------------
             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 =     0.0441, B  =    0.0021
Partial structure    1: scale =     0.3865, B  =   43.4585
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1929
Free R factor                        =     0.2355
Average Fourier shell correlation    =     0.9451
AverageFree Fourier shell correlation=     0.9311
Average correlation coefficient      =     0.9138
Overall figure of merit              =     0.8419
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    133126.06       8567.4414       723712.81       723587.00    

 fvalues    133126.06       8567.4414       723671.63       723669.19    
 fvalues    133126.06       8567.4414       723671.63       723669.19    


     CGMAT cycle number =      9

 Weight matrix   0.32681769    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    723683.00    

-------------------------------------------------------------------------------
             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 =     0.0441, B  =    0.0009
Partial structure    1: scale =     0.3863, B  =   43.4182
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1929
Free R factor                        =     0.2355
Average Fourier shell correlation    =     0.9451
AverageFree Fourier shell correlation=     0.9311
Average correlation coefficient      =     0.9138
Overall figure of merit              =     0.8419
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    133131.67       8553.4131       723681.88       723669.19    
 fvalues    133131.67       8553.4131       723681.88       723685.31    


     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.= 0.912 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        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Weight matrix   0.32663935    
 Actual weight    5.3716135      is applied to the X-ray term
Norm of X_ray positional gradient                38.5
Norm of Geom. positional gradient                38.6
Norm of X_ray B-factor gradient                  108.
Norm of Geom. B-factor gradient                  108.
Product of X_ray and Geom posit. gradients     -0.144E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.377E+08
 Cosine of angle between them                      -0.999


Residuals: XRAY=     0.7152E+06 GEOM=      8536.     TOTAL=     0.7237E+06
 function value    723689.31    

-------------------------------------------------------------------------------
             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     1.768     1.644
Bond angles  : others                          3242     1.499     1.582
Torsion angles, period  1. refined              184     6.959     5.000
Torsion angles, period  2. refined               90    35.889    22.778
Torsion angles, period  3. refined              268    13.510    15.000
Torsion angles, period  4. refined                9    13.106    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   311     0.263     0.200
VDW repulsions.others                          1376     0.201     0.200
VDW; torsion: refined_atoms                     722     0.173     0.200
VDW; torsion.others                             780     0.084     0.200
HBOND: refined_atoms                            217     0.197     0.200
HBOND.others                                      2     0.097     0.200
VDW repulsions: symmetry: refined_atoms           9     0.183     0.200
VDW repulsions: symmetry: others                 25     0.176     0.200
HBOND: symmetry: refined_atoms                   21     0.195     0.200
M. chain bond B values: refined atoms           745     1.676     1.510
M. chain bond B values: others                  745     1.671     1.510
M. chain angle B values: refined atoms          926     2.660     2.252
M. chain angle B values: others                 927     2.659     2.252
S. chain bond B values: refined atoms           811     3.006     1.903
S. chain bond B values: others                  810     3.003     1.902
S. chain angle B values: refined atoms         1177     4.651     2.690
S. chain angle B values: others                1178     4.649     2.689
Long range B values: refined atoms             1853     7.310    21.101
Long range B values: others                    1762     7.038    19.695
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =    0.0016
Partial structure    1: scale =     0.3863, B  =   43.3510
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3587 100.00   434.9   444.6  0.17  0.18     195   393.8   410.1  0.21  0.21
 0.147    6130  99.97   259.4   243.7  0.17  0.15     314   251.5   239.5  0.21  0.18
 0.244    7830 100.00   167.5   151.4  0.19  0.17     388   168.0   151.5  0.23  0.21
 0.342    9127 100.00    71.6    85.5  0.32  0.25     463    67.9    83.7  0.37  0.31
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2622   0.929    965   0.842   3587   0.905  0.949  0.9643  0.9736  0.9235  0.9357
  0.1468   5141   0.882    989   0.788   6130   0.867  1.021  0.9476  0.9608  0.8945  0.9387
  0.2444   6828   0.876   1002   0.769   7830   0.862  1.055  0.9467  0.9579  0.8879  0.9355
  0.3419   8148   0.792    983   0.711   9131   0.783  0.758  0.8928  0.9124  0.8244  0.8698
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26677
Percentage observed                  =    99.9893
Percentage of free reflections       =     4.8541
Overall R factor                     =     0.1930
Free R factor                        =     0.2355
Average Fourier shell correlation    =     0.9451
AverageFree Fourier shell correlation=     0.9310
Overall weighted R factor            =     0.1684
Free weighted R factor               =     0.2050
Overall weighted R2 factor           =     0.1994
Free weighted R2 factor              =     0.2364
Average correlation coefficient      =     0.9138
Overall correlation coefficient      =     0.9579
Free correlation coefficient         =     0.9381
Cruickshanks DPI for coordinate error=     0.0967
DPI based on free R factor           =     0.1005
Overall figure of merit              =     0.8419
ML based su of positional parameters =     0.0621
ML based su of thermal parameters    =     1.8132
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    133135.97       8535.9883       723691.94       723685.31    

 fvalues    133135.97       8535.9883       723683.06       723690.94    
 fvalues    133135.97       8535.9883       723683.06       723690.94    

    ****                              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.= 0.912 id.= 3.000 dev= -2.09 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_R05_1-60A.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     1.767     1.644
Bond angles  : others                          3242     1.498     1.582
Torsion angles, period  1. refined              184     6.958     5.000
Torsion angles, period  2. refined               90    35.872    22.778
Torsion angles, period  3. refined              268    13.483    15.000
Torsion angles, period  4. refined                9    13.103    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   310     0.263     0.200
VDW repulsions.others                          1375     0.201     0.200
VDW; torsion: refined_atoms                     723     0.173     0.200
VDW; torsion.others                             780     0.084     0.200
HBOND: refined_atoms                            217     0.197     0.200
HBOND.others                                      2     0.098     0.200
VDW repulsions: symmetry: refined_atoms           9     0.183     0.200
VDW repulsions: symmetry: others                 25     0.176     0.200
HBOND: symmetry: refined_atoms                   21     0.195     0.200
M. chain bond B values: refined atoms           745     1.675     1.510
M. chain bond B values: others                  745     1.670     1.510
M. chain angle B values: refined atoms          926     2.658     2.252
M. chain angle B values: others                 927     2.657     2.252
S. chain bond B values: refined atoms           811     3.005     1.902
S. chain bond B values: others                  810     3.001     1.902
S. chain angle B values: refined atoms         1177     4.647     2.689
S. chain angle B values: others                1178     4.645     2.689
Long range B values: refined atoms             1853     7.308    21.107
Long range B values: others                    1762     7.036    19.701
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =    0.0022
Partial structure    1: scale =     0.3863, B  =   43.2281
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3587 100.00   434.9   444.6  0.17  0.18     195   393.8   410.1  0.21  0.21
 0.147    6130  99.97   259.4   243.7  0.17  0.15     314   251.5   239.5  0.21  0.18
 0.244    7830 100.00   167.5   151.4  0.19  0.17     388   168.0   151.5  0.23  0.21
 0.342    9127 100.00    71.6    85.5  0.32  0.25     463    67.9    83.7  0.37  0.31
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2622   0.929    965   0.842   3587   0.905  0.949  0.9643  0.9736  0.9235  0.9357
  0.1468   5141   0.882    989   0.788   6130   0.867  1.021  0.9476  0.9608  0.8944  0.9387
  0.2444   6828   0.876   1002   0.769   7830   0.862  1.055  0.9466  0.9579  0.8879  0.9355
  0.3419   8148   0.792    983   0.711   9131   0.783  0.758  0.8928  0.9124  0.8243  0.8698
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26677
Percentage observed                  =    99.9893
Percentage of free reflections       =     4.8541
Overall R factor                     =     0.1930
Free R factor                        =     0.2355
Average Fourier shell correlation    =     0.9451
AverageFree Fourier shell correlation=     0.9310
Overall weighted R factor            =     0.1684
Free weighted R factor               =     0.2050
Overall weighted R2 factor           =     0.1994
Free weighted R2 factor              =     0.2365
Average correlation coefficient      =     0.9138
Overall correlation coefficient      =     0.9579
Free correlation coefficient         =     0.9381
Cruickshanks DPI for coordinate error=     0.0967
DPI based on free R factor           =     0.1005
Overall figure of merit              =     0.8419
ML based su of positional parameters =     0.0621
ML based su of thermal parameters    =     1.8132
-----------------------------------------------------------------------------
  Time in seconds: CPU =        21.41
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1936   0.2374   0.789      134833.    7032.3   0.0122  0.917   1.770  1.028   0.087
       1   0.1931   0.2373   0.832      133520.    6988.2   0.0121  0.905   1.744  1.014   0.086
       2   0.1921   0.2366   0.840      133163.    6978.6   0.0133  0.995   1.797  1.047   0.090
       3   0.1919   0.2360   0.842      133057.    6975.6   0.0134  1.008   1.822  1.063   0.091
       4   0.1919   0.2357   0.842      133017.    6974.7   0.0135  1.012   1.837  1.071   0.091
       5   0.1923   0.2355   0.842      133043.    6974.0   0.0129  0.969   1.815  1.058   0.090
       6   0.1928   0.2354   0.842      133095.    6974.4   0.0123  0.924   1.780  1.037   0.087
       7   0.1929   0.2355   0.842      133125.    6975.8   0.0122  0.920   1.770  1.032   0.087
       8   0.1929   0.2355   0.842      133131.    6976.3   0.0122  0.919   1.769  1.031   0.087
       9   0.1930   0.2355   0.842      133136.    6976.5   0.0122  0.919   1.768  1.030   0.087
      10   0.1930   0.2355   0.842      133136.    6976.5   0.0122  0.918   1.767  1.030   0.087
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1936   0.1930
             R free    0.2374   0.2355
     Rms BondLength    0.0122   0.0122
      Rms BondAngle    1.7705   1.7669
     Rms ChirVolume    0.0870   0.0869
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      53.8s System:    0.1s Elapsed:     0:54