###############################################################
 ###############################################################
 ###############################################################
 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 26/ 5/2020 Run time: 20:13:03 


 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 1.50     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- bins 4
  Data line--- ncyc 10
  Data line--- monitor MEDIum
  Data line--- free 18
  Data line--- END

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN   Filename: CDO_R.mtz 

 LABIN FP=FP SIGFP=SIGFP FREE=FreeR_flag

    ****                     Input and Default parameters#                      ****


Input coordinate file.  Logical name - XYZIN actual file name  - CDO_complete_R18_1-60A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R18_1-50A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R18_1-50A.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       0.1111
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.5000
  Estimated number of reflections :      43652
  Free R exclusion - flag equals:    18
  Auto weighting. An attempt
  Refinement cycles       :    10
  Scaling type                           :
          Wilson scaling type with Guassians

  Estimation of D/Sigma in resolution bins
  using  free set of reflns with experimental sigmas
  using  free set of reflns with experimental sigmas

  Scaling and SigmaA resln:    41.9635  1.5000

  Damping factors:     1.0000  1.0000  1.0000


    ****                    Geometry restraints and weights                     ****


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

 Planar groups (all and main chain)
          WEIGHT= 1.00 1.00

 Chiral centers
          Weight= 1.00

 NON-BONDED CONTACTS
          Overall weight                          =  1.00
          Sigma for simple VDW                    =  0.20
          Sigma for VDW trhough torsion angle     =  0.20
          Sigma for HBOND                         =  0.20
          Sigma for metal-ion                     =  0.20
          Sigma for DUMMY and other atom          =  0.30
          Distance for donor-accepetor = vdw1+vdw2+(-0.30)
          Distance for acceptor - H    = vdw1+     ( 0.10)
          VDW distance through torsion = vdw1+vdw2+(-0.30)
          Distance for DUMMY-others    = vdw1+vdw2+(-0.70)

 TORSION ANGLES
          Weight= 1.00

 THERMAL FACTORS
          Weight= 1.00
     Main chain bond (1-2 neighbour)          1.5A**2
     Main chain angle (1-3 neighbour)         2.0A**2
     Side chain bond                          3.0A**2
     Side chain angle                         4.5A**2

 RESTRAINTS AGAINST EXCESSIVE SHIFTS
     Positional parameters                   0.00A
     Thermal parameters                      0.00A
     Occupancy parameters                    0.00

 RADIUS OF CONFIDENCE
     Positional parameters 0.00A
     Thermal parameters    0.00A**2
     Occupancy parameters  0.00

Monitoring style is "MEDIUM". Complete information will be printed out in the
first and last cycle. In all other cycles minimum information will be printed out
Sigma cutoffs for printing out outliers
If deviation of restraint parameter > alpha*sigma then information will be printed out
Distance outliers      10.000
Angle outliers         10.000
Torsion outliers       10.000
Chiral volume outliers 10.000
Plane outliers         10.000
Non-bonding outliers   10.000
B value  outliers      10.000
Rigid bond outliers    10.000
Sphericity outliers    10.000
---------------------------------------------------------------

 Input file :CDO_complete_R18_1-60A.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=   2.055 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=   2.185 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=   1.812 ideal_dist=   1.720
            ch:AAA  res:  93  CYS              at:SG  .->ch:AAA  res: 157  TYR              at:CE1 .
  INFO:     link is found (not be used) dist=   2.203 ideal_dist=   2.090
            ch:AAA  res: 140  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.383 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=   2.387 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=   2.115 ideal_dist=   1.870
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:OD  .
  --------------------------------
  --- title of input coord file ---

  PDB_code:xxxx
  PDB_name:----
  PDB_date:26-MAY-20
  --------------------------------
  ATTENTION: atom:OXT  THR               171  AAA  is missing in the structure
  ATTENTION: atom:OXT  PRO               190  AAA  is missing in the structure
  Number of chains                  :       4
  Total number of monomers          :     502
  Number of atoms                   :    3948
  Number of missing atoms           :       0
  Number of rebuilt atoms           :    1482
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0

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


 loop_
     _atom_type_symbol
     _atom_type_scat_Cromer_Mann_a1
     _atom_type_scat_Cromer_Mann_b1
     _atom_type_scat_Cromer_Mann_a2
     _atom_type_scat_Cromer_Mann_b2
     _atom_type_scat_Cromer_Mann_a3
     _atom_type_scat_Cromer_Mann_b3
     _atom_type_scat_Cromer_Mann_a4
     _atom_type_scat_Cromer_Mann_b4
     _atom_type_scat_Cromer_Mann_c


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


 Number of distances         :           0
 Number of angles            :           0
 Number of torsions          :           0
 Number of planes            :           0
 Number of chirals           :           0
 Number of intervals         :           0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
                        Standard  External       All
                Bonds:      2950         0      2950
               Angles:      5345         0      5345
              Chirals:       196         0       196
               Planes:       451         0       451
             Torsions:      1553         0      1553
            Intervals:         0         0         0
--------------------------------------------------------------------------------


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


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

FreeR flag                           18
Number of "free" reflections       1723
Number of   all  reflections      33910
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          33910

   Current auto weighting coefficient =    6.2496691    

 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.= 0.880 id.= 3.000 dev= -2.12 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        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Weight matrix   0.28241363    
 Actual weight    6.2496691      is applied to the X-ray term
Norm of X_ray positional gradient                38.1
Norm of Geom. positional gradient                82.2
Norm of X_ray B-factor gradient                  105.
Norm of Geom. B-factor gradient                 0.227E+05
Product of X_ray and Geom posit. gradients     -0.150E+08
 Cosine of angle between them                      -0.494
Product of X_ray and Geom B-fact gradients     -0.350E+08
 Cosine of angle between them                      -0.005


Residuals: XRAY=     0.9768E+06 GEOM=     0.2710E+05 TOTAL=     0.1004E+07
 function value    1003868.4    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.844     1.644
Bond angles  : others                          3242     2.355     1.582
Torsion angles, period  1. refined              184     6.910     5.000
Torsion angles, period  2. refined               90    35.760    22.778
Torsion angles, period  3. refined              268    13.009    15.000
Torsion angles, period  4. refined                9    11.709    15.000
Chiral centres: refined atoms                   196     0.091     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.016     0.020
VDW repulsions: refined_atoms                   309     0.268     0.200
VDW repulsions.others                          1334     0.233     0.200
VDW; torsion: refined_atoms                     728     0.173     0.200
VDW; torsion.others                             712     0.082     0.200
HBOND: refined_atoms                            217     0.203     0.200
HBOND.others                                      2     0.104     0.200
VDW repulsions: symmetry: refined_atoms          10     0.203     0.200
VDW repulsions: symmetry: others                 25     0.194     0.200
HBOND: symmetry: refined_atoms                   24     0.215     0.200
HBOND: symmetry: others                           1     0.012     0.200
M. chain bond B values: refined atoms           745     1.752     1.503
M. chain bond B values: others                  745     1.749     1.503
M. chain angle B values: refined atoms          926     2.716     2.242
M. chain angle B values: others                 927     2.715     2.242
S. chain bond B values: refined atoms           811     3.160     1.909
S. chain bond B values: others                  810     3.156     1.909
S. chain angle B values: refined atoms         1177     4.849     2.693
S. chain angle B values: others                1178     4.847     2.693
Long range B values: refined atoms             1854     7.441    21.000
Long range B values: others                    1761     7.100    19.541
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0455, B  =    1.1597
Partial structure    1: scale =     0.3900, B  =   46.0035
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.37 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4308 100.00   404.5   413.5  0.17  0.18     239   447.0   461.0  0.19  0.21
 0.167    7399  99.97   228.9   208.7  0.18  0.16     399   221.4   204.2  0.23  0.20
 0.278    9418 100.00   124.0   114.4  0.21  0.18     492   126.4   117.4  0.24  0.21
 0.389   11049 100.00    50.3    62.7  0.41  0.36     592    50.5    63.3  0.42  0.38
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3212   0.895   1096   0.785   4308   0.867  0.943  0.9641  0.9654  0.9149  0.9345
  0.1670   6290   0.876   1109   0.775   7399   0.861  1.060  0.9438  0.9590  0.8818  0.9366
  0.2780   8294   0.840   1124   0.760   9418   0.830  1.019  0.9395  0.9480  0.9069  0.9309
  0.3890   9946   0.506   1114   0.441  11060   0.499  0.512  0.7608  0.7586  0.7377  0.7750
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32185
Percentage observed                  =    99.9912
Percentage of free reflections       =     5.0814
Overall R factor                     =     0.2075
Free R factor                        =     0.2386
Average Fourier shell correlation    =     0.8878
AverageFree Fourier shell correlation=     0.8824
Overall weighted R factor            =     0.1757
Free weighted R factor               =     0.2095
Overall weighted R2 factor           =     0.2049
Free weighted R2 factor              =     0.2466
Average correlation coefficient      =     0.8791
Overall correlation coefficient      =     0.9589
Free correlation coefficient         =     0.9479
Cruickshanks DPI for coordinate error=     0.0861
DPI based on free R factor           =     0.0870
Overall figure of merit              =     0.7284
ML based su of positional parameters =     0.0721
ML based su of thermal parameters    =     2.1039
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    156290.77       27102.859       1003868.4      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.34302160    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    980109.13    

-------------------------------------------------------------------------------
             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 =     0.0455, B  =   -0.0666
Partial structure    1: scale =     0.3905, B  =   45.3168
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2078
Free R factor                        =     0.2387
Average Fourier shell correlation    =     0.9018
AverageFree Fourier shell correlation=     0.8972
Average correlation coefficient      =     0.8787
Overall figure of merit              =     0.7578
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    155253.09       9828.6582       980109.13       1003868.4    


     CGMAT cycle number =      3

 Weight matrix   0.35614264    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    977665.88    

-------------------------------------------------------------------------------
             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 =     0.0455, B  =   -0.0303
Partial structure    1: scale =     0.3915, B  =   40.8877
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2069
Free R factor                        =     0.2383
Average Fourier shell correlation    =     0.9061
AverageFree Fourier shell correlation=     0.9012
Average correlation coefficient      =     0.8803
Overall figure of merit              =     0.7664
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    154978.94       9098.8164       977665.88       980109.13    


     CGMAT cycle number =      4

 Weight matrix   0.35980076    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    976958.88    

-------------------------------------------------------------------------------
             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 =     0.0455, B  =   -0.0155
Partial structure    1: scale =     0.3919, B  =   39.1329
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2067
Free R factor                        =     0.2381
Average Fourier shell correlation    =     0.9074
AverageFree Fourier shell correlation=     0.9025
Average correlation coefficient      =     0.8810
Overall figure of merit              =     0.7693
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    154901.75       8874.2100       976958.88       977665.88    


     CGMAT cycle number =      5

 Weight matrix   0.36068761    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    976777.69    

-------------------------------------------------------------------------------
             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 =     0.0455, B  =   -0.0031
Partial structure    1: scale =     0.3919, B  =   39.0195
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2066
Free R factor                        =     0.2379
Average Fourier shell correlation    =     0.9077
AverageFree Fourier shell correlation=     0.9027
Average correlation coefficient      =     0.8813
Overall figure of merit              =     0.7700
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    154873.89       8867.1172       976777.69       976958.88    


     CGMAT cycle number =      6

 Weight matrix   0.36098474    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    976732.50    

-------------------------------------------------------------------------------
             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 =     0.0455, B  =    0.0024
Partial structure    1: scale =     0.3923, B  =   38.9789
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2065
Free R factor                        =     0.2377
Average Fourier shell correlation    =     0.9078
AverageFree Fourier shell correlation=     0.9028
Average correlation coefficient      =     0.8814
Overall figure of merit              =     0.7701
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    154863.39       8887.5693       976732.50       976777.69    


     CGMAT cycle number =      7

 Weight matrix   0.36120856    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    976723.88    

-------------------------------------------------------------------------------
             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 =     0.0455, B  =    0.0000
Partial structure    1: scale =     0.3923, B  =   38.9789
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2065
Free R factor                        =     0.2377
Average Fourier shell correlation    =     0.9078
AverageFree Fourier shell correlation=     0.9028
Average correlation coefficient      =     0.8815
Overall figure of merit              =     0.7702
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    154860.92       8894.3457       976723.88       976732.50    


     CGMAT cycle number =      8

 Weight matrix   0.36091173    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    976754.19    

-------------------------------------------------------------------------------
             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 =     0.0455, B  =    0.0004
Partial structure    1: scale =     0.3923, B  =   38.9706
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2065
Free R factor                        =     0.2377
Average Fourier shell correlation    =     0.9078
AverageFree Fourier shell correlation=     0.9027
Average correlation coefficient      =     0.8815
Overall figure of merit              =     0.7701
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    154864.69       8899.3174       976763.00       976723.88    

 fvalues    154864.69       8899.3174       976759.38       976752.38    
 fvalues    154864.69       8899.3174       976759.38       976752.38    


     CGMAT cycle number =      9

 Weight matrix   0.36067757    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    976765.25    

-------------------------------------------------------------------------------
             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 =     0.0455, B  =    0.0031
Partial structure    1: scale =     0.3925, B  =   38.9947
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2065
Free R factor                        =     0.2377
Average Fourier shell correlation    =     0.9077
AverageFree Fourier shell correlation=     0.9027
Average correlation coefficient      =     0.8815
Overall figure of merit              =     0.7700
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    154866.27       8896.6670       976756.13       976752.38    
 fvalues    154866.27       8896.6670       976756.13       976759.63    


     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.= 0.897 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        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Weight matrix   0.36066580    
 Actual weight    6.2496691      is applied to the X-ray term
Norm of X_ray positional gradient                43.4
Norm of Geom. positional gradient                43.5
Norm of X_ray B-factor gradient                  109.
Norm of Geom. B-factor gradient                  108.
Product of X_ray and Geom posit. gradients     -0.183E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.379E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.9679E+06 GEOM=      8894.     TOTAL=     0.9768E+06
 function value    976763.19    

-------------------------------------------------------------------------------
             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     1.838     1.644
Bond angles  : others                          3242     1.505     1.582
Torsion angles, period  1. refined              184     6.898     5.000
Torsion angles, period  2. refined               90    35.515    22.778
Torsion angles, period  3. refined              268    12.939    15.000
Torsion angles, period  4. refined                9    11.891    15.000
Chiral centres: refined atoms                   196     0.092     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   311     0.268     0.200
VDW repulsions.others                          1361     0.204     0.200
VDW; torsion: refined_atoms                     724     0.173     0.200
VDW; torsion.others                             790     0.083     0.200
HBOND: refined_atoms                            218     0.200     0.200
HBOND.others                                      2     0.110     0.200
VDW repulsions: symmetry: refined_atoms          10     0.204     0.200
VDW repulsions: symmetry: others                 24     0.183     0.200
HBOND: symmetry: refined_atoms                   20     0.249     0.200
HBOND: symmetry: others                           1     0.019     0.200
M. chain bond B values: refined atoms           745     1.811     1.616
M. chain bond B values: others                  745     1.807     1.616
M. chain angle B values: refined atoms          926     2.786     2.412
M. chain angle B values: others                 927     2.784     2.411
S. chain bond B values: refined atoms           811     3.243     2.030
S. chain bond B values: others                  810     3.239     2.030
S. chain angle B values: refined atoms         1177     4.959     2.874
S. chain angle B values: others                1178     4.957     2.873
Long range B values: refined atoms             1853     7.510    22.444
Long range B values: others                    1756     7.201    20.854
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0455, B  =    0.0026
Partial structure    1: scale =     0.3924, B  =   38.9824
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4308 100.00   404.8   413.6  0.17  0.18     239   447.4   461.3  0.19  0.21
 0.167    7399  99.97   229.1   208.9  0.18  0.16     399   221.6   204.1  0.23  0.20
 0.278    9418 100.00   124.2   114.6  0.21  0.18     492   126.5   117.5  0.24  0.21
 0.389   11049 100.00    50.3    62.7  0.41  0.36     592    50.5    63.5  0.42  0.38
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3212   0.916   1096   0.818   4308   0.891  0.947  0.9685  0.9708  0.9152  0.9348
  0.1670   6290   0.886   1109   0.787   7399   0.871  1.062  0.9462  0.9616  0.8820  0.9373
  0.2780   8294   0.852   1124   0.774   9418   0.843  1.021  0.9454  0.9533  0.9082  0.9314
  0.3890   9946   0.599   1114   0.536  11060   0.593  0.557  0.8114  0.8083  0.7378  0.7807
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32185
Percentage observed                  =    99.9912
Percentage of free reflections       =     5.0814
Overall R factor                     =     0.2065
Free R factor                        =     0.2377
Average Fourier shell correlation    =     0.9077
AverageFree Fourier shell correlation=     0.9026
Overall weighted R factor            =     0.1749
Free weighted R factor               =     0.2086
Overall weighted R2 factor           =     0.2038
Free weighted R2 factor              =     0.2461
Average correlation coefficient      =     0.8815
Overall correlation coefficient      =     0.9592
Free correlation coefficient         =     0.9481
Cruickshanks DPI for coordinate error=     0.0857
DPI based on free R factor           =     0.0866
Overall figure of merit              =     0.7700
ML based su of positional parameters =     0.0637
ML based su of thermal parameters    =     1.8376
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    154867.20       8894.3184       976773.44       976759.63    

 fvalues    154867.20       8894.3184       976780.50       976763.06    
 fvalues    154867.20       8894.3184       976780.50       976763.06    

    ****                              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.= 0.897 id.= 3.000 dev= -2.10 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 LABOUT FreeR_flag=FreeR_flag FP=FP SIGFP=SIGFP FC=FC PHIC=PHIC FC_ALL=FC_ALL PHIC_ALL=PHIC_ALL FWT=FWT PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM FC_ALL_LS=FC_ALL_LS PHIC_ALL_LS=PHIC_ALL_LS

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R18_1-50A.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     1.838     1.644
Bond angles  : others                          3242     1.505     1.582
Torsion angles, period  1. refined              184     6.899     5.000
Torsion angles, period  2. refined               90    35.513    22.778
Torsion angles, period  3. refined              268    12.939    15.000
Torsion angles, period  4. refined                9    11.892    15.000
Chiral centres: refined atoms                   196     0.092     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   311     0.268     0.200
VDW repulsions.others                          1363     0.204     0.200
VDW; torsion: refined_atoms                     724     0.173     0.200
VDW; torsion.others                             790     0.084     0.200
HBOND: refined_atoms                            218     0.200     0.200
HBOND.others                                      2     0.110     0.200
VDW repulsions: symmetry: refined_atoms          10     0.204     0.200
VDW repulsions: symmetry: others                 24     0.183     0.200
HBOND: symmetry: refined_atoms                   20     0.250     0.200
HBOND: symmetry: others                           1     0.019     0.200
M. chain bond B values: refined atoms           745     1.811     1.616
M. chain bond B values: others                  745     1.807     1.616
M. chain angle B values: refined atoms          926     2.786     2.412
M. chain angle B values: others                 927     2.785     2.411
S. chain bond B values: refined atoms           811     3.243     2.030
S. chain bond B values: others                  810     3.239     2.030
S. chain angle B values: refined atoms         1177     4.960     2.874
S. chain angle B values: others                1178     4.957     2.873
Long range B values: refined atoms             1853     7.510    22.444
Long range B values: others                    1756     7.201    20.854
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0455, B  =    0.0022
Partial structure    1: scale =     0.3924, B  =   38.9684
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4308 100.00   404.8   413.6  0.17  0.18     239   447.4   461.3  0.19  0.21
 0.167    7399  99.97   229.1   208.9  0.18  0.16     399   221.6   204.1  0.23  0.20
 0.278    9418 100.00   124.2   114.6  0.21  0.18     492   126.5   117.5  0.24  0.21
 0.389   11049 100.00    50.3    62.7  0.41  0.36     592    50.5    63.5  0.42  0.38
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3212   0.916   1096   0.818   4308   0.891  0.947  0.9684  0.9708  0.9152  0.9348
  0.1670   6290   0.886   1109   0.787   7399   0.871  1.062  0.9462  0.9616  0.8819  0.9373
  0.2780   8294   0.852   1124   0.774   9418   0.843  1.021  0.9454  0.9533  0.9082  0.9314
  0.3890   9946   0.599   1114   0.536  11060   0.593  0.557  0.8114  0.8083  0.7377  0.7807
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32185
Percentage observed                  =    99.9912
Percentage of free reflections       =     5.0814
Overall R factor                     =     0.2065
Free R factor                        =     0.2377
Average Fourier shell correlation    =     0.9077
AverageFree Fourier shell correlation=     0.9026
Overall weighted R factor            =     0.1749
Free weighted R factor               =     0.2087
Overall weighted R2 factor           =     0.2038
Free weighted R2 factor              =     0.2461
Average correlation coefficient      =     0.8815
Overall correlation coefficient      =     0.9592
Free correlation coefficient         =     0.9480
Cruickshanks DPI for coordinate error=     0.0857
DPI based on free R factor           =     0.0867
Overall figure of merit              =     0.7700
ML based su of positional parameters =     0.0637
ML based su of thermal parameters    =     1.8376
-----------------------------------------------------------------------------
  Time in seconds: CPU =        25.97
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2075   0.2386   0.728      156291.    8572.3   0.0133  0.999   1.844  1.077   0.091
       1   0.2078   0.2387   0.758      155253.    8535.5   0.0122  0.918   1.777  1.037   0.089
       2   0.2069   0.2383   0.766      154979.    8525.4   0.0131  0.985   1.809  1.056   0.091
       3   0.2067   0.2381   0.769      154902.    8522.3   0.0132  0.994   1.823  1.065   0.092
       4   0.2066   0.2379   0.770      154874.    8520.9   0.0133  0.997   1.830  1.069   0.092
       5   0.2065   0.2377   0.770      154863.    8520.6   0.0133  0.998   1.834  1.072   0.092
       6   0.2065   0.2377   0.770      154861.    8520.7   0.0133  0.998   1.836  1.073   0.092
       7   0.2065   0.2377   0.770      154865.    8521.4   0.0133  0.999   1.838  1.074   0.092
       8   0.2065   0.2377   0.770      154867.    8521.4   0.0133  0.998   1.838  1.074   0.092
       9   0.2065   0.2377   0.770      154867.    8521.6   0.0133  0.998   1.838  1.074   0.092
      10   0.2065   0.2377   0.770      154869.    8521.7   0.0133  0.998   1.838  1.074   0.092
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2075   0.2065
             R free    0.2386   0.2377
     Rms BondLength    0.0133   0.0133
      Rms BondAngle    1.8441   1.8378
     Rms ChirVolume    0.0910   0.0924
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      58.5s System:    0.2s Elapsed:     0:58