###############################################################
 ###############################################################
 ###############################################################
 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 26/ 5/2020 Run time: 20:17:54 


 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 19
  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_R19_1-60A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R19_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_R19_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:    19
  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_R19_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=   2.054 ideal_dist=   2.090
            ch:AAA  res:  86  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.196 ideal_dist=   2.090
            ch:AAA  res:  88  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   1.832 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=   2.213 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=   2.398 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=   2.394 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=   2.090 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                           19
Number of "free" reflections       1721
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.= 0.900 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   0.29104373    
 Actual weight    6.2496691      is applied to the X-ray term
Norm of X_ray positional gradient                39.2
Norm of Geom. positional gradient                79.6
Norm of X_ray B-factor gradient                  110.
Norm of Geom. B-factor gradient                 0.219E+05
Product of X_ray and Geom posit. gradients     -0.138E+08
 Cosine of angle between them                      -0.455
Product of X_ray and Geom B-fact gradients     -0.343E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.9762E+06 GEOM=     0.2604E+05 TOTAL=     0.1002E+07
 function value    1002286.1    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.781     1.644
Bond angles  : others                          3242     2.340     1.582
Torsion angles, period  1. refined              184     6.860     5.000
Torsion angles, period  2. refined               90    36.147    22.778
Torsion angles, period  3. refined              268    13.168    15.000
Torsion angles, period  4. refined                9    11.345    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.017     0.020
VDW repulsions: refined_atoms                   318     0.263     0.200
VDW repulsions.others                          1358     0.229     0.200
VDW; torsion: refined_atoms                     725     0.173     0.200
VDW; torsion.others                             724     0.081     0.200
HBOND: refined_atoms                            228     0.188     0.200
HBOND.others                                      1     0.022     0.200
VDW repulsions: symmetry: refined_atoms           9     0.204     0.200
VDW repulsions: symmetry: others                 27     0.176     0.200
HBOND: symmetry: refined_atoms                   21     0.224     0.200
HBOND: symmetry: others                           1     0.041     0.200
M. chain bond B values: refined atoms           745     1.674     1.507
M. chain bond B values: others                  745     1.670     1.507
M. chain angle B values: refined atoms          926     2.626     2.247
M. chain angle B values: others                 927     2.625     2.247
S. chain bond B values: refined atoms           811     2.983     1.899
S. chain bond B values: others                  810     2.977     1.899
S. chain angle B values: refined atoms         1177     4.572     2.686
S. chain angle B values: others                1178     4.570     2.685
Long range B values: refined atoms             1873     7.383    21.413
Long range B values: others                    1781     7.138    19.956
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    1.1669
Partial structure    1: scale =     0.3928, B  =   46.0323
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    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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4321 100.00   405.3   415.0  0.17  0.18     226   420.5   428.9  0.21  0.21
 0.167    7421  99.97   227.9   207.8  0.18  0.16     377   234.6   217.0  0.21  0.18
 0.278    9403 100.00   123.8   114.0  0.21  0.19     507   127.1   118.7  0.25  0.21
 0.389   11030 100.00    50.2    62.6  0.41  0.36     611    50.3    62.0  0.41  0.37
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3223   0.901   1098   0.794   4321   0.874  0.942  0.9623  0.9664  0.9157  0.9324
  0.1670   6307   0.885   1114   0.779   7421   0.869  1.064  0.9540  0.9612  0.9093  0.9369
  0.2780   8289   0.832   1114   0.747   9403   0.822  1.017  0.9323  0.9435  0.8838  0.9285
  0.3890   9917   0.572   1125   0.500  11042   0.565  0.573  0.7667  0.7746  0.7501  0.7713
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32187
Percentage observed                  =    99.9912
Percentage of free reflections       =     5.0755
Overall R factor                     =     0.2086
Free R factor                        =     0.2410
Average Fourier shell correlation    =     0.8927
AverageFree Fourier shell correlation=     0.8822
Overall weighted R factor            =     0.1775
Free weighted R factor               =     0.2052
Overall weighted R2 factor           =     0.2075
Free weighted R2 factor              =     0.2282
Average correlation coefficient      =     0.8771
Overall correlation coefficient      =     0.9582
Free correlation coefficient         =     0.9468
Cruickshanks DPI for coordinate error=     0.0866
DPI based on free R factor           =     0.0878
Overall figure of merit              =     0.7515
ML based su of positional parameters =     0.0710
ML based su of thermal parameters    =     2.0800
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    156207.33       26042.004       1002286.1      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.35259274    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    979924.63    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =   -0.0428
Partial structure    1: scale =     0.3926, B  =   45.6250
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                     =     0.2083
Free R factor                        =     0.2404
Average Fourier shell correlation    =     0.9032
AverageFree Fourier shell correlation=     0.8924
Average correlation coefficient      =     0.8778
Overall figure of merit              =     0.7701
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    155242.33       9711.4150       979924.63       1002286.1    


     CGMAT cycle number =      3

 Weight matrix   0.35875595    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    978136.94    

-------------------------------------------------------------------------------
             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 =     0.0456, B  =   -0.0017
Partial structure    1: scale =     0.3945, B  =   41.5611
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                     =     0.2072
Free R factor                        =     0.2400
Average Fourier shell correlation    =     0.9042
AverageFree Fourier shell correlation=     0.8930
Average correlation coefficient      =     0.8794
Overall figure of merit              =     0.7700
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    155048.81       9133.1807       978136.94       979924.63    


     CGMAT cycle number =      4

 Weight matrix   0.36583051    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    976989.06    

-------------------------------------------------------------------------------
             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 =     0.0456, B  =    0.0026
Partial structure    1: scale =     0.3946, B  =   40.0848
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                     =     0.2070
Free R factor                        =     0.2398
Average Fourier shell correlation    =     0.9074
AverageFree Fourier shell correlation=     0.8960
Average correlation coefficient      =     0.8800
Overall figure of merit              =     0.7793
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    154894.38       8950.4961       976989.06       978136.94    


     CGMAT cycle number =      5

 Weight matrix   0.32988876    
 Actual weight    5.6815171      is applied to the X-ray term


 function value    889200.13    

-------------------------------------------------------------------------------
             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 =     0.0456, B  =    0.0002
Partial structure    1: scale =     0.3946, B  =   40.0833
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                     =     0.2068
Free R factor                        =     0.2397
Average Fourier shell correlation    =     0.9057
AverageFree Fourier shell correlation=     0.8942
Average correlation coefficient      =     0.8803
Overall figure of merit              =     0.7737
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    154929.34       8966.3477       889200.13       976989.06    


     CGMAT cycle number =      6

 Weight matrix   0.29756430    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    809353.69    

-------------------------------------------------------------------------------
             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 =     0.0456, B  =    0.0021
Partial structure    1: scale =     0.3948, B  =   40.0432
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                     =     0.2072
Free R factor                        =     0.2399
Average Fourier shell correlation    =     0.9045
AverageFree Fourier shell correlation=     0.8931
Average correlation coefficient      =     0.8800
Overall figure of merit              =     0.7702
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    155012.63       8711.1152       809353.69       889200.13    


     CGMAT cycle number =      7

 Weight matrix   0.29647657    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    809534.19    

-------------------------------------------------------------------------------
             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 =     0.0456, B  =    0.0012
Partial structure    1: scale =     0.3947, B  =   39.9480
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                     =     0.2076
Free R factor                        =     0.2402
Average Fourier shell correlation    =     0.9040
AverageFree Fourier shell correlation=     0.8927
Average correlation coefficient      =     0.8794
Overall figure of merit              =     0.7692
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    155112.28       8382.6074       809591.38       809353.69    

 fvalues    155112.28       8382.6074       809573.38       809539.94    
 fvalues    155112.28       8382.6074       809573.38       809539.94    


     CGMAT cycle number =      8

 Weight matrix   0.29630533    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    809573.81    

-------------------------------------------------------------------------------
             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 =     0.0456, B  =   -0.0002
Partial structure    1: scale =     0.3948, B  =   39.9531
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                     =     0.2076
Free R factor                        =     0.2402
Average Fourier shell correlation    =     0.9040
AverageFree Fourier shell correlation=     0.8927
Average correlation coefficient      =     0.8794
Overall figure of merit              =     0.7691
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    155125.38       8359.3359       809581.63       809539.94    
 fvalues    155125.38       8359.3359       809581.63       809584.25    


     CGMAT cycle number =      9

 Weight matrix   0.29622039    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    809590.75    

-------------------------------------------------------------------------------
             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 =     0.0456, B  =    0.0007
Partial structure    1: scale =     0.3949, B  =   39.9737
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                     =     0.2076
Free R factor                        =     0.2403
Average Fourier shell correlation    =     0.9040
AverageFree Fourier shell correlation=     0.8927
Average correlation coefficient      =     0.8794
Overall figure of merit              =     0.7691
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    155132.25       8332.7832       809590.94       809584.25    
 fvalues    155132.25       8332.7832       809590.94       809593.25    


     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.= 0.918 id.= 3.000 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   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   0.29632977    
 Actual weight    5.1650152      is applied to the X-ray term
Norm of X_ray positional gradient                37.6
Norm of Geom. positional gradient                37.8
Norm of X_ray B-factor gradient                  98.4
Norm of Geom. B-factor gradient                  99.4
Product of X_ray and Geom posit. gradients     -0.138E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.316E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.8013E+06 GEOM=      8306.     TOTAL=     0.8096E+06
 function value    809579.31    

-------------------------------------------------------------------------------
             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     1.772     1.644
Bond angles  : others                          3242     1.504     1.582
Torsion angles, period  1. refined              184     6.865     5.000
Torsion angles, period  2. refined               90    36.004    22.778
Torsion angles, period  3. refined              268    13.044    15.000
Torsion angles, period  4. refined                9    11.540    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   315     0.263     0.200
VDW repulsions.others                          1364     0.203     0.200
VDW; torsion: refined_atoms                     728     0.172     0.200
VDW; torsion.others                             775     0.083     0.200
HBOND: refined_atoms                            226     0.187     0.200
HBOND.others                                      1     0.039     0.200
VDW repulsions: symmetry: refined_atoms           9     0.201     0.200
VDW repulsions: symmetry: others                 31     0.150     0.200
HBOND: symmetry: refined_atoms                   19     0.235     0.200
HBOND: symmetry: others                           1     0.047     0.200
M. chain bond B values: refined atoms           745     1.720     1.620
M. chain bond B values: others                  745     1.716     1.620
M. chain angle B values: refined atoms          926     2.677     2.417
M. chain angle B values: others                 927     2.676     2.416
S. chain bond B values: refined atoms           811     3.061     2.021
S. chain bond B values: others                  810     3.055     2.020
S. chain angle B values: refined atoms         1177     4.684     2.865
S. chain angle B values: others                1178     4.682     2.865
Long range B values: refined atoms             1869     7.499    22.770
Long range B values: others                    1779     7.266    21.297
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    0.0011
Partial structure    1: scale =     0.3948, B  =   39.9047
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4321 100.00   405.6   415.3  0.17  0.18     226   420.7   428.9  0.21  0.21
 0.167    7421  99.97   228.0   208.0  0.18  0.16     377   234.8   217.3  0.21  0.18
 0.278    9403 100.00   123.9   114.2  0.21  0.19     507   127.2   118.7  0.24  0.21
 0.389   11030 100.00    50.2    62.6  0.41  0.36     611    50.4    62.0  0.41  0.37
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3223   0.916   1098   0.821   4321   0.892  0.945  0.9662  0.9701  0.9161  0.9320
  0.1670   6307   0.897   1114   0.795   7421   0.882  1.066  0.9567  0.9643  0.9098  0.9383
  0.2780   8289   0.849   1114   0.766   9403   0.839  1.019  0.9387  0.9493  0.8867  0.9285
  0.3890   9917   0.592   1125   0.525  11042   0.585  0.574  0.7880  0.7990  0.7503  0.7771
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32187
Percentage observed                  =    99.9912
Percentage of free reflections       =     5.0755
Overall R factor                     =     0.2077
Free R factor                        =     0.2402
Average Fourier shell correlation    =     0.9040
AverageFree Fourier shell correlation=     0.8928
Overall weighted R factor            =     0.1769
Free weighted R factor               =     0.2043
Overall weighted R2 factor           =     0.2070
Free weighted R2 factor              =     0.2264
Average correlation coefficient      =     0.8793
Overall correlation coefficient      =     0.9584
Free correlation coefficient         =     0.9473
Cruickshanks DPI for coordinate error=     0.0862
DPI based on free R factor           =     0.0876
Overall figure of merit              =     0.7692
ML based su of positional parameters =     0.0639
ML based su of thermal parameters    =     1.8640
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    155134.70       8306.1572       809579.31       809593.25    

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.919 id.= 3.000 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 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_R19_1-50A.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     1.769     1.644
Bond angles  : others                          3242     1.503     1.582
Torsion angles, period  1. refined              184     6.865     5.000
Torsion angles, period  2. refined               90    35.997    22.778
Torsion angles, period  3. refined              268    13.034    15.000
Torsion angles, period  4. refined                9    11.530    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   314     0.263     0.200
VDW repulsions.others                          1366     0.202     0.200
VDW; torsion: refined_atoms                     728     0.172     0.200
VDW; torsion.others                             777     0.083     0.200
HBOND: refined_atoms                            226     0.186     0.200
HBOND.others                                      1     0.039     0.200
VDW repulsions: symmetry: refined_atoms           9     0.201     0.200
VDW repulsions: symmetry: others                 31     0.149     0.200
HBOND: symmetry: refined_atoms                   20     0.230     0.200
HBOND: symmetry: others                           1     0.047     0.200
M. chain bond B values: refined atoms           745     1.716     1.620
M. chain bond B values: others                  745     1.713     1.620
M. chain angle B values: refined atoms          926     2.673     2.417
M. chain angle B values: others                 927     2.672     2.417
S. chain bond B values: refined atoms           811     3.055     2.020
S. chain bond B values: others                  810     3.049     2.020
S. chain angle B values: refined atoms         1177     4.675     2.865
S. chain angle B values: others                1178     4.673     2.864
Long range B values: refined atoms             1868     7.493    22.748
Long range B values: others                    1778     7.258    21.273
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    0.0002
Partial structure    1: scale =     0.3948, B  =   39.9006
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4321 100.00   405.6   415.3  0.17  0.18     226   420.7   429.0  0.21  0.21
 0.167    7421  99.97   228.0   208.0  0.18  0.16     377   234.8   217.4  0.21  0.18
 0.278    9403 100.00   123.9   114.2  0.21  0.19     507   127.2   118.7  0.24  0.21
 0.389   11030 100.00    50.2    62.6  0.41  0.36     611    50.4    62.0  0.41  0.37
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3223   0.917   1098   0.821   4321   0.892  0.945  0.9662  0.9701  0.9161  0.9320
  0.1670   6307   0.897   1114   0.795   7421   0.882  1.066  0.9567  0.9643  0.9096  0.9383
  0.2780   8289   0.849   1114   0.766   9403   0.839  1.019  0.9387  0.9492  0.8867  0.9284
  0.3890   9917   0.592   1125   0.525  11042   0.585  0.574  0.7881  0.7990  0.7504  0.7770
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32187
Percentage observed                  =    99.9912
Percentage of free reflections       =     5.0755
Overall R factor                     =     0.2077
Free R factor                        =     0.2404
Average Fourier shell correlation    =     0.9040
AverageFree Fourier shell correlation=     0.8928
Overall weighted R factor            =     0.1769
Free weighted R factor               =     0.2043
Overall weighted R2 factor           =     0.2070
Free weighted R2 factor              =     0.2263
Average correlation coefficient      =     0.8793
Overall correlation coefficient      =     0.9584
Free correlation coefficient         =     0.9473
Cruickshanks DPI for coordinate error=     0.0862
DPI based on free R factor           =     0.0876
Overall figure of merit              =     0.7692
ML based su of positional parameters =     0.0639
ML based su of thermal parameters    =     1.8640
-----------------------------------------------------------------------------
  Time in seconds: CPU =        26.01
             Elapsed =           0.00

    ****           Things for loggraph, R factor and others vs cycle            ****


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS: vs cycle :N:1,2,3:
:FOM vs cycle :N:1,4:
:-LL vs cycle :N:1,5:
:-LLfree vs cycle :N:1,6:
:Geometry vs cycle:N:1,7,8,9,10,11:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2086   0.2410   0.751      156207.    8530.2   0.0122  0.923   1.781  1.034   0.088
       1   0.2083   0.2404   0.770      155242.    8499.1   0.0121  0.913   1.761  1.022   0.089
       2   0.2072   0.2400   0.770      155049.    8494.4   0.0131  0.991   1.810  1.051   0.091
       3   0.2070   0.2398   0.779      154894.    8487.0   0.0133  1.000   1.832  1.063   0.092
       4   0.2068   0.2397   0.774      154929.    8489.2   0.0133  1.005   1.842  1.069   0.092
       5   0.2072   0.2399   0.770      155013.    8491.6   0.0127  0.961   1.818  1.054   0.091
       6   0.2076   0.2402   0.769      155111.    8494.2   0.0121  0.916   1.782  1.033   0.088
       7   0.2076   0.2402   0.769      155123.    8494.7   0.0121  0.915   1.779  1.032   0.088
       8   0.2076   0.2403   0.769      155132.    8495.0   0.0121  0.913   1.776  1.030   0.088
       9   0.2077   0.2402   0.769      155135.    8494.8   0.0121  0.911   1.772  1.028   0.088
      10   0.2077   0.2404   0.769      155139.    8494.7   0.0120  0.910   1.769  1.026   0.088
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2086   0.2077
             R free    0.2410   0.2404
     Rms BondLength    0.0122   0.0120
      Rms BondAngle    1.7809   1.7694
     Rms ChirVolume    0.0883   0.0880
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      58.0s System:    0.2s Elapsed:     0:58