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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 26/ 5/2020 Run time: 18:40:54 


 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 1.60     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- bins 4
  Data line--- ncyc 10
  Data line--- monitor MEDIum
  Data line--- free 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_1-70A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R19_1-60A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R19_1-60A.mtz

Cell from mtz :    57.632    57.632   122.391    90.000    90.000    90.000
Space group from mtz: number -   96; name - P 43 21 2

  Refinement type                        : Restrained

    ****                           Makecif parameters                           ****

Dictionary files for restraints : /protein2/ccp4/ccp4-7.0/ccp4-7.0/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /protein2/ccp4/ccp4-7.0/ccp4-7.0/lib/data/monomers/ener_lib.cif
    Program will rely on residue and atom names. No checking
    If this option is used then monomers should be checked carefully before using
    Hydrogens will be restored in their riding positions
    Links between monomers will be checked. Only those links present in the coordinate file will be used
    Standard sugar links will be analysed and used
    For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
    Symmetry related links will be analysed and used
    Cis peptides will be found and used automatically


  Residual                               : Rice Maximum Likelihood for Fs

    ****                    Least-square scaling parameters                     ****

Overall scale
Overall B value
Overall anisotropic B with tr(B) = 0.0
Constant bulk solvent in non protein region
Probe radii for non-ions     1.200
Probe radii for ions         0.800
Shrinkage of the mask  by    0.800


    ****                 Map sharpening parameters and methods                  ****

No map sharpening will be performed

  Method of minimisation                 : Sparse Matrix
  Experimental sigmas used for weighting
  Number of Bins and width:     4       0.0977
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.6000
  Estimated number of reflections :      36894
  Free R exclusion - flag equals:    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  1.6000

  Damping factors:     1.0000  1.0000  1.0000


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


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

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

 Chiral centers
          Weight= 1.00

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

 TORSION ANGLES
          Weight= 1.00

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

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

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

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

 Input file :CDO_complete_R19_1-70A.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.51
 _lib_update       11/07/18
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 24624
                with complete description    : 24624
  NUMBER OF MODIFICATIONS                    :    70
  NUMBER OF LINKS                            :    77
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  Number of atoms    :    1836
  Number of residues :     502
  Number of chains   :       4
  I am reading library. Please wait.
                mon_lib.cif
  INFO:     link is found (not be used) dist=   2.044 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=   2.205 ideal_dist=   2.090
            ch:AAA  res:  88  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   1.842 ideal_dist=   1.720
            ch:AAA  res:  93  CYS              at:SG  .->ch:AAA  res: 157  TYR              at:CE1 .
  INFO:     link is found (not be used) dist=   2.212 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=   2.403 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=   2.389 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=   2.079 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       1420
Number of   all  reflections      28041
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          28041

   Current auto weighting coefficient =    6.4996524    

 mode : HKRF


######  TLS Group Definitions ######



     CGMAT cycle number =      1

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.909 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Weight matrix   0.30988348    
 Actual weight    6.4996524      is applied to the X-ray term
Norm of X_ray positional gradient                40.8
Norm of Geom. positional gradient                79.1
Norm of X_ray B-factor gradient                  122.
Norm of Geom. B-factor gradient                 0.211E+05
Product of X_ray and Geom posit. gradients     -0.135E+08
 Cosine of angle between them                      -0.431
Product of X_ray and Geom B-fact gradients     -0.397E+08
 Cosine of angle between them                      -0.005


Residuals: XRAY=     0.8719E+06 GEOM=     0.2568E+05 TOTAL=     0.8976E+06
 function value    897567.06    

-------------------------------------------------------------------------------
             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     1.766     1.644
Bond angles  : others                          3242     2.336     1.582
Torsion angles, period  1. refined              184     6.903     5.000
Torsion angles, period  2. refined               90    36.474    22.778
Torsion angles, period  3. refined              268    13.613    15.000
Torsion angles, period  4. refined                9    11.293    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.017     0.020
VDW repulsions: refined_atoms                   305     0.266     0.200
VDW repulsions.others                          1347     0.228     0.200
VDW; torsion: refined_atoms                     719     0.172     0.200
VDW; torsion.others                             719     0.080     0.200
HBOND: refined_atoms                            225     0.186     0.200
HBOND.others                                      1     0.009     0.200
VDW repulsions: symmetry: refined_atoms           9     0.201     0.200
VDW repulsions: symmetry: others                 26     0.173     0.200
HBOND: symmetry: refined_atoms                   23     0.221     0.200
HBOND: symmetry: others                           1     0.028     0.200
M. chain bond B values: refined atoms           745     1.626     1.387
M. chain bond B values: others                  745     1.623     1.387
M. chain angle B values: refined atoms          926     2.568     2.064
M. chain angle B values: others                 927     2.567     2.064
S. chain bond B values: refined atoms           811     2.863     1.771
S. chain bond B values: others                  810     2.856     1.771
S. chain angle B values: refined atoms         1177     4.428     2.497
S. chain angle B values: others                1178     4.426     2.496
Long range B values: refined atoms             1851     7.146    19.722
Long range B values: others                    1759     6.887    18.266
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =    1.2537
Partial structure    1: scale =     0.3884, B  =   47.7635
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.42 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

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


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3589 100.00   431.5   441.2  0.17  0.18     193   452.8   456.2  0.20  0.21
 0.147    6131  99.97   258.6   243.2  0.17  0.15     313   264.2   252.8  0.20  0.18
 0.244    7802 100.00   167.4   151.6  0.19  0.17     416   166.5   152.2  0.23  0.20
 0.342    9093 100.00    71.4    85.8  0.33  0.26     497    71.2    86.8  0.35  0.28
$$

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

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2630   0.908    959   0.812   3589   0.882  0.944  0.9648  0.9680  0.9181  0.9328
  0.1468   5151   0.886    980   0.783   6131   0.870  1.025  0.9540  0.9609  0.9106  0.9408
  0.2444   6822   0.868    980   0.758   7802   0.854  1.054  0.9414  0.9564  0.8780  0.9373
  0.3419   8113   0.683    984   0.600   9097   0.674  0.711  0.8657  0.8706  0.8442  0.8540
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26618
Percentage observed                  =    99.9893
Percentage of free reflections       =     5.0646
Overall R factor                     =     0.1942
Free R factor                        =     0.2295
Average Fourier shell correlation    =     0.9297
AverageFree Fourier shell correlation=     0.9208
Overall weighted R factor            =     0.1691
Free weighted R factor               =     0.1978
Overall weighted R2 factor           =     0.2010
Free weighted R2 factor              =     0.2205
Average correlation coefficient      =     0.9090
Overall correlation coefficient      =     0.9570
Free correlation coefficient         =     0.9442
Cruickshanks DPI for coordinate error=     0.0976
DPI based on free R factor           =     0.0981
Overall figure of merit              =     0.7998
ML based su of positional parameters =     0.0702
ML based su of thermal parameters    =     2.1155
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    134143.75       25679.293       897567.06      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.38267255    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    875181.75    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0696
Partial structure    1: scale =     0.3884, B  =   47.4243
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1935
Free R factor                        =     0.2291
Average Fourier shell correlation    =     0.9407
AverageFree Fourier shell correlation=     0.9321
Average correlation coefficient      =     0.9101
Overall figure of merit              =     0.8312
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    133152.31       9737.9824       875181.75       897567.06    


     CGMAT cycle number =      3

 Weight matrix   0.39375710    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    872933.38    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0245
Partial structure    1: scale =     0.3888, B  =   43.5734
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1924
Free R factor                        =     0.2283
Average Fourier shell correlation    =     0.9428
AverageFree Fourier shell correlation=     0.9339
Average correlation coefficient      =     0.9124
Overall figure of merit              =     0.8365
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    132872.92       9305.5918       872933.38       875181.75    


     CGMAT cycle number =      4

 Weight matrix   0.39592412    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    872300.00    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0208
Partial structure    1: scale =     0.3891, B  =   43.3151
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1921
Free R factor                        =     0.2278
Average Fourier shell correlation    =     0.9433
AverageFree Fourier shell correlation=     0.9342
Average correlation coefficient      =     0.9132
Overall figure of merit              =     0.8376
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    132790.14       9210.2773       872300.00       872933.38    


     CGMAT cycle number =      5

 Weight matrix   0.36018717    
 Actual weight    5.9087749      is applied to the X-ray term


 function value    793706.75    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0113
Partial structure    1: scale =     0.3892, B  =   43.2975
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1920
Free R factor                        =     0.2276
Average Fourier shell correlation    =     0.9434
AverageFree Fourier shell correlation=     0.9343
Average correlation coefficient      =     0.9136
Overall figure of merit              =     0.8376
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    132758.56       9266.3330       793706.75       872300.00    


     CGMAT cycle number =      6

 Weight matrix   0.32637820    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    722373.44    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0000
Partial structure    1: scale =     0.3892, B  =   43.2975
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1924
Free R factor                        =     0.2277
Average Fourier shell correlation    =     0.9432
AverageFree Fourier shell correlation=     0.9341
Average correlation coefficient      =     0.9134
Overall figure of merit              =     0.8373
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    132800.92       9018.1670       722373.44       793706.75    


     CGMAT cycle number =      7

 Weight matrix   0.32569143    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    722436.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0227
Partial structure    1: scale =     0.3891, B  =   43.3097
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1929
Free R factor                        =     0.2280
Average Fourier shell correlation    =     0.9431
AverageFree Fourier shell correlation=     0.9340
Average correlation coefficient      =     0.9129
Overall figure of merit              =     0.8372
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    132883.55       8676.8193       722481.25       722373.44    

 fvalues    132883.55       8676.8193       722482.25       722475.88    
 fvalues    132883.55       8676.8193       722482.25       722475.88    


     CGMAT cycle number =      8

 Weight matrix   0.32566249    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    722477.94    

-------------------------------------------------------------------------------
             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 =     0.0441, B  =   -0.0268
Partial structure    1: scale =     0.3889, B  =   43.2929
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1929
Free R factor                        =     0.2280
Average Fourier shell correlation    =     0.9430
AverageFree Fourier shell correlation=     0.9340
Average correlation coefficient      =     0.9129
Overall figure of merit              =     0.8372
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    132889.22       8653.1689       722476.88       722475.88    
 fvalues    132889.22       8653.1689       722476.88       722482.69    


     CGMAT cycle number =      9

 Weight matrix   0.32553521    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    722476.50    

-------------------------------------------------------------------------------
             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 =     0.0441, B  =   -0.0224
Partial structure    1: scale =     0.3889, B  =   43.2635
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1930
Free R factor                        =     0.2281
Average Fourier shell correlation    =     0.9430
AverageFree Fourier shell correlation=     0.9340
Average correlation coefficient      =     0.9129
Overall figure of merit              =     0.8372
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    132893.11       8626.0918       722476.50       722482.69    


     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.= 0.915 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Weight matrix   0.32534522    
 Actual weight    5.3716135      is applied to the X-ray term
Norm of X_ray positional gradient                38.2
Norm of Geom. positional gradient                38.4
Norm of X_ray B-factor gradient                  107.
Norm of Geom. B-factor gradient                  109.
Product of X_ray and Geom posit. gradients     -0.142E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.375E+08
 Cosine of angle between them                      -0.999


Residuals: XRAY=     0.7139E+06 GEOM=      8598.     TOTAL=     0.7225E+06
 function value    722469.81    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2103     1.783     1.644
Bond angles  : others                          3242     1.511     1.582
Torsion angles, period  1. refined              184     6.859     5.000
Torsion angles, period  2. refined               90    36.161    22.778
Torsion angles, period  3. refined              268    13.190    15.000
Torsion angles, period  4. refined                9    11.356    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                   318     0.263     0.200
VDW repulsions.others                          1375     0.204     0.200
VDW; torsion: refined_atoms                     726     0.173     0.200
VDW; torsion.others                             780     0.084     0.200
HBOND: refined_atoms                            229     0.188     0.200
HBOND.others                                      1     0.049     0.200
VDW repulsions: symmetry: refined_atoms           9     0.204     0.200
VDW repulsions: symmetry: others                 28     0.163     0.200
HBOND: symmetry: refined_atoms                   21     0.224     0.200
HBOND: symmetry: others                           1     0.053     0.200
M. chain bond B values: refined atoms           745     1.676     1.507
M. chain bond B values: others                  745     1.673     1.507
M. chain angle B values: refined atoms          926     2.630     2.247
M. chain angle B values: others                 927     2.628     2.247
S. chain bond B values: refined atoms           811     2.989     1.900
S. chain bond B values: others                  810     2.983     1.899
S. chain angle B values: refined atoms         1177     4.582     2.686
S. chain angle B values: others                1178     4.580     2.686
Long range B values: refined atoms             1875     7.381    21.426
Long range B values: others                    1783     7.138    19.972
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0169
Partial structure    1: scale =     0.3888, B  =   43.2056
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

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


$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10.  v. resln :N:1,6,7,11,12:
:Cycle   10.  and  v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3589 100.00   432.2   441.5  0.17  0.18     193   453.5   456.2  0.20  0.20
 0.147    6131  99.97   259.0   243.2  0.17  0.15     313   264.6   252.9  0.20  0.17
 0.244    7802 100.00   167.7   151.8  0.19  0.17     416   166.8   152.2  0.23  0.20
 0.342    9093 100.00    71.5    85.6  0.32  0.26     497    71.3    86.9  0.35  0.28
$$

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

 $TABLE: Cycle   10. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2630   0.921    959   0.833   3589   0.898  0.946  0.9685  0.9713  0.9205  0.9338
  0.1468   5151   0.892    980   0.790   6131   0.875  1.026  0.9553  0.9621  0.9112  0.9404
  0.2444   6822   0.878    980   0.769   7802   0.864  1.055  0.9445  0.9597  0.8779  0.9378
  0.3419   8113   0.774    984   0.690   9097   0.765  0.750  0.8983  0.9047  0.8486  0.8647
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26618
Percentage observed                  =    99.9893
Percentage of free reflections       =     5.0646
Overall R factor                     =     0.1930
Free R factor                        =     0.2281
Average Fourier shell correlation    =     0.9430
AverageFree Fourier shell correlation=     0.9340
Overall weighted R factor            =     0.1685
Free weighted R factor               =     0.1956
Overall weighted R2 factor           =     0.1998
Free weighted R2 factor              =     0.2180
Average correlation coefficient      =     0.9129
Overall correlation coefficient      =     0.9575
Free correlation coefficient         =     0.9450
Cruickshanks DPI for coordinate error=     0.0970
DPI based on free R factor           =     0.0975
Overall figure of merit              =     0.8372
ML based su of positional parameters =     0.0622
ML based su of thermal parameters    =     1.8357
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    132897.05       8598.2480       722469.81       722476.50    

    ****                              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.= 0.915 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_1-60A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.781     1.644
Bond angles  : others                          3242     1.510     1.582
Torsion angles, period  1. refined              184     6.859     5.000
Torsion angles, period  2. refined               90    36.144    22.778
Torsion angles, period  3. refined              268    13.166    15.000
Torsion angles, period  4. refined                9    11.350    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                   318     0.263     0.200
VDW repulsions.others                          1378     0.203     0.200
VDW; torsion: refined_atoms                     726     0.173     0.200
VDW; torsion.others                             779     0.084     0.200
HBOND: refined_atoms                            228     0.188     0.200
HBOND.others                                      1     0.050     0.200
VDW repulsions: symmetry: refined_atoms           9     0.204     0.200
VDW repulsions: symmetry: others                 28     0.163     0.200
HBOND: symmetry: refined_atoms                   21     0.224     0.200
HBOND: symmetry: others                           1     0.053     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     2.982     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             1874     7.381    21.412
Long range B values: others                    1782     7.136    19.956
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0164
Partial structure    1: scale =     0.3888, B  =   43.1626
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

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


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3589 100.00   432.2   441.5  0.17  0.18     193   453.6   456.1  0.20  0.20
 0.147    6131  99.97   259.0   243.2  0.17  0.15     313   264.6   252.9  0.20  0.17
 0.244    7802 100.00   167.7   151.8  0.19  0.17     416   166.8   152.2  0.23  0.20
 0.342    9093 100.00    71.5    85.6  0.32  0.26     497    71.3    86.9  0.35  0.28
$$

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

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2630   0.922    959   0.833   3589   0.898  0.946  0.9686  0.9713  0.9207  0.9338
  0.1468   5151   0.892    980   0.790   6131   0.875  1.026  0.9553  0.9620  0.9110  0.9404
  0.2444   6822   0.878    980   0.769   7802   0.864  1.055  0.9445  0.9596  0.8779  0.9377
  0.3419   8113   0.774    984   0.690   9097   0.764  0.750  0.8983  0.9047  0.8486  0.8647
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26618
Percentage observed                  =    99.9893
Percentage of free reflections       =     5.0646
Overall R factor                     =     0.1931
Free R factor                        =     0.2280
Average Fourier shell correlation    =     0.9430
AverageFree Fourier shell correlation=     0.9340
Overall weighted R factor            =     0.1685
Free weighted R factor               =     0.1955
Overall weighted R2 factor           =     0.1998
Free weighted R2 factor              =     0.2178
Average correlation coefficient      =     0.9129
Overall correlation coefficient      =     0.9575
Free correlation coefficient         =     0.9451
Cruickshanks DPI for coordinate error=     0.0970
DPI based on free R factor           =     0.0975
Overall figure of merit              =     0.8372
ML based su of positional parameters =     0.0622
ML based su of thermal parameters    =     1.8357
-----------------------------------------------------------------------------
  Time in seconds: CPU =        20.20
             Elapsed =         128.00

    ****           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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1942   0.2295   0.800      134144.    7331.1   0.0121  0.911   1.766  1.024   0.088
       1   0.1935   0.2291   0.831      133152.    7293.8   0.0123  0.921   1.760  1.021   0.089
       2   0.1924   0.2283   0.837      132873.    7285.5   0.0133  0.999   1.811  1.052   0.091
       3   0.1921   0.2278   0.838      132790.    7283.1   0.0134  1.012   1.835  1.066   0.092
       4   0.1920   0.2276   0.838      132759.    7282.1   0.0135  1.016   1.849  1.074   0.092
       5   0.1924   0.2277   0.837      132801.    7283.1   0.0129  0.974   1.828  1.061   0.091
       6   0.1929   0.2280   0.837      132876.    7284.9   0.0123  0.928   1.793  1.040   0.088
       7   0.1929   0.2280   0.837      132888.    7285.4   0.0123  0.926   1.790  1.039   0.088
       8   0.1930   0.2281   0.837      132893.    7285.7   0.0122  0.925   1.787  1.037   0.088
       9   0.1930   0.2281   0.837      132897.    7285.7   0.0122  0.923   1.783  1.035   0.088
      10   0.1931   0.2280   0.837      132902.    7285.7   0.0122  0.922   1.781  1.034   0.088
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1942   0.1931
             R free    0.2295   0.2280
     Rms BondLength    0.0121   0.0122
      Rms BondAngle    1.7662   1.7811
     Rms ChirVolume    0.0883   0.0881
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      52.5s System:    0.1s Elapsed:     0:53