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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: 19:04:40 


 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 4
  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_R04_1-60A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R04_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_R04_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:     4
  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_R04_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=   2.059 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=   2.192 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=   1.824 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=   2.214 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=   2.396 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=   2.396 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=   2.091 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                            4
Number of "free" reflections       1760
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.= 0.889 id.= 3.000 dev= -2.11 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   0.28801623    
 Actual weight    6.2496691      is applied to the X-ray term
Norm of X_ray positional gradient                40.1
Norm of Geom. positional gradient                80.4
Norm of X_ray B-factor gradient                  113.
Norm of Geom. B-factor gradient                 0.212E+05
Product of X_ray and Geom posit. gradients     -0.148E+08
 Cosine of angle between them                      -0.474
Product of X_ray and Geom B-fact gradients     -0.360E+08
 Cosine of angle between them                      -0.005


Residuals: XRAY=     0.9762E+06 GEOM=     0.2573E+05 TOTAL=     0.1002E+07
 function value    1001961.1    

-------------------------------------------------------------------------------
             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     1.796     1.644
Bond angles  : others                          3242     2.345     1.582
Torsion angles, period  1. refined              184     6.844     5.000
Torsion angles, period  2. refined               90    35.960    22.778
Torsion angles, period  3. refined              268    13.481    15.000
Torsion angles, period  4. refined                9    11.268    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.015     0.020
VDW repulsions: refined_atoms                   314     0.266     0.200
VDW repulsions.others                          1356     0.231     0.200
VDW; torsion: refined_atoms                     729     0.171     0.200
VDW; torsion.others                             716     0.081     0.200
HBOND: refined_atoms                            213     0.208     0.200
HBOND.others                                      2     0.111     0.200
VDW repulsions: symmetry: refined_atoms           8     0.232     0.200
VDW repulsions: symmetry: others                 24     0.201     0.200
HBOND: symmetry: refined_atoms                   23     0.202     0.200
HBOND: symmetry: others                           1     0.011     0.200
M. chain bond B values: refined atoms           745     1.686     1.509
M. chain bond B values: others                  745     1.682     1.509
M. chain angle B values: refined atoms          926     2.651     2.251
M. chain angle B values: others                 927     2.650     2.251
S. chain bond B values: refined atoms           811     3.048     1.908
S. chain bond B values: others                  810     3.042     1.907
S. chain angle B values: refined atoms         1177     4.723     2.695
S. chain angle B values: others                1178     4.721     2.694
Long range B values: refined atoms             1857     7.340    21.078
Long range B values: others                    1770     7.078    19.718
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    1.1802
Partial structure    1: scale =     0.3919, B  =   46.4848
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4304 100.00   406.9   416.3  0.17  0.17     243   395.4   406.6  0.19  0.20
 0.167    7426  99.97   228.3   208.0  0.18  0.16     372   229.0   210.9  0.23  0.20
 0.278    9389 100.00   124.2   114.4  0.21  0.18     521   120.6   111.3  0.24  0.21
 0.389   11018 100.00    50.2    62.4  0.41  0.36     623    50.6    63.8  0.43  0.38
$$

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

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3199   0.918   1105   0.814   4304   0.891  0.952  0.9681  0.9706  0.9307  0.9355
  0.1670   6315   0.874   1111   0.774   7426   0.859  1.060  0.9484  0.9582  0.8935  0.9339
  0.2780   8273   0.844   1116   0.766   9389   0.835  1.022  0.9371  0.9478  0.9024  0.9301
  0.3890   9918   0.496   1111   0.438  11029   0.490  0.519  0.7416  0.7498  0.7172  0.7740
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32148
Percentage observed                  =    99.9912
Percentage of free reflections       =     5.1905
Overall R factor                     =     0.2073
Free R factor                        =     0.2410
Average Fourier shell correlation    =     0.8853
AverageFree Fourier shell correlation=     0.8745
Overall weighted R factor            =     0.1754
Free weighted R factor               =     0.2053
Overall weighted R2 factor           =     0.2035
Free weighted R2 factor              =     0.2469
Average correlation coefficient      =     0.8782
Overall correlation coefficient      =     0.9590
Free correlation coefficient         =     0.9482
Cruickshanks DPI for coordinate error=     0.0861
DPI based on free R factor           =     0.0879
Overall figure of merit              =     0.7299
ML based su of positional parameters =     0.0714
ML based su of thermal parameters    =     2.0982
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    156206.03       25725.141       1001961.1      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.36056277    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    978765.06    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =   -0.0476
Partial structure    1: scale =     0.3931, B  =   46.1256
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                        =     0.2405
Average Fourier shell correlation    =     0.9016
AverageFree Fourier shell correlation=     0.8924
Average correlation coefficient      =     0.8781
Overall figure of merit              =     0.7629
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    155042.89       9798.2930       978765.06       1001961.1    


     CGMAT cycle number =      3

 Weight matrix   0.37124276    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    976266.00    

-------------------------------------------------------------------------------
             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 =     0.0456, B  =   -0.0062
Partial structure    1: scale =     0.3933, B  =   41.9372
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                     =     0.2059
Free R factor                        =     0.2405
Average Fourier shell correlation    =     0.9058
AverageFree Fourier shell correlation=     0.8963
Average correlation coefficient      =     0.8801
Overall figure of merit              =     0.7706
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    154725.69       9281.5996       976266.00       978765.06    


     CGMAT cycle number =      4

 Weight matrix   0.34043479    
 Actual weight    5.6815171      is applied to the X-ray term


 function value    887729.94    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.014     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    0.0105
Partial structure    1: scale =     0.3935, B  =   40.7113
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                     =     0.2057
Free R factor                        =     0.2403
Average Fourier shell correlation    =     0.9071
AverageFree Fourier shell correlation=     0.8974
Average correlation coefficient      =     0.8809
Overall figure of merit              =     0.7728
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    154642.16       9127.8965       887729.94       976266.00    


     CGMAT cycle number =      5

 Weight matrix   0.31009981    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    807695.31    

-------------------------------------------------------------------------------
             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  =    0.0066
Partial structure    1: scale =     0.3937, B  =   40.5630
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                     =     0.2059
Free R factor                        =     0.2401
Average Fourier shell correlation    =     0.9073
AverageFree Fourier shell correlation=     0.8978
Average correlation coefficient      =     0.8808
Overall figure of merit              =     0.7735
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    154663.05       8858.3096       807695.31       887729.94    


     CGMAT cycle number =      6

 Weight matrix   0.30952355    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    807725.69    

-------------------------------------------------------------------------------
             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  =    0.0124
Partial structure    1: scale =     0.3937, B  =   40.3235
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                     =     0.2063
Free R factor                        =     0.2402
Average Fourier shell correlation    =     0.9072
AverageFree Fourier shell correlation=     0.8977
Average correlation coefficient      =     0.8805
Overall figure of merit              =     0.7734
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    154727.94       8551.3525       807716.50       807695.31    
 fvalues    154727.94       8551.3525       807716.50       807723.50    


     CGMAT cycle number =      7

 Weight matrix   0.30905104    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    807790.19    

-------------------------------------------------------------------------------
             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  =    0.0146
Partial structure    1: scale =     0.3937, B  =   40.1302
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                     =     0.2064
Free R factor                        =     0.2402
Average Fourier shell correlation    =     0.9071
AverageFree Fourier shell correlation=     0.8977
Average correlation coefficient      =     0.8804
Overall figure of merit              =     0.7733
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    154752.03       8476.0645       807801.44       807723.50    

 fvalues    154752.03       8476.0645       807783.13       807772.69    
 fvalues    154752.03       8476.0645       807783.13       807772.69    


     CGMAT cycle number =      8

 Weight matrix   0.30928054    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    807784.13    

-------------------------------------------------------------------------------
             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  =    0.0105
Partial structure    1: scale =     0.3937, B  =   40.1441
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                     =     0.2064
Free R factor                        =     0.2403
Average Fourier shell correlation    =     0.9071
AverageFree Fourier shell correlation=     0.8977
Average correlation coefficient      =     0.8804
Overall figure of merit              =     0.7734
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02

 fvalues    154753.63       8463.6230       807768.44       807772.69    


     CGMAT cycle number =      9

 Weight matrix   0.30902287    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    807800.81    

-------------------------------------------------------------------------------
             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  =    0.0156
Partial structure    1: scale =     0.3937, B  =   40.1077
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                     =     0.2064
Free R factor                        =     0.2403
Average Fourier shell correlation    =     0.9071
AverageFree Fourier shell correlation=     0.8977
Average correlation coefficient      =     0.8804
Overall figure of merit              =     0.7733
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    154757.72       8452.3223       807830.69       807768.44    

 fvalues    154757.72       8452.3223       807795.06       807778.31    
 fvalues    154757.72       8452.3223       807795.06       807778.31    


     CGMAT cycle number =     10

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.907 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        :   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   0.30991796    
 Actual weight    5.1650152      is applied to the X-ray term
Norm of X_ray positional gradient                39.1
Norm of Geom. positional gradient                39.1
Norm of X_ray B-factor gradient                  100.
Norm of Geom. B-factor gradient                  100.
Product of X_ray and Geom posit. gradients     -0.148E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.325E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.7993E+06 GEOM=      8450.     TOTAL=     0.8078E+06
 function value    807777.94    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2103     1.788     1.644
Bond angles  : others                          3242     1.493     1.582
Torsion angles, period  1. refined              184     6.835     5.000
Torsion angles, period  2. refined               90    35.696    22.778
Torsion angles, period  3. refined              268    13.325    15.000
Torsion angles, period  4. refined                9    11.467    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     0.266     0.200
VDW repulsions.others                          1366     0.205     0.200
VDW; torsion: refined_atoms                     725     0.171     0.200
VDW; torsion.others                             766     0.084     0.200
HBOND: refined_atoms                            210     0.205     0.200
HBOND.others                                      2     0.118     0.200
VDW repulsions: symmetry: refined_atoms           8     0.226     0.200
VDW repulsions: symmetry: others                 21     0.210     0.200
HBOND: symmetry: refined_atoms                   24     0.194     0.200
M. chain bond B values: refined atoms           745     1.740     1.622
M. chain bond B values: others                  745     1.736     1.622
M. chain angle B values: refined atoms          926     2.716     2.421
M. chain angle B values: others                 927     2.715     2.421
S. chain bond B values: refined atoms           811     3.132     2.032
S. chain bond B values: others                  810     3.126     2.031
S. chain angle B values: refined atoms         1177     4.844     2.878
S. chain angle B values: others                1178     4.842     2.877
Long range B values: refined atoms             1851     7.384    22.433
Long range B values: others                    1763     7.120    21.038
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    0.0004
Partial structure    1: scale =     0.3937, B  =   40.1074
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4304 100.00   407.2   416.7  0.17  0.17     243   395.7   407.2  0.19  0.20
 0.167    7426  99.97   228.4   208.4  0.18  0.16     372   229.1   211.2  0.23  0.20
 0.278    9389 100.00   124.3   114.8  0.21  0.18     521   120.7   111.7  0.24  0.21
 0.389   11018 100.00    50.2    62.5  0.41  0.36     623    50.6    63.9  0.43  0.38
$$

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

 $TABLE: Cycle   10. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3199   0.931   1105   0.837   4304   0.907  0.953  0.9711  0.9736  0.9304  0.9352
  0.1670   6315   0.885   1111   0.787   7426   0.870  1.062  0.9510  0.9609  0.8937  0.9343
  0.2780   8273   0.864   1116   0.787   9389   0.854  1.023  0.9448  0.9549  0.9040  0.9312
  0.3890   9918   0.594   1111   0.533  11029   0.588  0.571  0.7983  0.8045  0.7200  0.7792
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32148
Percentage observed                  =    99.9912
Percentage of free reflections       =     5.1905
Overall R factor                     =     0.2064
Free R factor                        =     0.2404
Average Fourier shell correlation    =     0.9072
AverageFree Fourier shell correlation=     0.8978
Overall weighted R factor            =     0.1748
Free weighted R factor               =     0.2052
Overall weighted R2 factor           =     0.2032
Free weighted R2 factor              =     0.2471
Average correlation coefficient      =     0.8804
Overall correlation coefficient      =     0.9591
Free correlation coefficient         =     0.9483
Cruickshanks DPI for coordinate error=     0.0858
DPI based on free R factor           =     0.0877
Overall figure of merit              =     0.7736
ML based su of positional parameters =     0.0625
ML based su of thermal parameters    =     1.8123
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    154758.09       8450.0059       807777.94       807778.31    

    ****                              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.= 0.907 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

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

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R04_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     1.788     1.644
Bond angles  : others                          3242     1.493     1.582
Torsion angles, period  1. refined              184     6.835     5.000
Torsion angles, period  2. refined               90    35.692    22.778
Torsion angles, period  3. refined              268    13.313    15.000
Torsion angles, period  4. refined                9    11.464    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     0.265     0.200
VDW repulsions.others                          1366     0.205     0.200
VDW; torsion: refined_atoms                     724     0.171     0.200
VDW; torsion.others                             766     0.084     0.200
HBOND: refined_atoms                            210     0.205     0.200
HBOND.others                                      2     0.118     0.200
VDW repulsions: symmetry: refined_atoms           8     0.226     0.200
VDW repulsions: symmetry: others                 21     0.210     0.200
HBOND: symmetry: refined_atoms                   24     0.194     0.200
M. chain bond B values: refined atoms           745     1.740     1.622
M. chain bond B values: others                  745     1.736     1.622
M. chain angle B values: refined atoms          926     2.716     2.421
M. chain angle B values: others                 927     2.714     2.421
S. chain bond B values: refined atoms           811     3.132     2.032
S. chain bond B values: others                  810     3.126     2.031
S. chain angle B values: refined atoms         1177     4.843     2.878
S. chain angle B values: others                1178     4.841     2.877
Long range B values: refined atoms             1851     7.384    22.432
Long range B values: others                    1763     7.120    21.037
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0455, B  =    0.0163
Partial structure    1: scale =     0.3937, B  =   40.1111
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4304 100.00   407.2   416.6  0.17  0.17     243   395.7   407.1  0.19  0.20
 0.167    7426  99.97   228.5   208.2  0.18  0.16     372   229.2   211.0  0.23  0.20
 0.278    9389 100.00   124.3   114.7  0.21  0.18     521   120.7   111.6  0.24  0.21
 0.389   11018 100.00    50.3    62.4  0.41  0.36     623    50.6    63.8  0.43  0.38
$$

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

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3199   0.931   1105   0.837   4304   0.907  0.953  0.9711  0.9736  0.9304  0.9352
  0.1670   6315   0.885   1111   0.786   7426   0.870  1.062  0.9510  0.9609  0.8936  0.9343
  0.2780   8273   0.863   1116   0.786   9389   0.854  1.023  0.9448  0.9549  0.9040  0.9312
  0.3890   9918   0.593   1111   0.533  11029   0.587  0.571  0.7979  0.8042  0.7201  0.7793
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32148
Percentage observed                  =    99.9912
Percentage of free reflections       =     5.1905
Overall R factor                     =     0.2064
Free R factor                        =     0.2402
Average Fourier shell correlation    =     0.9071
AverageFree Fourier shell correlation=     0.8977
Overall weighted R factor            =     0.1749
Free weighted R factor               =     0.2052
Overall weighted R2 factor           =     0.2033
Free weighted R2 factor              =     0.2472
Average correlation coefficient      =     0.8804
Overall correlation coefficient      =     0.9591
Free correlation coefficient         =     0.9483
Cruickshanks DPI for coordinate error=     0.0858
DPI based on free R factor           =     0.0877
Overall figure of merit              =     0.7733
ML based su of positional parameters =     0.0625
ML based su of thermal parameters    =     1.8123
-----------------------------------------------------------------------------
  Time in seconds: CPU =        28.52
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2073   0.2410   0.730      156206.    8685.8   0.0125  0.931   1.796  1.046   0.088
       1   0.2070   0.2405   0.763      155043.    8646.2   0.0124  0.925   1.780  1.036   0.088
       2   0.2059   0.2405   0.771      154726.    8636.8   0.0135  1.003   1.834  1.069   0.091
       3   0.2057   0.2403   0.773      154642.    8633.6   0.0136  1.013   1.855  1.081   0.092
       4   0.2059   0.2401   0.774      154663.    8632.2   0.0130  0.971   1.835  1.069   0.091
       5   0.2063   0.2402   0.773      154728.    8633.2   0.0124  0.927   1.801  1.048   0.088
       6   0.2064   0.2402   0.773      154755.    8634.0   0.0123  0.923   1.791  1.042   0.088
       7   0.2064   0.2403   0.773      154757.    8634.3   0.0123  0.922   1.790  1.042   0.088
       8   0.2064   0.2403   0.773      154762.    8634.2   0.0123  0.921   1.788  1.041   0.088
       9   0.2064   0.2404   0.774      154758.    8634.3   0.0123  0.921   1.788  1.041   0.088
      10   0.2064   0.2402   0.773      154769.    8634.4   0.0123  0.921   1.788  1.041   0.088
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2073   0.2064
             R free    0.2410   0.2402
     Rms BondLength    0.0125   0.0123
      Rms BondAngle    1.7965   1.7877
     Rms ChirVolume    0.0877   0.0881
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      60.8s System:    0.2s Elapsed:     1:01