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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
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 User: maly  Run date: 26/ 5/2020 Run time: 14:33:58 


 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 1.90     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 6
  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_R06_2-00A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R06_1-90A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R06_1-90A.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       0.0693
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.9000
  Estimated number of reflections :      21862
  Free R exclusion - flag equals:     6
  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  1.9000

  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_R06_2-00A.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=   2.017 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=   2.233 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=   1.820 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=   2.184 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=   2.349 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=   2.483 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=   1.975 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                            6
Number of "free" reflections        888
Number of   all  reflections      16986
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          16986

   Current auto weighting coefficient =    7.2495699    

 mode : HKRF


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



     CGMAT cycle number =      1

    ****                         Bond distance outliers                         ****

Bond distance deviations from the ideal >10.000Sigma will be monitored

A    125 LEU C   . - A    126 ARG N   . mod.= 1.537 id.= 1.337 dev= -0.200 sig.= 0.011

    ****                              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.= 0.881 id.= 3.000 dev= -2.12 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    31   31   65
 Minimum acceptable grid spacing:    73   73  154
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    31   31   65
 Minimum acceptable grid spacing:    73   73  154
 Weight matrix   0.23935731    
 Actual weight    7.2495699      is applied to the X-ray term
Norm of X_ray positional gradient                42.6
Norm of Geom. positional gradient                86.1
Norm of X_ray B-factor gradient                  143.
Norm of Geom. B-factor gradient                 0.210E+05
Product of X_ray and Geom posit. gradients     -0.696E+07
 Cosine of angle between them                      -0.196
Product of X_ray and Geom B-fact gradients     -0.384E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.6374E+06 GEOM=     0.2563E+05 TOTAL=     0.6630E+06
 function value    663003.00    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.792     1.644
Bond angles  : others                          3242     2.351     1.582
Torsion angles, period  1. refined              184     7.276     5.000
Torsion angles, period  2. refined               90    36.656    22.778
Torsion angles, period  3. refined              268    14.456    15.000
Torsion angles, period  4. refined                9    10.943    15.000
Chiral centres: refined atoms                   196     0.083     0.200
Planar groups: refined atoms                   1736     0.012     0.020
Planar groups: others                           331     0.017     0.020
VDW repulsions: refined_atoms                   318     0.256     0.200
VDW repulsions.others                          1320     0.233     0.200
VDW; torsion: refined_atoms                     707     0.170     0.200
VDW; torsion.others                             697     0.081     0.200
HBOND: refined_atoms                            235     0.209     0.200
HBOND.others                                      3     0.043     0.200
VDW repulsions: symmetry: refined_atoms          10     0.207     0.200
VDW repulsions: symmetry: others                 31     0.152     0.200
HBOND: symmetry: refined_atoms                   18     0.229     0.200
HBOND: symmetry: others                           1     0.062     0.200
M. chain bond B values: refined atoms           745     1.518     1.178
M. chain bond B values: others                  745     1.517     1.178
M. chain angle B values: refined atoms          926     2.423     1.748
M. chain angle B values: others                 927     2.422     1.748
S. chain bond B values: refined atoms           811     2.351     1.498
S. chain bond B values: others                  810     2.347     1.497
S. chain angle B values: refined atoms         1177     3.730     2.107
S. chain angle B values: others                1178     3.728     2.107
Long range B values: refined atoms             1869     6.629    16.653
Long range B values: others                    1772     6.293    15.253
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =    0.3335
Partial structure    1: scale =     0.3754, B  =   49.2037
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2184 100.00   480.6   483.9  0.16  0.18     127   480.6   501.9  0.21  0.23
 0.104    3726 100.00   384.8   368.0  0.16  0.15     198   406.4   395.5  0.19  0.18
 0.173    4711  99.96   248.7   243.7  0.15  0.13     231   235.6   225.1  0.22  0.19
 0.242    5473 100.00   188.0   188.9  0.19  0.15     331   196.7   197.1  0.22  0.17
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1505   0.893    679   0.792   2184   0.861  0.948  0.9571  0.9650  0.9018  0.9385
  0.1042   3026   0.897    700   0.793   3726   0.877  1.002  0.9603  0.9658  0.9209  0.9459
  0.1733   4019   0.870    692   0.768   4711   0.855  0.980  0.9396  0.9590  0.8799  0.9421
  0.2425   4789   0.873    686   0.765   5475   0.860  0.951  0.9500  0.9528  0.8983  0.9175
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16096
Percentage observed                  =    99.9823
Percentage of free reflections       =     5.2285
Overall R factor                     =     0.1635
Free R factor                        =     0.2083
Average Fourier shell correlation    =     0.9593
AverageFree Fourier shell correlation=     0.9506
Overall weighted R factor            =     0.1513
Free weighted R factor               =     0.1965
Overall weighted R2 factor           =     0.1847
Free weighted R2 factor              =     0.2389
Average correlation coefficient      =     0.9341
Overall correlation coefficient      =     0.9533
Free correlation coefficient         =     0.9281
Cruickshanks DPI for coordinate error=     0.1449
DPI based on free R factor           =     0.1361
Overall figure of merit              =     0.8626
ML based su of positional parameters =     0.0844
ML based su of thermal parameters    =     2.8026
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    87918.055       25634.961       663003.00      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.25539488    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    644339.38    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.011     0.013
Bond distances: others                         1393     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.1193
Partial structure    1: scale =     0.3749, B  =   49.2063
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1612
Free R factor                        =     0.2056
Average Fourier shell correlation    =     0.9619
AverageFree Fourier shell correlation=     0.9529
Average correlation coefficient      =     0.9382
Overall figure of merit              =     0.8691
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    87435.211       10471.719       644339.38       663003.00    


     CGMAT cycle number =      3

 Weight matrix   0.25667068    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    642127.25    

-------------------------------------------------------------------------------
             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 =     0.0402, B  =   -0.0513
Partial structure    1: scale =     0.3752, B  =   47.3775
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1600
Free R factor                        =     0.2051
Average Fourier shell correlation    =     0.9624
AverageFree Fourier shell correlation=     0.9531
Average correlation coefficient      =     0.9396
Overall figure of merit              =     0.8694
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    87302.602       9220.9590       642127.25       644339.38    


     CGMAT cycle number =      4

 Weight matrix   0.25700760    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    641300.50    

-------------------------------------------------------------------------------
             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 =     0.0403, B  =   -0.0505
Partial structure    1: scale =     0.3760, B  =   47.4829
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1596
Free R factor                        =     0.2051
Average Fourier shell correlation    =     0.9625
AverageFree Fourier shell correlation=     0.9532
Average correlation coefficient      =     0.9401
Overall figure of merit              =     0.8694
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    87249.781       8777.1162       641300.50       642127.25    


     CGMAT cycle number =      5

 Weight matrix   0.25709882    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    641071.25    

-------------------------------------------------------------------------------
             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 =     0.0403, B  =   -0.0502
Partial structure    1: scale =     0.3763, B  =   47.4221
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1594
Free R factor                        =     0.2053
Average Fourier shell correlation    =     0.9626
AverageFree Fourier shell correlation=     0.9531
Average correlation coefficient      =     0.9404
Overall figure of merit              =     0.8694
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    87230.563       8687.1611       641071.25       641300.50    


     CGMAT cycle number =      6

 Weight matrix   0.25770274    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    640833.50    

-------------------------------------------------------------------------------
             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 =     0.0403, B  =   -0.0891
Partial structure    1: scale =     0.3757, B  =   47.3100
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1593
Free R factor                        =     0.2052
Average Fourier shell correlation    =     0.9627
AverageFree Fourier shell correlation=     0.9532
Average correlation coefficient      =     0.9406
Overall figure of merit              =     0.8696
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    87201.070       8663.2783       640833.50       641071.25    


     CGMAT cycle number =      7

 Weight matrix   0.25742894    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    640777.88    

-------------------------------------------------------------------------------
             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 =     0.0403, B  =   -0.0919
Partial structure    1: scale =     0.3755, B  =   47.2406
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1592
Free R factor                        =     0.2049
Average Fourier shell correlation    =     0.9627
AverageFree Fourier shell correlation=     0.9532
Average correlation coefficient      =     0.9408
Overall figure of merit              =     0.8696
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    87191.109       8679.8066       640777.88       640833.50    


     CGMAT cycle number =      8

 Weight matrix   0.25719199    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    640714.94    

-------------------------------------------------------------------------------
             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 =     0.0403, B  =   -0.0844
Partial structure    1: scale =     0.3753, B  =   46.9897
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1591
Free R factor                        =     0.2050
Average Fourier shell correlation    =     0.9627
AverageFree Fourier shell correlation=     0.9531
Average correlation coefficient      =     0.9408
Overall figure of merit              =     0.8696
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    87181.391       8687.3936       640714.94       640777.88    


     CGMAT cycle number =      9

 Weight matrix   0.25648198    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    640746.63    

-------------------------------------------------------------------------------
             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 =     0.0403, B  =   -0.0829
Partial structure    1: scale =     0.3753, B  =   46.9740
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1591
Free R factor                        =     0.2052
Average Fourier shell correlation    =     0.9627
AverageFree Fourier shell correlation=     0.9530
Average correlation coefficient      =     0.9409
Overall figure of merit              =     0.8694
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    87187.586       8674.2734       640772.25       640714.94    

 fvalues    87187.586       8674.2734       640748.94       640746.75    
 fvalues    87187.586       8674.2734       640748.94       640746.75    


     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.= 0.903 id.= 3.000 dev= -2.10 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    31   31   65
 Minimum acceptable grid spacing:    73   73  154
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    31   31   65
 Minimum acceptable grid spacing:    73   73  154
 Weight matrix   0.25644985    
 Actual weight    7.2495699      is applied to the X-ray term
Norm of X_ray positional gradient                34.6
Norm of Geom. positional gradient                34.6
Norm of X_ray B-factor gradient                  115.
Norm of Geom. B-factor gradient                  119.
Product of X_ray and Geom posit. gradients     -0.116E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.438E+08
 Cosine of angle between them                      -0.991


Residuals: XRAY=     0.6321E+06 GEOM=      8673.     TOTAL=     0.6407E+06
 function value    640747.06    

-------------------------------------------------------------------------------
             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     1.745     1.644
Bond angles  : others                          3242     1.446     1.582
Torsion angles, period  1. refined              184     6.997     5.000
Torsion angles, period  2. refined               90    36.504    22.778
Torsion angles, period  3. refined              268    14.021    15.000
Torsion angles, period  4. refined                9    10.862    15.000
Chiral centres: refined atoms                   196     0.083     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   311     0.259     0.200
VDW repulsions.others                          1360     0.205     0.200
VDW; torsion: refined_atoms                     708     0.172     0.200
VDW; torsion.others                             774     0.084     0.200
HBOND: refined_atoms                            238     0.194     0.200
HBOND.others                                      1     0.007     0.200
VDW repulsions: symmetry: refined_atoms           7     0.243     0.200
VDW repulsions: symmetry: others                 27     0.176     0.200
HBOND: symmetry: refined_atoms                   22     0.184     0.200
HBOND: symmetry: others                           1     0.018     0.200
M. chain bond B values: refined atoms           745     1.582     1.206
M. chain bond B values: others                  745     1.581     1.206
M. chain angle B values: refined atoms          926     2.464     1.790
M. chain angle B values: others                 927     2.463     1.789
S. chain bond B values: refined atoms           812     2.589     1.553
S. chain bond B values: others                  811     2.586     1.553
S. chain angle B values: refined atoms         1177     4.053     2.183
S. chain angle B values: others                1178     4.051     2.183
Long range B values: refined atoms             1864     6.973    17.153
Long range B values: others                    1767     6.668    15.767
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =   -0.0827
Partial structure    1: scale =     0.3752, B  =   46.9556
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2184 100.00   480.5   484.4  0.16  0.17     127   480.5   506.9  0.21  0.23
 0.104    3726 100.00   384.7   367.2  0.16  0.15     198   406.3   394.2  0.18  0.18
 0.173    4711  99.96   248.6   243.2  0.16  0.13     231   235.6   226.0  0.22  0.19
 0.242    5473 100.00   188.0   189.1  0.16  0.13     331   196.7   196.4  0.21  0.17
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1505   0.910    679   0.816   2184   0.881  0.953  0.9603  0.9686  0.8989  0.9387
  0.1042   3026   0.899    700   0.796   3726   0.879  1.002  0.9618  0.9662  0.9250  0.9449
  0.1733   4019   0.875    692   0.768   4711   0.859  0.980  0.9415  0.9599  0.8816  0.9406
  0.2425   4789   0.880    686   0.772   5475   0.867  0.954  0.9531  0.9604  0.9029  0.9393
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16096
Percentage observed                  =    99.9823
Percentage of free reflections       =     5.2285
Overall R factor                     =     0.1591
Free R factor                        =     0.2052
Average Fourier shell correlation    =     0.9627
AverageFree Fourier shell correlation=     0.9531
Overall weighted R factor            =     0.1497
Free weighted R factor               =     0.1944
Overall weighted R2 factor           =     0.1847
Free weighted R2 factor              =     0.2402
Average correlation coefficient      =     0.9409
Overall correlation coefficient      =     0.9547
Free correlation coefficient         =     0.9290
Cruickshanks DPI for coordinate error=     0.1409
DPI based on free R factor           =     0.1340
Overall figure of merit              =     0.8694
ML based su of positional parameters =     0.0814
ML based su of thermal parameters    =     2.6964
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    87187.867       8673.0508       640727.44       640746.75    
 fvalues    87187.867       8673.0508       640727.44       640747.63    

    ****                              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.= 0.903 id.= 3.000 dev= -2.10 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

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

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R06_1-90A.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     1.745     1.644
Bond angles  : others                          3242     1.446     1.582
Torsion angles, period  1. refined              184     6.996     5.000
Torsion angles, period  2. refined               90    36.494    22.778
Torsion angles, period  3. refined              268    14.020    15.000
Torsion angles, period  4. refined                9    10.869    15.000
Chiral centres: refined atoms                   196     0.083     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   311     0.259     0.200
VDW repulsions.others                          1360     0.205     0.200
VDW; torsion: refined_atoms                     708     0.172     0.200
VDW; torsion.others                             775     0.084     0.200
HBOND: refined_atoms                            239     0.193     0.200
HBOND.others                                      1     0.007     0.200
VDW repulsions: symmetry: refined_atoms           7     0.243     0.200
VDW repulsions: symmetry: others                 27     0.176     0.200
HBOND: symmetry: refined_atoms                   22     0.184     0.200
HBOND: symmetry: others                           1     0.019     0.200
M. chain bond B values: refined atoms           745     1.581     1.206
M. chain bond B values: others                  745     1.581     1.206
M. chain angle B values: refined atoms          926     2.464     1.789
M. chain angle B values: others                 927     2.463     1.789
S. chain bond B values: refined atoms           812     2.590     1.553
S. chain bond B values: others                  811     2.587     1.553
S. chain angle B values: refined atoms         1177     4.054     2.183
S. chain angle B values: others                1178     4.052     2.183
Long range B values: refined atoms             1865     6.988    17.202
Long range B values: others                    1767     6.686    15.793
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =   -0.0822
Partial structure    1: scale =     0.3752, B  =   46.9954
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2184 100.00   480.5   484.4  0.16  0.18     127   480.5   507.0  0.21  0.23
 0.104    3726 100.00   384.8   367.2  0.16  0.15     198   406.3   394.2  0.18  0.18
 0.173    4711  99.96   248.6   243.2  0.16  0.13     231   235.6   226.0  0.22  0.19
 0.242    5473 100.00   188.0   189.0  0.16  0.13     331   196.7   196.4  0.21  0.17
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1505   0.910    679   0.817   2184   0.881  0.953  0.9603  0.9686  0.8988  0.9387
  0.1042   3026   0.899    700   0.796   3726   0.879  1.002  0.9618  0.9662  0.9252  0.9449
  0.1733   4019   0.875    692   0.768   4711   0.859  0.980  0.9415  0.9599  0.8816  0.9406
  0.2425   4789   0.880    686   0.772   5475   0.867  0.954  0.9531  0.9604  0.9028  0.9393
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16096
Percentage observed                  =    99.9823
Percentage of free reflections       =     5.2285
Overall R factor                     =     0.1591
Free R factor                        =     0.2051
Average Fourier shell correlation    =     0.9627
AverageFree Fourier shell correlation=     0.9530
Overall weighted R factor            =     0.1498
Free weighted R factor               =     0.1943
Overall weighted R2 factor           =     0.1848
Free weighted R2 factor              =     0.2402
Average correlation coefficient      =     0.9409
Overall correlation coefficient      =     0.9547
Free correlation coefficient         =     0.9290
Cruickshanks DPI for coordinate error=     0.1410
DPI based on free R factor           =     0.1340
Overall figure of merit              =     0.8694
ML based su of positional parameters =     0.0814
ML based su of thermal parameters    =     2.6964
-----------------------------------------------------------------------------
  Time in seconds: CPU =        14.74
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1635   0.2083   0.863       87918.    4985.5   0.0129  1.002   1.792  1.041   0.083
       1   0.1612   0.2056   0.869       87435.    4973.7   0.0115  0.843   1.728  1.000   0.084
       2   0.1600   0.2051   0.869       87303.    4971.4   0.0118  0.873   1.740  1.006   0.084
       3   0.1596   0.2051   0.869       87250.    4970.6   0.0118  0.877   1.742  1.009   0.084
       4   0.1594   0.2053   0.869       87231.    4971.1   0.0118  0.879   1.743  1.010   0.084
       5   0.1593   0.2052   0.870       87201.    4970.7   0.0118  0.880   1.743  1.010   0.084
       6   0.1592   0.2049   0.870       87191.    4970.9   0.0118  0.880   1.744  1.011   0.084
       7   0.1591   0.2050   0.870       87181.    4971.0   0.0118  0.879   1.745  1.011   0.083
       8   0.1591   0.2052   0.869       87188.    4972.0   0.0118  0.879   1.745  1.012   0.083
       9   0.1591   0.2052   0.869       87188.    4971.9   0.0118  0.879   1.745  1.012   0.083
      10   0.1591   0.2051   0.869       87188.    4972.1   0.0118  0.879   1.745  1.012   0.083
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1635   0.1591
             R free    0.2083   0.2051
     Rms BondLength    0.0129   0.0118
      Rms BondAngle    1.7916   1.7453
     Rms ChirVolume    0.0834   0.0834
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      46.8s System:    0.2s Elapsed:     0:47