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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: 14:55:57 


 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 15
  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_R15_2-00A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R15_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_R15_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:    15
  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_R15_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=   2.042 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=   2.245 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=   1.833 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=   2.231 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=   2.373 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=   2.462 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=   1.934 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                           15
Number of "free" reflections        878
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.= 1.567 id.= 1.337 dev= -0.230 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.= 0.902 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   0.23248431    
 Actual weight    7.2495699      is applied to the X-ray term
Norm of X_ray positional gradient                43.0
Norm of Geom. positional gradient                87.9
Norm of X_ray B-factor gradient                  141.
Norm of Geom. B-factor gradient                 0.207E+05
Product of X_ray and Geom posit. gradients     -0.705E+07
 Cosine of angle between them                      -0.192
Product of X_ray and Geom B-fact gradients     -0.373E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.6381E+06 GEOM=     0.2578E+05 TOTAL=     0.6639E+06
 function value    663887.75    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.014     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.834     1.644
Bond angles  : others                          3242     2.347     1.582
Torsion angles, period  1. refined              184     7.286     5.000
Torsion angles, period  2. refined               90    36.724    22.778
Torsion angles, period  3. refined              268    14.675    15.000
Torsion angles, period  4. refined                9    10.948    15.000
Chiral centres: refined atoms                   196     0.086     0.200
Planar groups: refined atoms                   1736     0.012     0.020
Planar groups: others                           331     0.017     0.020
VDW repulsions: refined_atoms                   316     0.259     0.200
VDW repulsions.others                          1343     0.230     0.200
VDW; torsion: refined_atoms                     720     0.170     0.200
VDW; torsion.others                             705     0.081     0.200
HBOND: refined_atoms                            237     0.216     0.200
HBOND.others                                      3     0.045     0.200
Metal-ion: refined_atoms                          1     0.026     0.200
VDW repulsions: symmetry: refined_atoms           9     0.244     0.200
VDW repulsions: symmetry: others                 26     0.175     0.200
HBOND: symmetry: refined_atoms                   16     0.263     0.200
HBOND: symmetry: others                           1     0.049     0.200
M. chain bond B values: refined atoms           745     1.524     1.180
M. chain bond B values: others                  745     1.523     1.180
M. chain angle B values: refined atoms          926     2.485     1.751
M. chain angle B values: others                 927     2.483     1.751
S. chain bond B values: refined atoms           811     2.398     1.506
S. chain bond B values: others                  810     2.391     1.506
S. chain angle B values: refined atoms         1177     3.824     2.115
S. chain angle B values: others                1178     3.823     2.115
Long range B values: refined atoms             1877     6.753    16.623
Long range B values: others                    1778     6.297    15.282
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =    0.3535
Partial structure    1: scale =     0.3772, B  =   48.2678
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2205 100.00   478.7   481.7  0.15  0.16     106   524.9   541.9  0.17  0.19
 0.104    3714 100.00   385.2   368.6  0.16  0.15     210   400.8   376.6  0.19  0.18
 0.173    4691  99.96   248.5   243.4  0.16  0.14     251   241.3   237.0  0.24  0.20
 0.242    5493 100.00   188.7   189.3  0.19  0.15     311   186.4   188.0  0.22  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1517   0.928    688   0.831   2205   0.898  0.963  0.9757  0.9738  0.9438  0.9438
  0.1042   3013   0.895    701   0.789   3714   0.875  1.001  0.9573  0.9645  0.9098  0.9447
  0.1733   3992   0.856    699   0.763   4691   0.842  0.973  0.9338  0.9540  0.8751  0.9366
  0.2425   4788   0.874    708   0.764   5496   0.860  0.951  0.9446  0.9529  0.8980  0.9170
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16106
Percentage observed                  =    99.9823
Percentage of free reflections       =     5.1696
Overall R factor                     =     0.1636
Free R factor                        =     0.2038
Average Fourier shell correlation    =     0.9588
AverageFree Fourier shell correlation=     0.9483
Overall weighted R factor            =     0.1498
Free weighted R factor               =     0.1884
Overall weighted R2 factor           =     0.1801
Free weighted R2 factor              =     0.2212
Average correlation coefficient      =     0.9328
Overall correlation coefficient      =     0.9535
Free correlation coefficient         =     0.9365
Cruickshanks DPI for coordinate error=     0.1449
DPI based on free R factor           =     0.1331
Overall figure of merit              =     0.8635
ML based su of positional parameters =     0.0856
ML based su of thermal parameters    =     2.8637
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    88019.656       25783.152       663887.75      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.25085789    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    644930.88    

-------------------------------------------------------------------------------
             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 =     0.0402, B  =   -0.0959
Partial structure    1: scale =     0.3773, B  =   48.1098
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                        =     0.2021
Average Fourier shell correlation    =     0.9615
AverageFree Fourier shell correlation=     0.9508
Average correlation coefficient      =     0.9370
Overall figure of merit              =     0.8701
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    87506.758       10544.488       644930.88       663887.75    


     CGMAT cycle number =      3

 Weight matrix   0.25419858    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    642603.63    

-------------------------------------------------------------------------------
             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 =     0.0402, B  =   -0.0192
Partial structure    1: scale =     0.3769, B  =   46.1288
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                     =     0.1598
Free R factor                        =     0.2012
Average Fourier shell correlation    =     0.9622
AverageFree Fourier shell correlation=     0.9513
Average correlation coefficient      =     0.9385
Overall figure of merit              =     0.8710
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    87346.164       9381.4736       642603.63       644930.88    


     CGMAT cycle number =      4

 Weight matrix   0.25551555    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    641741.13    

-------------------------------------------------------------------------------
             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 =     0.0402, B  =   -0.0610
Partial structure    1: scale =     0.3770, B  =   46.1558
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                        =     0.2005
Average Fourier shell correlation    =     0.9624
AverageFree Fourier shell correlation=     0.9515
Average correlation coefficient      =     0.9391
Overall figure of merit              =     0.8713
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    87286.875       8948.8047       641741.13       642603.63    


     CGMAT cycle number =      5

 Weight matrix   0.25625509    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    641388.00    

-------------------------------------------------------------------------------
             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  =   -0.0522
Partial structure    1: scale =     0.3766, B  =   46.2313
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                     =     0.1591
Free R factor                        =     0.2003
Average Fourier shell correlation    =     0.9625
AverageFree Fourier shell correlation=     0.9516
Average correlation coefficient      =     0.9394
Overall figure of merit              =     0.8715
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    87245.539       8895.3652       641388.00       641741.13    


     CGMAT cycle number =      6

 Weight matrix   0.25599486    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    641327.31    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.0586
Partial structure    1: scale =     0.3766, B  =   46.3010
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                     =     0.1590
Free R factor                        =     0.2002
Average Fourier shell correlation    =     0.9626
AverageFree Fourier shell correlation=     0.9515
Average correlation coefficient      =     0.9397
Overall figure of merit              =     0.8714
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    87235.938       8904.3359       641327.31       641388.00    


     CGMAT cycle number =      7

 Weight matrix   0.25571790    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    641342.50    

-------------------------------------------------------------------------------
             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 =     0.0402, B  =   -0.0596
Partial structure    1: scale =     0.3767, B  =   46.4921
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                     =     0.1590
Free R factor                        =     0.2003
Average Fourier shell correlation    =     0.9626
AverageFree Fourier shell correlation=     0.9514
Average correlation coefficient      =     0.9398
Overall figure of merit              =     0.8713
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    87238.164       8911.0479       641292.19       641327.31    
 fvalues    87238.164       8911.0479       641292.19       641350.25    


     CGMAT cycle number =      8

 Weight matrix   0.25532037    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    641342.06    

-------------------------------------------------------------------------------
             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 =     0.0402, B  =   -0.0590
Partial structure    1: scale =     0.3767, B  =   46.4312
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                     =     0.1590
Free R factor                        =     0.2006
Average Fourier shell correlation    =     0.9625
AverageFree Fourier shell correlation=     0.9513
Average correlation coefficient      =     0.9398
Overall figure of merit              =     0.8711
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    87236.023       8918.4180       641342.06       641350.25    


     CGMAT cycle number =      9

 Weight matrix   0.25471237    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    641333.63    

-------------------------------------------------------------------------------
             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 =     0.0402, B  =   -0.0502
Partial structure    1: scale =     0.3765, B  =   46.3298
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                     =     0.1589
Free R factor                        =     0.2009
Average Fourier shell correlation    =     0.9625
AverageFree Fourier shell correlation=     0.9512
Average correlation coefficient      =     0.9399
Overall figure of merit              =     0.8710
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    87236.102       8909.4326       641333.63       641342.06    


     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.= 0.921 id.= 3.000 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   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   0.25417790    
 Actual weight    7.2495699      is applied to the X-ray term
Norm of X_ray positional gradient                34.9
Norm of Geom. positional gradient                34.9
Norm of X_ray B-factor gradient                  117.
Norm of Geom. B-factor gradient                  120.
Product of X_ray and Geom posit. gradients     -0.118E+08
 Cosine of angle between them                      -0.998
Product of X_ray and Geom B-fact gradients     -0.450E+08
 Cosine of angle between them                      -0.997


Residuals: XRAY=     0.6324E+06 GEOM=      8902.     TOTAL=     0.6413E+06
 function value    641305.13    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2103     1.773     1.644
Bond angles  : others                          3242     1.453     1.582
Torsion angles, period  1. refined              184     6.987     5.000
Torsion angles, period  2. refined               90    36.752    22.778
Torsion angles, period  3. refined              268    14.109    15.000
Torsion angles, period  4. refined                9    10.831    15.000
Chiral centres: refined atoms                   196     0.086     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   303     0.266     0.200
VDW repulsions.others                          1363     0.205     0.200
VDW; torsion: refined_atoms                     723     0.171     0.200
VDW; torsion.others                             788     0.084     0.200
HBOND: refined_atoms                            237     0.204     0.200
HBOND.others                                      2     0.050     0.200
VDW repulsions: symmetry: refined_atoms           9     0.254     0.200
VDW repulsions: symmetry: others                 25     0.195     0.200
HBOND: symmetry: refined_atoms                   22     0.221     0.200
HBOND: symmetry: others                           1     0.042     0.200
M. chain bond B values: refined atoms           745     1.578     1.208
M. chain bond B values: others                  745     1.577     1.208
M. chain angle B values: refined atoms          926     2.541     1.793
M. chain angle B values: others                 927     2.539     1.793
S. chain bond B values: refined atoms           811     2.640     1.561
S. chain bond B values: others                  810     2.636     1.560
S. chain angle B values: refined atoms         1177     4.156     2.188
S. chain angle B values: others                1178     4.155     2.188
Long range B values: refined atoms             1867     7.018    17.147
Long range B values: others                    1770     6.607    15.763
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.0491
Partial structure    1: scale =     0.3767, B  =   46.3914
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2205 100.00   478.9   482.7  0.15  0.16     106   525.1   547.9  0.18  0.20
 0.104    3714 100.00   385.4   367.8  0.16  0.15     210   401.0   373.6  0.19  0.18
 0.173    4691  99.96   248.6   242.9  0.16  0.14     251   241.4   237.4  0.23  0.19
 0.242    5493 100.00   188.8   189.7  0.16  0.13     311   186.5   188.9  0.21  0.17
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1517   0.941    688   0.850   2205   0.912  0.963  0.9777  0.9760  0.9425  0.9441
  0.1042   3013   0.896    701   0.792   3714   0.877  1.001  0.9573  0.9649  0.9085  0.9446
  0.1733   3992   0.863    699   0.768   4691   0.848  0.973  0.9375  0.9557  0.8794  0.9354
  0.2425   4788   0.884    708   0.772   5496   0.869  0.955  0.9487  0.9611  0.9028  0.9389
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16106
Percentage observed                  =    99.9823
Percentage of free reflections       =     5.1696
Overall R factor                     =     0.1589
Free R factor                        =     0.2010
Average Fourier shell correlation    =     0.9624
AverageFree Fourier shell correlation=     0.9510
Overall weighted R factor            =     0.1478
Free weighted R factor               =     0.1884
Overall weighted R2 factor           =     0.1798
Free weighted R2 factor              =     0.2261
Average correlation coefficient      =     0.9399
Overall correlation coefficient      =     0.9553
Free correlation coefficient         =     0.9362
Cruickshanks DPI for coordinate error=     0.1407
DPI based on free R factor           =     0.1313
Overall figure of merit              =     0.8708
ML based su of positional parameters =     0.0818
ML based su of thermal parameters    =     2.7268
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    87233.242       8901.6221       641305.13       641333.63    

    ****                              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.= 0.921 id.= 3.000 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

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

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R15_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     1.772     1.644
Bond angles  : others                          3242     1.453     1.582
Torsion angles, period  1. refined              184     6.985     5.000
Torsion angles, period  2. refined               90    36.743    22.778
Torsion angles, period  3. refined              268    14.090    15.000
Torsion angles, period  4. refined                9    10.856    15.000
Chiral centres: refined atoms                   196     0.086     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   303     0.266     0.200
VDW repulsions.others                          1368     0.204     0.200
VDW; torsion: refined_atoms                     724     0.171     0.200
VDW; torsion.others                             793     0.084     0.200
HBOND: refined_atoms                            237     0.205     0.200
HBOND.others                                      2     0.054     0.200
VDW repulsions: symmetry: refined_atoms           9     0.255     0.200
VDW repulsions: symmetry: others                 25     0.196     0.200
HBOND: symmetry: refined_atoms                   22     0.222     0.200
HBOND: symmetry: others                           1     0.042     0.200
M. chain bond B values: refined atoms           745     1.578     1.209
M. chain bond B values: others                  745     1.578     1.209
M. chain angle B values: refined atoms          926     2.542     1.794
M. chain angle B values: others                 927     2.541     1.793
S. chain bond B values: refined atoms           811     2.641     1.561
S. chain bond B values: others                  810     2.636     1.560
S. chain angle B values: refined atoms         1177     4.157     2.189
S. chain angle B values: others                1178     4.156     2.188
Long range B values: refined atoms             1867     7.024    17.154
Long range B values: others                    1770     6.601    15.774
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.0507
Partial structure    1: scale =     0.3763, B  =   46.2744
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2205 100.00   478.9   482.8  0.15  0.16     106   525.0   547.7  0.18  0.20
 0.104    3714 100.00   385.4   367.8  0.16  0.15     210   401.0   373.3  0.19  0.18
 0.173    4691  99.96   248.6   242.9  0.16  0.14     251   241.4   237.3  0.23  0.20
 0.242    5493 100.00   188.8   189.6  0.16  0.13     311   186.5   189.0  0.21  0.17
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1517   0.940    688   0.849   2205   0.912  0.963  0.9776  0.9761  0.9424  0.9444
  0.1042   3013   0.896    701   0.792   3714   0.876  1.001  0.9571  0.9648  0.9083  0.9445
  0.1733   3992   0.862    699   0.768   4691   0.848  0.973  0.9373  0.9557  0.8791  0.9354
  0.2425   4788   0.884    708   0.771   5496   0.869  0.955  0.9486  0.9610  0.9026  0.9390
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16106
Percentage observed                  =    99.9823
Percentage of free reflections       =     5.1696
Overall R factor                     =     0.1589
Free R factor                        =     0.2011
Average Fourier shell correlation    =     0.9624
AverageFree Fourier shell correlation=     0.9509
Overall weighted R factor            =     0.1478
Free weighted R factor               =     0.1885
Overall weighted R2 factor           =     0.1797
Free weighted R2 factor              =     0.2264
Average correlation coefficient      =     0.9400
Overall correlation coefficient      =     0.9554
Free correlation coefficient         =     0.9360
Cruickshanks DPI for coordinate error=     0.1406
DPI based on free R factor           =     0.1313
Overall figure of merit              =     0.8706
ML based su of positional parameters =     0.0818
ML based su of thermal parameters    =     2.7268
-----------------------------------------------------------------------------
  Time in seconds: CPU =        12.88
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1636   0.2038   0.863       88020.    4911.4   0.0139  1.073   1.834  1.063   0.086
       1   0.1612   0.2021   0.870       87507.    4900.9   0.0118  0.862   1.756  1.014   0.087
       2   0.1598   0.2012   0.871       87346.    4897.1   0.0123  0.900   1.770  1.022   0.087
       3   0.1594   0.2005   0.871       87287.    4895.5   0.0124  0.906   1.773  1.024   0.087
       4   0.1591   0.2003   0.871       87246.    4894.2   0.0124  0.909   1.774  1.025   0.087
       5   0.1590   0.2002   0.871       87236.    4894.9   0.0124  0.910   1.775  1.026   0.086
       6   0.1590   0.2003   0.871       87237.    4895.5   0.0124  0.910   1.774  1.027   0.086
       7   0.1590   0.2006   0.871       87236.    4896.3   0.0124  0.911   1.774  1.027   0.086
       8   0.1589   0.2009   0.871       87236.    4897.2   0.0124  0.910   1.774  1.027   0.086
       9   0.1589   0.2010   0.871       87233.    4897.5   0.0124  0.910   1.773  1.027   0.086
      10   0.1589   0.2011   0.871       87235.    4898.1   0.0124  0.909   1.772  1.027   0.086
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1636   0.1589
             R free    0.2038   0.2011
     Rms BondLength    0.0139   0.0124
      Rms BondAngle    1.8335   1.7721
     Rms ChirVolume    0.0861   0.0859
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      44.8s System:    0.1s Elapsed:     0:45