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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 26/ 5/2020 Run time: 14:51:03 


 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 13
  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_R13_2-00A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R13_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_R13_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:    13
  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_R13_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=   2.043 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=   2.241 ideal_dist=   2.090
            ch:AAA  res:  88  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   1.842 ideal_dist=   1.720
            ch:AAA  res:  93  CYS              at:SG  .->ch:AAA  res: 157  TYR              at:CE1 .
  INFO:     link is found (not be used) dist=   2.229 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=   2.350 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=   2.451 ideal_dist=   2.235
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:SG  .
  INFO:     link is found (not be used) dist=   2.039 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  PRO               190  AAA  is missing in the structure
  Number of chains                  :       4
  Total number of monomers          :     502
  Number of atoms                   :    3945
  Number of missing atoms           :       1
  Number of rebuilt atoms           :    1480
  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:      2949         0      2949
               Angles:      5344         0      5344
              Chirals:       196         0       196
               Planes:       453         0       453
             Torsions:      1556         0      1556
            Intervals:         0         0         0
--------------------------------------------------------------------------------


  Number of harmonic restraints       =            0
  Number of atoms in special position =            0
 -----------------------------------------------------


    ****                           Info from mtz file                           ****

FreeR flag                           13
Number of "free" reflections        839
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.= 1.532 id.= 1.337 dev= -0.195 sig.= 0.011
A    171 THR C   . - A    172 GLY N   . mod.= 1.732 id.= 1.337 dev= -0.395 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.= 0.906 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   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   0.26455027    
 Actual weight    7.2495699      is applied to the X-ray term
Norm of X_ray positional gradient                42.0
Norm of Geom. positional gradient                100.
Norm of X_ray B-factor gradient                  140.
Norm of Geom. B-factor gradient                  120.
Product of X_ray and Geom posit. gradients     -0.867E+07
 Cosine of angle between them                      -0.213
Product of X_ray and Geom B-fact gradients     -0.419E+08
 Cosine of angle between them                      -0.774


Residuals: XRAY=     0.6351E+06 GEOM=     0.1490E+05 TOTAL=     0.6500E+06
 function value    649986.44    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.017     0.013
Bond distances: others                         1391     0.035     0.017
Bond angles  : refined atoms                   2106     1.945     1.644
Bond angles  : others                          3238     2.373     1.580
Torsion angles, period  1. refined              185     7.456     5.000
Torsion angles, period  2. refined               90    37.173    22.778
Torsion angles, period  3. refined              268    14.830    15.000
Torsion angles, period  4. refined                9    11.032    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1743     0.013     0.020
Planar groups: others                           332     0.018     0.020
VDW repulsions: refined_atoms                   316     0.238     0.200
VDW repulsions.others                          1347     0.224     0.200
VDW; torsion: refined_atoms                     716     0.172     0.200
VDW; torsion.others                             712     0.082     0.200
HBOND: refined_atoms                            233     0.214     0.200
HBOND.others                                      4     0.044     0.200
VDW repulsions: symmetry: refined_atoms          12     0.208     0.200
VDW repulsions: symmetry: others                 29     0.164     0.200
HBOND: symmetry: refined_atoms                   19     0.219     0.200
HBOND: symmetry: others                           1     0.016     0.200
M. chain bond B values: refined atoms           746     1.640     1.177
M. chain bond B values: others                  746     1.639     1.177
M. chain angle B values: refined atoms          929     2.640     1.750
M. chain angle B values: others                 930     2.639     1.750
S. chain bond B values: refined atoms           811     2.650     1.534
S. chain bond B values: others                  810     2.645     1.533
S. chain angle B values: refined atoms         1177     4.208     2.145
S. chain angle B values: others                1178     4.206     2.145
Long range B values: refined atoms             1869     7.135    16.641
Long range B values: others                    1774     6.758    15.375
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =    0.3388
Partial structure    1: scale =     0.3764, B  =   46.3043
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2211 100.00   479.5   484.6  0.15  0.16     100   483.8   485.1  0.17  0.17
 0.104    3720 100.00   384.5   368.2  0.16  0.15     204   397.8   379.1  0.19  0.18
 0.173    4679  99.96   247.9   243.2  0.16  0.13     263   241.2   232.9  0.20  0.17
 0.242    5532 100.00   188.3   189.4  0.18  0.14     272   185.3   182.0  0.22  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1527   0.941    684   0.855   2211   0.914  0.963  0.9735  0.9767  0.9247  0.9465
  0.1042   3024   0.896    696   0.796   3720   0.877  1.000  0.9612  0.9667  0.9222  0.9446
  0.1733   3981   0.892    698   0.799   4679   0.878  0.986  0.9514  0.9647  0.9032  0.9412
  0.2425   4827   0.869    708   0.759   5535   0.855  0.949  0.9428  0.9518  0.9044  0.9196
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16145
Percentage observed                  =    99.9823
Percentage of free reflections       =     4.9399
Overall R factor                     =     0.1612
Free R factor                        =     0.1952
Average Fourier shell correlation    =     0.9624
AverageFree Fourier shell correlation=     0.9536
Overall weighted R factor            =     0.1480
Free weighted R factor               =     0.1780
Overall weighted R2 factor           =     0.1786
Free weighted R2 factor              =     0.2086
Average correlation coefficient      =     0.9353
Overall correlation coefficient      =     0.9551
Free correlation coefficient         =     0.9369
Cruickshanks DPI for coordinate error=     0.1422
DPI based on free R factor           =     0.1272
Overall figure of merit              =     0.8749
ML based su of positional parameters =     0.0802
ML based su of thermal parameters    =     2.7180
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    87602.891       14903.213       649986.44      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.28074336    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    641359.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =   -0.1104
Partial structure    1: scale =     0.3768, B  =   47.0139
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                     =     0.1591
Free R factor                        =     0.1936
Average Fourier shell correlation    =     0.9646
AverageFree Fourier shell correlation=     0.9556
Average correlation coefficient      =     0.9386
Overall figure of merit              =     0.8805
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    87229.766       8980.9570       641359.25       649986.44    


     CGMAT cycle number =      3

 Weight matrix   0.28393790    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    640570.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =   -0.0917
Partial structure    1: scale =     0.3769, B  =   47.1008
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                     =     0.1579
Free R factor                        =     0.1928
Average Fourier shell correlation    =     0.9651
AverageFree Fourier shell correlation=     0.9561
Average correlation coefficient      =     0.9399
Overall figure of merit              =     0.8815
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    87091.906       9191.4004       640570.25       641359.25    


     CGMAT cycle number =      4

 Weight matrix   0.28511399    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    640243.06    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =   -0.0857
Partial structure    1: scale =     0.3770, B  =   47.1644
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                     =     0.1575
Free R factor                        =     0.1926
Average Fourier shell correlation    =     0.9653
AverageFree Fourier shell correlation=     0.9563
Average correlation coefficient      =     0.9404
Overall figure of merit              =     0.8818
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    87035.477       9273.2832       640243.06       640570.25    


     CGMAT cycle number =      5

 Weight matrix   0.28523397    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    639929.81    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =   -0.0623
Partial structure    1: scale =     0.3817, B  =   48.1912
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                     =     0.1572
Free R factor                        =     0.1926
Average Fourier shell correlation    =     0.9654
AverageFree Fourier shell correlation=     0.9564
Average correlation coefficient      =     0.9405
Overall figure of merit              =     0.8819
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    86986.859       9312.5156       639929.81       640243.06    


     CGMAT cycle number =      6

 Weight matrix   0.28566584    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    639799.44    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =   -0.0798
Partial structure    1: scale =     0.3824, B  =   48.1917
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                     =     0.1572
Free R factor                        =     0.1923
Average Fourier shell correlation    =     0.9655
AverageFree Fourier shell correlation=     0.9565
Average correlation coefficient      =     0.9407
Overall figure of merit              =     0.8821
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    86969.039       9311.2910       639799.44       639929.81    


     CGMAT cycle number =      7

 Weight matrix   0.28577125    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    639754.88    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =   -0.0816
Partial structure    1: scale =     0.3824, B  =   48.2911
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                     =     0.1571
Free R factor                        =     0.1925
Average Fourier shell correlation    =     0.9655
AverageFree Fourier shell correlation=     0.9565
Average correlation coefficient      =     0.9408
Overall figure of merit              =     0.8821
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    86960.664       9327.4404       639754.88       639799.44    


     CGMAT cycle number =      8

 Weight matrix   0.28622055    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    639704.63    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =   -0.0788
Partial structure    1: scale =     0.3825, B  =   48.3063
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                     =     0.1571
Free R factor                        =     0.1925
Average Fourier shell correlation    =     0.9656
AverageFree Fourier shell correlation=     0.9566
Average correlation coefficient      =     0.9408
Overall figure of merit              =     0.8822
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    86952.281       9338.0176       639704.63       639754.88    


     CGMAT cycle number =      9

 Weight matrix   0.28571579    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    639712.94    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =   -0.0688
Partial structure    1: scale =     0.3835, B  =   48.6549
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                     =     0.1572
Free R factor                        =     0.1928
Average Fourier shell correlation    =     0.9655
AverageFree Fourier shell correlation=     0.9565
Average correlation coefficient      =     0.9408
Overall figure of merit              =     0.8821
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    86954.055       9341.0801       639689.50       639704.63    
 fvalues    86954.055       9341.0801       639689.50       639720.56    


     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.= 0.923 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   0.28581116    
 Actual weight    7.2495699      is applied to the X-ray term
Norm of X_ray positional gradient                37.4
Norm of Geom. positional gradient                37.3
Norm of X_ray B-factor gradient                  124.
Norm of Geom. B-factor gradient                  128.
Product of X_ray and Geom posit. gradients     -0.135E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.508E+08
 Cosine of angle between them                      -0.993


Residuals: XRAY=     0.6304E+06 GEOM=      9343.     TOTAL=     0.6397E+06
 function value    639730.50    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.840     1.644
Bond angles  : others                          3238     1.461     1.580
Torsion angles, period  1. refined              185     7.125     5.000
Torsion angles, period  2. refined               90    37.306    22.778
Torsion angles, period  3. refined              268    14.536    15.000
Torsion angles, period  4. refined                9    10.641    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   310     0.242     0.200
VDW repulsions.others                          1357     0.198     0.200
VDW; torsion: refined_atoms                     720     0.172     0.200
VDW; torsion.others                             794     0.085     0.200
HBOND: refined_atoms                            230     0.204     0.200
HBOND.others                                      1     0.073     0.200
VDW repulsions: symmetry: refined_atoms          10     0.223     0.200
VDW repulsions: symmetry: others                 27     0.184     0.200
HBOND: symmetry: refined_atoms                   21     0.204     0.200
HBOND: symmetry: others                           1     0.035     0.200
M. chain bond B values: refined atoms           746     1.660     1.210
M. chain bond B values: others                  746     1.659     1.211
M. chain angle B values: refined atoms          929     2.627     1.800
M. chain angle B values: others                 930     2.625     1.800
S. chain bond B values: refined atoms           811     2.853     1.588
S. chain bond B values: others                  810     2.849     1.587
S. chain angle B values: refined atoms         1177     4.474     2.220
S. chain angle B values: others                1178     4.472     2.219
Long range B values: refined atoms             1865     7.370    17.200
Long range B values: others                    1770     6.964    15.851
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =   -0.0755
Partial structure    1: scale =     0.3832, B  =   48.4959
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2211 100.00   478.9   484.3  0.15  0.16     100   483.1   484.6  0.17  0.18
 0.104    3720 100.00   384.0   367.2  0.16  0.15     204   397.2   378.6  0.19  0.18
 0.173    4679  99.96   247.6   242.6  0.15  0.13     263   240.8   232.2  0.20  0.18
 0.242    5532 100.00   188.0   189.4  0.17  0.13     272   185.1   182.9  0.21  0.17
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1527   0.946    684   0.863   2211   0.921  0.961  0.9744  0.9774  0.9245  0.9446
  0.1042   3024   0.902    696   0.802   3720   0.883  1.001  0.9627  0.9680  0.9233  0.9449
  0.1733   3981   0.894    698   0.800   4679   0.880  0.986  0.9527  0.9658  0.9069  0.9435
  0.2425   4827   0.882    708   0.772   5535   0.868  0.953  0.9490  0.9589  0.9124  0.9342
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16145
Percentage observed                  =    99.9823
Percentage of free reflections       =     4.9399
Overall R factor                     =     0.1572
Free R factor                        =     0.1929
Average Fourier shell correlation    =     0.9655
AverageFree Fourier shell correlation=     0.9565
Overall weighted R factor            =     0.1460
Free weighted R factor               =     0.1774
Overall weighted R2 factor           =     0.1780
Free weighted R2 factor              =     0.2080
Average correlation coefficient      =     0.9408
Overall correlation coefficient      =     0.9562
Free correlation coefficient         =     0.9385
Cruickshanks DPI for coordinate error=     0.1388
DPI based on free R factor           =     0.1257
Overall figure of merit              =     0.8822
ML based su of positional parameters =     0.0771
ML based su of thermal parameters    =     2.5997
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    86954.508       9342.9199       639693.00       639720.56    
 fvalues    86954.508       9342.9199       639693.00       639725.75    

    ****                              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.= 0.923 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_R13_1-90A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.839     1.644
Bond angles  : others                          3238     1.462     1.580
Torsion angles, period  1. refined              185     7.116     5.000
Torsion angles, period  2. refined               90    37.317    22.778
Torsion angles, period  3. refined              268    14.552    15.000
Torsion angles, period  4. refined                9    10.659    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   310     0.242     0.200
VDW repulsions.others                          1370     0.197     0.200
VDW; torsion: refined_atoms                     720     0.172     0.200
VDW; torsion.others                             794     0.085     0.200
HBOND: refined_atoms                            230     0.205     0.200
HBOND.others                                      1     0.076     0.200
VDW repulsions: symmetry: refined_atoms          10     0.223     0.200
VDW repulsions: symmetry: others                 27     0.186     0.200
HBOND: symmetry: refined_atoms                   21     0.204     0.200
HBOND: symmetry: others                           1     0.036     0.200
M. chain bond B values: refined atoms           746     1.660     1.210
M. chain bond B values: others                  746     1.659     1.211
M. chain angle B values: refined atoms          929     2.626     1.800
M. chain angle B values: others                 930     2.625     1.800
S. chain bond B values: refined atoms           811     2.857     1.588
S. chain bond B values: others                  810     2.853     1.588
S. chain angle B values: refined atoms         1177     4.477     2.220
S. chain angle B values: others                1178     4.475     2.220
Long range B values: refined atoms             1865     7.377    17.212
Long range B values: others                    1770     6.977    15.864
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =   -0.0747
Partial structure    1: scale =     0.3828, B  =   48.6263
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.53 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2211 100.00   478.8   484.3  0.15  0.16     100   483.1   484.3  0.17  0.18
 0.104    3720 100.00   383.9   367.1  0.16  0.15     204   397.2   378.6  0.19  0.18
 0.173    4679  99.96   247.6   242.6  0.15  0.13     263   240.8   232.2  0.20  0.18
 0.242    5532 100.00   188.0   189.4  0.17  0.13     272   185.1   182.9  0.21  0.17
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1527   0.947    684   0.864   2211   0.921  0.961  0.9748  0.9775  0.9254  0.9446
  0.1042   3024   0.902    696   0.802   3720   0.883  1.001  0.9628  0.9680  0.9235  0.9448
  0.1733   3981   0.894    698   0.800   4679   0.880  0.986  0.9526  0.9658  0.9067  0.9435
  0.2425   4827   0.882    708   0.772   5535   0.868  0.953  0.9491  0.9590  0.9128  0.9343
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16145
Percentage observed                  =    99.9823
Percentage of free reflections       =     4.9399
Overall R factor                     =     0.1573
Free R factor                        =     0.1927
Average Fourier shell correlation    =     0.9656
AverageFree Fourier shell correlation=     0.9566
Overall weighted R factor            =     0.1461
Free weighted R factor               =     0.1773
Overall weighted R2 factor           =     0.1782
Free weighted R2 factor              =     0.2078
Average correlation coefficient      =     0.9408
Overall correlation coefficient      =     0.9562
Free correlation coefficient         =     0.9387
Cruickshanks DPI for coordinate error=     0.1388
DPI based on free R factor           =     0.1256
Overall figure of merit              =     0.8823
ML based su of positional parameters =     0.0771
ML based su of thermal parameters    =     2.5997
-----------------------------------------------------------------------------
  Time in seconds: CPU =        14.27
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1612   0.1952   0.875       87603.    4663.4   0.0175  1.418   1.945  1.125   0.090
       1   0.1591   0.1936   0.881       87230.    4655.6   0.0126  0.922   1.839  1.056   0.088
       2   0.1579   0.1928   0.881       87092.    4652.5   0.0129  0.946   1.839  1.055   0.088
       3   0.1575   0.1926   0.882       87035.    4651.2   0.0129  0.950   1.840  1.055   0.088
       4   0.1572   0.1926   0.882       86987.    4650.4   0.0130  0.951   1.840  1.056   0.088
       5   0.1572   0.1923   0.882       86969.    4649.7   0.0129  0.951   1.839  1.055   0.088
       6   0.1571   0.1925   0.882       86961.    4649.8   0.0130  0.953   1.839  1.056   0.088
       7   0.1571   0.1925   0.882       86952.    4649.4   0.0129  0.953   1.839  1.056   0.088
       8   0.1572   0.1928   0.882       86953.    4650.0   0.0130  0.955   1.840  1.057   0.087
       9   0.1572   0.1929   0.882       86955.    4650.2   0.0130  0.954   1.840  1.057   0.087
      10   0.1573   0.1927   0.882       86951.    4649.4   0.0130  0.955   1.839  1.057   0.087
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1612   0.1573
             R free    0.1952   0.1927
     Rms BondLength    0.0175   0.0130
      Rms BondAngle    1.9455   1.8393
     Rms ChirVolume    0.0897   0.0872
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      46.4s System:    0.1s Elapsed:     0:47