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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: 14:58:23 


 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 16
  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_R16_2-00A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R16_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_R16_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:    16
  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_R16_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=   2.024 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=   2.221 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=   1.826 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=   2.216 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=   2.319 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=   2.463 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=   1.987 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                           16
Number of "free" reflections        868
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     10 ARG C   . - A     11 THR N   . mod.= 1.482 id.= 1.337 dev= -0.145 sig.= 0.011
A    125 LEU C   . - A    126 ARG N   . mod.= 1.561 id.= 1.337 dev= -0.224 sig.= 0.011

    ****                          Bond angle outliers                           ****

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

A     10 ARG O     - A     11 THR N     mod.= 107.13 id.= 123.47 dev= 16.341 sig.=  1.500

    ****                Large deviation of atoms from planarity                 ****

Deviations from the planarity >10.000Sigma will be monitored
Atom: A     10 ARG C     deviation=   0.25 sigma.=   0.02

    ****                              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.= 0.886 id.= 3.000 dev= -2.11 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   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   0.24015419    
 Actual weight    7.2495699      is applied to the X-ray term
Norm of X_ray positional gradient                40.4
Norm of Geom. positional gradient                88.9
Norm of X_ray B-factor gradient                  136.
Norm of Geom. B-factor gradient                 0.221E+05
Product of X_ray and Geom posit. gradients     -0.736E+07
 Cosine of angle between them                      -0.211
Product of X_ray and Geom B-fact gradients     -0.388E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.6362E+06 GEOM=     0.2673E+05 TOTAL=     0.6630E+06
 function value    662980.38    

-------------------------------------------------------------------------------
             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     1.826     1.644
Bond angles  : others                          3242     2.354     1.582
Torsion angles, period  1. refined              184     7.345     5.000
Torsion angles, period  2. refined               90    36.681    22.778
Torsion angles, period  3. refined              268    14.678    15.000
Torsion angles, period  4. refined                9    11.264    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.013     0.020
Planar groups: others                           331     0.015     0.020
VDW repulsions: refined_atoms                   319     0.260     0.200
VDW repulsions.others                          1346     0.231     0.200
VDW; torsion: refined_atoms                     705     0.171     0.200
VDW; torsion.others                             684     0.081     0.200
HBOND: refined_atoms                            238     0.206     0.200
HBOND.others                                      5     0.057     0.200
VDW repulsions: symmetry: refined_atoms           7     0.248     0.200
VDW repulsions: symmetry: others                 25     0.160     0.200
HBOND: symmetry: refined_atoms                   15     0.261     0.200
HBOND: symmetry: others                           1     0.075     0.200
M. chain bond B values: refined atoms           745     1.548     1.185
M. chain bond B values: others                  745     1.547     1.185
M. chain angle B values: refined atoms          926     2.491     1.759
M. chain angle B values: others                 927     2.490     1.759
S. chain bond B values: refined atoms           812     2.421     1.510
S. chain bond B values: others                  811     2.416     1.509
S. chain angle B values: refined atoms         1177     3.861     2.123
S. chain angle B values: others                1178     3.859     2.122
Long range B values: refined atoms             1870     6.764    16.614
Long range B values: others                    1771     6.359    15.213
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =    0.3340
Partial structure    1: scale =     0.3767, B  =   49.1005
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2186 100.00   479.3   484.4  0.16  0.17     125   486.9   491.2  0.18  0.19
 0.104    3735 100.00   386.1   369.7  0.15  0.14     189   367.7   351.6  0.19  0.18
 0.173    4675  99.96   247.8   242.4  0.16  0.13     267   243.6   239.5  0.22  0.20
 0.242    5517 100.00   188.7   189.6  0.19  0.15     287   178.0   179.7  0.24  0.20
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1512   0.925    674   0.818   2186   0.892  0.955  0.9672  0.9724  0.9104  0.9404
  0.1042   3032   0.906    703   0.808   3735   0.887  1.004  0.9571  0.9691  0.9163  0.9493
  0.1733   3980   0.871    695   0.771   4675   0.856  0.980  0.9415  0.9588  0.8693  0.9400
  0.2425   4815   0.861    705   0.755   5520   0.847  0.946  0.9284  0.9494  0.8535  0.9175
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16116
Percentage observed                  =    99.9823
Percentage of free reflections       =     5.1107
Overall R factor                     =     0.1627
Free R factor                        =     0.2081
Average Fourier shell correlation    =     0.9598
AverageFree Fourier shell correlation=     0.9443
Overall weighted R factor            =     0.1496
Free weighted R factor               =     0.1924
Overall weighted R2 factor           =     0.1823
Free weighted R2 factor              =     0.2235
Average correlation coefficient      =     0.9345
Overall correlation coefficient      =     0.9543
Free correlation coefficient         =     0.9262
Cruickshanks DPI for coordinate error=     0.1439
DPI based on free R factor           =     0.1358
Overall figure of merit              =     0.8652
ML based su of positional parameters =     0.0843
ML based su of thermal parameters    =     2.8524
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    87763.602       26732.020       662980.38      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.25560424    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    644054.38    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =   -0.0962
Partial structure    1: scale =     0.3770, B  =   49.1760
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1605
Free R factor                        =     0.2067
Average Fourier shell correlation    =     0.9623
AverageFree Fourier shell correlation=     0.9470
Average correlation coefficient      =     0.9380
Overall figure of merit              =     0.8710
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    87362.555       10713.440       644054.38       662980.38    


     CGMAT cycle number =      3

 Weight matrix   0.25904363    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    641651.06    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =   -0.0788
Partial structure    1: scale =     0.3768, B  =   47.2153
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1591
Free R factor                        =     0.2061
Average Fourier shell correlation    =     0.9630
AverageFree Fourier shell correlation=     0.9475
Average correlation coefficient      =     0.9397
Overall figure of merit              =     0.8720
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    87215.063       9379.3574       641651.06       644054.38    


     CGMAT cycle number =      4

 Weight matrix   0.26017517    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    640800.00    

-------------------------------------------------------------------------------
             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 =     0.0403, B  =   -0.0722
Partial structure    1: scale =     0.3770, B  =   47.3757
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1585
Free R factor                        =     0.2060
Average Fourier shell correlation    =     0.9632
AverageFree Fourier shell correlation=     0.9477
Average correlation coefficient      =     0.9403
Overall figure of merit              =     0.8724
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    87155.602       8959.3467       640800.00       641651.06    


     CGMAT cycle number =      5

 Weight matrix   0.26078105    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    640477.50    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =   -0.0685
Partial structure    1: scale =     0.3771, B  =   47.2937
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1582
Free R factor                        =     0.2060
Average Fourier shell correlation    =     0.9634
AverageFree Fourier shell correlation=     0.9478
Average correlation coefficient      =     0.9406
Overall figure of merit              =     0.8726
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    87121.750       8882.2871       640477.50       640800.00    


     CGMAT cycle number =      6

 Weight matrix   0.26062793    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    640383.56    

-------------------------------------------------------------------------------
             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 =     0.0404, B  =   -0.0664
Partial structure    1: scale =     0.3775, B  =   47.3627
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1581
Free R factor                        =     0.2061
Average Fourier shell correlation    =     0.9634
AverageFree Fourier shell correlation=     0.9478
Average correlation coefficient      =     0.9408
Overall figure of merit              =     0.8727
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    87107.391       8892.4199       640383.56       640477.50    


     CGMAT cycle number =      7

 Weight matrix   0.26013887    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    640349.00    

-------------------------------------------------------------------------------
             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 =     0.0404, B  =   -0.0672
Partial structure    1: scale =     0.3775, B  =   47.2271
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1580
Free R factor                        =     0.2065
Average Fourier shell correlation    =     0.9634
AverageFree Fourier shell correlation=     0.9477
Average correlation coefficient      =     0.9409
Overall figure of merit              =     0.8726
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    87102.008       8896.9541       640349.00       640383.56    


     CGMAT cycle number =      8

 Weight matrix   0.25938901    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    640337.44    

-------------------------------------------------------------------------------
             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 =     0.0404, B  =   -0.0717
Partial structure    1: scale =     0.3776, B  =   47.2511
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1580
Free R factor                        =     0.2069
Average Fourier shell correlation    =     0.9634
AverageFree Fourier shell correlation=     0.9476
Average correlation coefficient      =     0.9410
Overall figure of merit              =     0.8724
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    87100.609       8895.4756       640337.44       640349.00    


     CGMAT cycle number =      9

 Weight matrix   0.25904340    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    640319.13    

-------------------------------------------------------------------------------
             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 =     0.0404, B  =   -0.0704
Partial structure    1: scale =     0.3770, B  =   46.9927
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1579
Free R factor                        =     0.2071
Average Fourier shell correlation    =     0.9634
AverageFree Fourier shell correlation=     0.9475
Average correlation coefficient      =     0.9410
Overall figure of merit              =     0.8724
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    87099.102       8888.1191       640319.13       640337.44    


     CGMAT cycle number =     10

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.907 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   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   0.25868791    
 Actual weight    7.2495699      is applied to the X-ray term
Norm of X_ray positional gradient                35.0
Norm of Geom. positional gradient                35.0
Norm of X_ray B-factor gradient                  116.
Norm of Geom. B-factor gradient                  120.
Product of X_ray and Geom posit. gradients     -0.118E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.446E+08
 Cosine of angle between them                      -0.994


Residuals: XRAY=     0.6314E+06 GEOM=      8886.     TOTAL=     0.6403E+06
 function value    640336.19    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.770     1.644
Bond angles  : others                          3242     1.449     1.582
Torsion angles, period  1. refined              184     6.983     5.000
Torsion angles, period  2. refined               90    36.713    22.778
Torsion angles, period  3. refined              268    14.134    15.000
Torsion angles, period  4. refined                9    11.249    15.000
Chiral centres: refined atoms                   196     0.085     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   311     0.265     0.200
VDW repulsions.others                          1358     0.206     0.200
VDW; torsion: refined_atoms                     713     0.172     0.200
VDW; torsion.others                             782     0.083     0.200
HBOND: refined_atoms                            236     0.198     0.200
HBOND.others                                      2     0.068     0.200
VDW repulsions: symmetry: refined_atoms           7     0.252     0.200
VDW repulsions: symmetry: others                 24     0.174     0.200
HBOND: symmetry: refined_atoms                   17     0.245     0.200
HBOND: symmetry: others                           1     0.052     0.200
M. chain bond B values: refined atoms           745     1.609     1.215
M. chain bond B values: others                  745     1.608     1.215
M. chain angle B values: refined atoms          926     2.544     1.803
M. chain angle B values: others                 927     2.542     1.802
S. chain bond B values: refined atoms           812     2.654     1.570
S. chain bond B values: others                  811     2.649     1.569
S. chain angle B values: refined atoms         1177     4.202     2.203
S. chain angle B values: others                1178     4.200     2.202
Long range B values: refined atoms             1867     7.036    17.163
Long range B values: others                    1770     6.670    15.757
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =   -0.0734
Partial structure    1: scale =     0.3768, B  =   47.0585
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   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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2186 100.00   479.1   485.3  0.16  0.17     125   486.8   492.9  0.17  0.19
 0.104    3735 100.00   385.9   368.6  0.15  0.14     189   367.6   352.9  0.20  0.19
 0.173    4675  99.96   247.7   242.3  0.16  0.13     267   243.6   240.5  0.22  0.20
 0.242    5517 100.00   188.6   189.7  0.17  0.13     287   177.9   181.3  0.24  0.20
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1512   0.935    674   0.830   2186   0.902  0.955  0.9703  0.9746  0.9143  0.9425
  0.1042   3032   0.908    703   0.812   3735   0.890  1.004  0.9582  0.9695  0.9156  0.9477
  0.1733   3980   0.876    695   0.775   4675   0.861  0.980  0.9438  0.9604  0.8692  0.9402
  0.2425   4815   0.872    705   0.763   5520   0.858  0.950  0.9340  0.9572  0.8575  0.9366
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16116
Percentage observed                  =    99.9823
Percentage of free reflections       =     5.1107
Overall R factor                     =     0.1579
Free R factor                        =     0.2072
Average Fourier shell correlation    =     0.9633
AverageFree Fourier shell correlation=     0.9475
Overall weighted R factor            =     0.1474
Free weighted R factor               =     0.1908
Overall weighted R2 factor           =     0.1813
Free weighted R2 factor              =     0.2211
Average correlation coefficient      =     0.9410
Overall correlation coefficient      =     0.9560
Free correlation coefficient         =     0.9275
Cruickshanks DPI for coordinate error=     0.1397
DPI based on free R factor           =     0.1352
Overall figure of merit              =     0.8723
ML based su of positional parameters =     0.0811
ML based su of thermal parameters    =     2.7364
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    87100.883       8886.3359       640357.06       640319.13    

 fvalues    87100.883       8886.3359       640352.56       640330.25    
 fvalues    87100.883       8886.3359       640352.56       640330.25    

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.907 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

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

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R16_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     1.770     1.644
Bond angles  : others                          3242     1.449     1.582
Torsion angles, period  1. refined              184     6.981     5.000
Torsion angles, period  2. refined               90    36.719    22.778
Torsion angles, period  3. refined              268    14.130    15.000
Torsion angles, period  4. refined                9    11.249    15.000
Chiral centres: refined atoms                   196     0.085     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   311     0.265     0.200
VDW repulsions.others                          1358     0.206     0.200
VDW; torsion: refined_atoms                     713     0.172     0.200
VDW; torsion.others                             782     0.083     0.200
HBOND: refined_atoms                            236     0.198     0.200
HBOND.others                                      2     0.068     0.200
VDW repulsions: symmetry: refined_atoms           7     0.252     0.200
VDW repulsions: symmetry: others                 24     0.174     0.200
HBOND: symmetry: refined_atoms                   17     0.245     0.200
HBOND: symmetry: others                           1     0.052     0.200
M. chain bond B values: refined atoms           745     1.609     1.215
M. chain bond B values: others                  745     1.608     1.215
M. chain angle B values: refined atoms          926     2.544     1.802
M. chain angle B values: others                 927     2.543     1.802
S. chain bond B values: refined atoms           812     2.654     1.570
S. chain bond B values: others                  811     2.650     1.570
S. chain angle B values: refined atoms         1177     4.203     2.203
S. chain angle B values: others                1178     4.201     2.202
Long range B values: refined atoms             1867     7.038    17.162
Long range B values: others                    1770     6.671    15.757
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =   -0.0739
Partial structure    1: scale =     0.3767, B  =   47.0662
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   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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2186 100.00   479.1   485.3  0.16  0.17     125   486.8   492.9  0.17  0.19
 0.104    3735 100.00   385.9   368.6  0.15  0.14     189   367.6   352.9  0.20  0.19
 0.173    4675  99.96   247.7   242.4  0.16  0.13     267   243.6   240.5  0.22  0.20
 0.242    5517 100.00   188.6   189.7  0.17  0.13     287   177.9   181.3  0.24  0.20
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1512   0.935    674   0.830   2186   0.902  0.955  0.9703  0.9746  0.9143  0.9425
  0.1042   3032   0.908    703   0.812   3735   0.890  1.004  0.9581  0.9694  0.9155  0.9477
  0.1733   3980   0.876    695   0.775   4675   0.861  0.980  0.9437  0.9604  0.8692  0.9401
  0.2425   4815   0.872    705   0.763   5520   0.858  0.950  0.9339  0.9572  0.8573  0.9366
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16116
Percentage observed                  =    99.9823
Percentage of free reflections       =     5.1107
Overall R factor                     =     0.1580
Free R factor                        =     0.2073
Average Fourier shell correlation    =     0.9633
AverageFree Fourier shell correlation=     0.9475
Overall weighted R factor            =     0.1475
Free weighted R factor               =     0.1908
Overall weighted R2 factor           =     0.1813
Free weighted R2 factor              =     0.2211
Average correlation coefficient      =     0.9410
Overall correlation coefficient      =     0.9561
Free correlation coefficient         =     0.9274
Cruickshanks DPI for coordinate error=     0.1397
DPI based on free R factor           =     0.1353
Overall figure of merit              =     0.8723
ML based su of positional parameters =     0.0811
ML based su of thermal parameters    =     2.7364
-----------------------------------------------------------------------------
  Time in seconds: CPU =        13.45
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1627   0.2081   0.865       87764.    4875.9   0.0138  1.076   1.826  1.061   0.087
       1   0.1605   0.2067   0.871       87363.    4867.0   0.0117  0.861   1.745  1.008   0.087
       2   0.1591   0.2061   0.872       87215.    4862.8   0.0120  0.886   1.756  1.014   0.087
       3   0.1585   0.2060   0.872       87156.    4861.5   0.0121  0.892   1.762  1.017   0.086
       4   0.1582   0.2060   0.873       87122.    4860.5   0.0121  0.895   1.765  1.019   0.086
       5   0.1581   0.2061   0.873       87107.    4860.2   0.0121  0.896   1.767  1.021   0.086
       6   0.1580   0.2065   0.873       87102.    4860.6   0.0121  0.897   1.769  1.022   0.086
       7   0.1580   0.2069   0.872       87101.    4861.3   0.0121  0.896   1.770  1.022   0.086
       8   0.1579   0.2071   0.872       87099.    4861.8   0.0121  0.896   1.770  1.022   0.086
       9   0.1579   0.2072   0.872       87102.    4862.1   0.0121  0.896   1.770  1.023   0.085
      10   0.1580   0.2073   0.872       87103.    4862.3   0.0121  0.895   1.770  1.023   0.085
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1627   0.1580
             R free    0.2081   0.2073
     Rms BondLength    0.0138   0.0121
      Rms BondAngle    1.8258   1.7701
     Rms ChirVolume    0.0867   0.0854
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      45.6s System:    0.1s Elapsed:     0:45