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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: 14:48:34 


 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 12
  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_R12_2-00A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R12_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_R12_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:    12
  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_R12_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=   2.026 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=   2.244 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=   1.809 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=   2.206 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=   2.331 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=   2.468 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=   1.966 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                           12
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.= 1.540 id.= 1.337 dev= -0.203 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.= 0.874 id.= 3.000 dev= -2.13 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   0.24878585    
 Actual weight    7.2495699      is applied to the X-ray term
Norm of X_ray positional gradient                43.4
Norm of Geom. positional gradient                86.9
Norm of X_ray B-factor gradient                  142.
Norm of Geom. B-factor gradient                 0.212E+05
Product of X_ray and Geom posit. gradients     -0.803E+07
 Cosine of angle between them                      -0.220
Product of X_ray and Geom B-fact gradients     -0.391E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.6377E+06 GEOM=     0.2613E+05 TOTAL=     0.6639E+06
 function value    663870.56    

-------------------------------------------------------------------------------
             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     1.857     1.644
Bond angles  : others                          3242     2.350     1.582
Torsion angles, period  1. refined              184     7.220     5.000
Torsion angles, period  2. refined               90    36.992    22.778
Torsion angles, period  3. refined              268    14.807    15.000
Torsion angles, period  4. refined                9    10.933    15.000
Chiral centres: refined atoms                   196     0.085     0.200
Planar groups: refined atoms                   1736     0.012     0.020
Planar groups: others                           331     0.016     0.020
VDW repulsions: refined_atoms                   314     0.257     0.200
VDW repulsions.others                          1342     0.230     0.200
VDW; torsion: refined_atoms                     708     0.171     0.200
VDW; torsion.others                             703     0.081     0.200
HBOND: refined_atoms                            238     0.214     0.200
HBOND.others                                      2     0.062     0.200
VDW repulsions: symmetry: refined_atoms          13     0.197     0.200
VDW repulsions: symmetry: others                 30     0.139     0.200
HBOND: symmetry: refined_atoms                   17     0.233     0.200
M. chain bond B values: refined atoms           745     1.584     1.176
M. chain bond B values: others                  745     1.584     1.176
M. chain angle B values: refined atoms          926     2.537     1.746
M. chain angle B values: others                 927     2.535     1.746
S. chain bond B values: refined atoms           811     2.435     1.510
S. chain bond B values: others                  810     2.432     1.510
S. chain angle B values: refined atoms         1177     3.884     2.118
S. chain angle B values: others                1178     3.883     2.117
Long range B values: refined atoms             1870     6.860    16.495
Long range B values: others                    1772     6.489    15.115
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =    0.3602
Partial structure    1: scale =     0.3752, B  =   49.0589
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2203 100.00   481.5   485.7  0.16  0.17     108   470.8   479.4  0.17  0.18
 0.104    3721 100.00   385.7   368.6  0.16  0.15     203   396.3   375.9  0.22  0.21
 0.173    4703  99.96   248.4   242.8  0.15  0.13     239   245.5   243.9  0.21  0.18
 0.242    5515 100.00   188.6   189.6  0.19  0.15     289   189.5   190.1  0.23  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1524   0.928    679   0.843   2203   0.902  0.961  0.9683  0.9730  0.9248  0.9432
  0.1042   3035   0.895    686   0.789   3721   0.876  1.003  0.9499  0.9640  0.8897  0.9453
  0.1733   4007   0.881    696   0.783   4703   0.867  0.984  0.9493  0.9625  0.8878  0.9433
  0.2425   4818   0.866    700   0.756   5518   0.852  0.947  0.9383  0.9495  0.8570  0.9138
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16145
Percentage observed                  =    99.9823
Percentage of free reflections       =     4.9399
Overall R factor                     =     0.1631
Free R factor                        =     0.2108
Average Fourier shell correlation    =     0.9598
AverageFree Fourier shell correlation=     0.9481
Overall weighted R factor            =     0.1494
Free weighted R factor               =     0.1902
Overall weighted R2 factor           =     0.1806
Free weighted R2 factor              =     0.2187
Average correlation coefficient      =     0.9337
Overall correlation coefficient      =     0.9541
Free correlation coefficient         =     0.9210
Cruickshanks DPI for coordinate error=     0.1439
DPI based on free R factor           =     0.1374
Overall figure of merit              =     0.8687
ML based su of positional parameters =     0.0828
ML based su of thermal parameters    =     2.7859
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    87968.977       26133.334       663870.56      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.26520792    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    645532.25    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.1256
Partial structure    1: scale =     0.3751, B  =   49.3065
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                     =     0.1607
Free R factor                        =     0.2087
Average Fourier shell correlation    =     0.9622
AverageFree Fourier shell correlation=     0.9499
Average correlation coefficient      =     0.9379
Overall figure of merit              =     0.8738
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    87563.711       10732.980       645532.25       663870.56    


     CGMAT cycle number =      3

 Weight matrix   0.26844287    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    643243.69    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.0543
Partial structure    1: scale =     0.3751, B  =   47.5566
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                     =     0.1594
Free R factor                        =     0.2081
Average Fourier shell correlation    =     0.9627
AverageFree Fourier shell correlation=     0.9503
Average correlation coefficient      =     0.9393
Overall figure of merit              =     0.8745
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    87412.305       9542.0879       643243.69       645532.25    


     CGMAT cycle number =      4

 Weight matrix   0.26927987    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    642391.44    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.0835
Partial structure    1: scale =     0.3754, B  =   47.5797
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                     =     0.1589
Free R factor                        =     0.2081
Average Fourier shell correlation    =     0.9629
AverageFree Fourier shell correlation=     0.9504
Average correlation coefficient      =     0.9400
Overall figure of merit              =     0.8747
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    87354.320       9110.2070       642391.44       643243.69    


     CGMAT cycle number =      5

 Weight matrix   0.26854664    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    642165.38    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.0651
Partial structure    1: scale =     0.3756, B  =   47.7071
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                     =     0.1587
Free R factor                        =     0.2083
Average Fourier shell correlation    =     0.9629
AverageFree Fourier shell correlation=     0.9503
Average correlation coefficient      =     0.9403
Overall figure of merit              =     0.8745
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    87331.219       9051.6504       642165.38       642391.44    


     CGMAT cycle number =      6

 Weight matrix   0.26852432    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    642012.38    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.0679
Partial structure    1: scale =     0.3758, B  =   47.8946
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                     =     0.1585
Free R factor                        =     0.2084
Average Fourier shell correlation    =     0.9629
AverageFree Fourier shell correlation=     0.9502
Average correlation coefficient      =     0.9405
Overall figure of merit              =     0.8744
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    87310.359       9049.8359       642012.38       642165.38    


     CGMAT cycle number =      7

 Weight matrix   0.26741064    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    642109.06    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.0869
Partial structure    1: scale =     0.3760, B  =   48.1762
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                     =     0.1585
Free R factor                        =     0.2090
Average Fourier shell correlation    =     0.9628
AverageFree Fourier shell correlation=     0.9499
Average correlation coefficient      =     0.9406
Overall figure of merit              =     0.8739
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    87321.758       9049.3320       642169.38       642012.38    

 fvalues    87321.758       9049.3320       642120.81       642094.50    
 fvalues    87321.758       9049.3320       642120.81       642094.50    


     CGMAT cycle number =      8

 Weight matrix   0.26718691    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    642130.88    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.0885
Partial structure    1: scale =     0.3759, B  =   48.2298
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                     =     0.1585
Free R factor                        =     0.2091
Average Fourier shell correlation    =     0.9628
AverageFree Fourier shell correlation=     0.9499
Average correlation coefficient      =     0.9406
Overall figure of merit              =     0.8738
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    87327.297       9046.0039       642155.50       642094.50    

 fvalues    87327.297       9046.0039       642152.31       642131.31    
 fvalues    87327.297       9046.0039       642152.31       642131.31    


     CGMAT cycle number =      9

 Weight matrix   0.26720321    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    642115.19    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.0872
Partial structure    1: scale =     0.3759, B  =   48.2022
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                     =     0.1585
Free R factor                        =     0.2091
Average Fourier shell correlation    =     0.9628
AverageFree Fourier shell correlation=     0.9499
Average correlation coefficient      =     0.9406
Overall figure of merit              =     0.8738
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    87325.086       9045.8984       642115.19       642131.31    


     CGMAT cycle number =     10

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.885 id.= 3.000 dev= -2.12 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    31   31   65
 Minimum acceptable grid spacing:    73   73  154
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    31   31   65
 Minimum acceptable grid spacing:    73   73  154
 Weight matrix   0.26687559    
 Actual weight    7.2495699      is applied to the X-ray term
Norm of X_ray positional gradient                36.2
Norm of Geom. positional gradient                36.3
Norm of X_ray B-factor gradient                  119.
Norm of Geom. B-factor gradient                  123.
Product of X_ray and Geom posit. gradients     -0.127E+08
 Cosine of angle between them                      -0.997
Product of X_ray and Geom B-fact gradients     -0.466E+08
 Cosine of angle between them                      -0.991


Residuals: XRAY=     0.6331E+06 GEOM=      9045.     TOTAL=     0.6422E+06
 function value    642154.88    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.801     1.644
Bond angles  : others                          3242     1.462     1.582
Torsion angles, period  1. refined              184     6.917     5.000
Torsion angles, period  2. refined               90    37.024    22.778
Torsion angles, period  3. refined              268    14.361    15.000
Torsion angles, period  4. refined                9    10.356    15.000
Chiral centres: refined atoms                   196     0.084     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   293     0.268     0.200
VDW repulsions.others                          1367     0.206     0.200
VDW; torsion: refined_atoms                     713     0.171     0.200
VDW; torsion.others                             758     0.085     0.200
HBOND: refined_atoms                            240     0.208     0.200
HBOND.others                                      1     0.012     0.200
VDW repulsions: symmetry: refined_atoms          11     0.224     0.200
VDW repulsions: symmetry: others                 27     0.170     0.200
HBOND: symmetry: refined_atoms                   25     0.184     0.200
M. chain bond B values: refined atoms           745     1.644     1.211
M. chain bond B values: others                  745     1.644     1.211
M. chain angle B values: refined atoms          926     2.579     1.798
M. chain angle B values: others                 927     2.578     1.798
S. chain bond B values: refined atoms           811     2.686     1.571
S. chain bond B values: others                  810     2.684     1.571
S. chain angle B values: refined atoms         1177     4.235     2.201
S. chain angle B values: others                1178     4.233     2.200
Long range B values: refined atoms             1852     7.169    16.944
Long range B values: others                    1752     6.708    15.495
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.0863
Partial structure    1: scale =     0.3759, B  =   48.1857
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2203 100.00   481.7   486.6  0.15  0.16     108   470.9   480.2  0.17  0.18
 0.104    3721 100.00   385.8   367.8  0.16  0.15     203   396.4   375.9  0.22  0.20
 0.173    4703  99.96   248.5   242.6  0.16  0.13     239   245.5   243.7  0.21  0.17
 0.242    5515 100.00   188.7   189.9  0.17  0.13     289   189.5   190.0  0.23  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1524   0.934    679   0.857   2203   0.910  0.961  0.9687  0.9738  0.9222  0.9436
  0.1042   3035   0.895    686   0.789   3721   0.876  1.003  0.9504  0.9641  0.8904  0.9444
  0.1733   4007   0.885    696   0.786   4703   0.870  0.984  0.9516  0.9630  0.8933  0.9421
  0.2425   4818   0.875    700   0.763   5518   0.861  0.951  0.9409  0.9573  0.8607  0.9354
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16145
Percentage observed                  =    99.9823
Percentage of free reflections       =     4.9399
Overall R factor                     =     0.1585
Free R factor                        =     0.2092
Average Fourier shell correlation    =     0.9628
AverageFree Fourier shell correlation=     0.9498
Overall weighted R factor            =     0.1476
Free weighted R factor               =     0.1883
Overall weighted R2 factor           =     0.1802
Free weighted R2 factor              =     0.2173
Average correlation coefficient      =     0.9406
Overall correlation coefficient      =     0.9557
Free correlation coefficient         =     0.9217
Cruickshanks DPI for coordinate error=     0.1399
DPI based on free R factor           =     0.1363
Overall figure of merit              =     0.8737
ML based su of positional parameters =     0.0798
ML based su of thermal parameters    =     2.6676
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    87329.305       9045.3428       642150.50       642115.19    

 fvalues    87329.305       9045.3428       642156.69       642145.19    
 fvalues    87329.305       9045.3428       642156.69       642145.19    

    ****                              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.= 0.885 id.= 3.000 dev= -2.12 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_R12_1-90A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.800     1.644
Bond angles  : others                          3242     1.462     1.582
Torsion angles, period  1. refined              184     6.916     5.000
Torsion angles, period  2. refined               90    37.024    22.778
Torsion angles, period  3. refined              268    14.359    15.000
Torsion angles, period  4. refined                9    10.356    15.000
Chiral centres: refined atoms                   196     0.084     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   293     0.268     0.200
VDW repulsions.others                          1367     0.206     0.200
VDW; torsion: refined_atoms                     713     0.171     0.200
VDW; torsion.others                             758     0.085     0.200
HBOND: refined_atoms                            240     0.208     0.200
HBOND.others                                      1     0.012     0.200
VDW repulsions: symmetry: refined_atoms          11     0.224     0.200
VDW repulsions: symmetry: others                 27     0.170     0.200
HBOND: symmetry: refined_atoms                   25     0.184     0.200
M. chain bond B values: refined atoms           745     1.644     1.211
M. chain bond B values: others                  745     1.643     1.211
M. chain angle B values: refined atoms          926     2.579     1.798
M. chain angle B values: others                 927     2.578     1.797
S. chain bond B values: refined atoms           811     2.686     1.571
S. chain bond B values: others                  810     2.684     1.571
S. chain angle B values: refined atoms         1177     4.235     2.201
S. chain angle B values: others                1178     4.233     2.200
Long range B values: refined atoms             1852     7.169    16.944
Long range B values: others                    1752     6.708    15.495
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.0875
Partial structure    1: scale =     0.3759, B  =   48.1979
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2203 100.00   481.6   486.6  0.15  0.16     108   470.9   480.2  0.17  0.18
 0.104    3721 100.00   385.8   367.8  0.16  0.15     203   396.4   375.9  0.22  0.20
 0.173    4703  99.96   248.5   242.6  0.16  0.13     239   245.5   243.7  0.21  0.17
 0.242    5515 100.00   188.6   189.9  0.17  0.13     289   189.5   190.0  0.23  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1524   0.934    679   0.857   2203   0.910  0.961  0.9687  0.9738  0.9222  0.9436
  0.1042   3035   0.895    686   0.789   3721   0.876  1.003  0.9504  0.9641  0.8904  0.9444
  0.1733   4007   0.885    696   0.786   4703   0.870  0.984  0.9517  0.9630  0.8933  0.9421
  0.2425   4818   0.875    700   0.763   5518   0.861  0.951  0.9409  0.9573  0.8606  0.9355
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16145
Percentage observed                  =    99.9823
Percentage of free reflections       =     4.9399
Overall R factor                     =     0.1585
Free R factor                        =     0.2092
Average Fourier shell correlation    =     0.9628
AverageFree Fourier shell correlation=     0.9498
Overall weighted R factor            =     0.1476
Free weighted R factor               =     0.1883
Overall weighted R2 factor           =     0.1802
Free weighted R2 factor              =     0.2173
Average correlation coefficient      =     0.9406
Overall correlation coefficient      =     0.9557
Free correlation coefficient         =     0.9217
Cruickshanks DPI for coordinate error=     0.1399
DPI based on free R factor           =     0.1363
Overall figure of merit              =     0.8737
ML based su of positional parameters =     0.0798
ML based su of thermal parameters    =     2.6676
-----------------------------------------------------------------------------
  Time in seconds: CPU =        16.68
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1631   0.2108   0.869       87969.    4717.8   0.0141  1.067   1.857  1.070   0.085
       1   0.1607   0.2087   0.874       87564.    4710.1   0.0124  0.892   1.787  1.027   0.085
       2   0.1594   0.2081   0.874       87412.    4707.1   0.0128  0.925   1.798  1.034   0.085
       3   0.1589   0.2081   0.875       87354.    4706.6   0.0128  0.931   1.801  1.036   0.085
       4   0.1587   0.2083   0.874       87331.    4707.4   0.0128  0.932   1.803  1.038   0.085
       5   0.1585   0.2084   0.874       87310.    4707.3   0.0128  0.931   1.802  1.038   0.084
       6   0.1585   0.2090   0.874       87324.    4709.0   0.0128  0.931   1.802  1.038   0.084
       7   0.1585   0.2091   0.874       87327.    4709.5   0.0128  0.930   1.801  1.038   0.084
       8   0.1585   0.2091   0.874       87325.    4709.5   0.0128  0.930   1.801  1.038   0.084
       9   0.1585   0.2092   0.874       87331.    4709.9   0.0128  0.930   1.801  1.038   0.084
      10   0.1585   0.2092   0.874       87329.    4709.9   0.0128  0.930   1.800  1.038   0.084
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1631   0.1585
             R free    0.2108   0.2092
     Rms BondLength    0.0141   0.0128
      Rms BondAngle    1.8572   1.8004
     Rms ChirVolume    0.0854   0.0840
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      48.7s System:    0.1s Elapsed:     0:49