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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: 15:00:49 


 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 17
  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_R17_2-00A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R17_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_R17_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:    17
  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_R17_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=   2.032 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=   2.267 ideal_dist=   2.090
            ch:AAA  res:  88  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   1.833 ideal_dist=   1.720
            ch:AAA  res:  93  CYS              at:SG  .->ch:AAA  res: 157  TYR              at:CE1 .
  INFO:     link is found (not be used) dist=   2.233 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=   2.346 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=   2.431 ideal_dist=   2.235
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:SG  .
  INFO:     link is found (not be used) dist=   2.131 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                           17
Number of "free" reflections        841
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.= 1.460 id.= 1.337 dev= -0.123 sig.= 0.011
A    125 LEU C   . - A    126 ARG N   . mod.= 1.548 id.= 1.337 dev= -0.211 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.= 108.13 id.= 123.47 dev= 15.335 sig.=  1.500

    ****                              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.= 0.901 id.= 3.000 dev= -2.10 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    31   31   65
 Minimum acceptable grid spacing:    73   73  154
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    31   31   65
 Minimum acceptable grid spacing:    73   73  154
 Weight matrix   0.22743447    
 Actual weight    7.2495699      is applied to the X-ray term
Norm of X_ray positional gradient                39.6
Norm of Geom. positional gradient                88.1
Norm of X_ray B-factor gradient                  134.
Norm of Geom. B-factor gradient                 0.222E+05
Product of X_ray and Geom posit. gradients     -0.728E+07
 Cosine of angle between them                      -0.216
Product of X_ray and Geom B-fact gradients     -0.364E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.6388E+06 GEOM=     0.2662E+05 TOTAL=     0.6654E+06
 function value    665403.88    

-------------------------------------------------------------------------------
             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     2.352     1.582
Torsion angles, period  1. refined              184     7.296     5.000
Torsion angles, period  2. refined               90    37.033    22.778
Torsion angles, period  3. refined              268    14.462    15.000
Torsion angles, period  4. refined                9    10.777    15.000
Chiral centres: refined atoms                   196     0.082     0.200
Planar groups: refined atoms                   1736     0.012     0.020
Planar groups: others                           331     0.015     0.020
VDW repulsions: refined_atoms                   307     0.258     0.200
VDW repulsions.others                          1356     0.229     0.200
VDW; torsion: refined_atoms                     706     0.171     0.200
VDW; torsion.others                             706     0.081     0.200
HBOND: refined_atoms                            234     0.215     0.200
HBOND.others                                      4     0.044     0.200
VDW repulsions: symmetry: refined_atoms           9     0.234     0.200
VDW repulsions: symmetry: others                 25     0.157     0.200
HBOND: symmetry: refined_atoms                   18     0.238     0.200
HBOND: symmetry: others                           1     0.071     0.200
M. chain bond B values: refined atoms           745     1.528     1.185
M. chain bond B values: others                  745     1.527     1.185
M. chain angle B values: refined atoms          926     2.466     1.759
M. chain angle B values: others                 927     2.465     1.759
S. chain bond B values: refined atoms           811     2.385     1.508
S. chain bond B values: others                  810     2.383     1.508
S. chain angle B values: refined atoms         1177     3.797     2.121
S. chain angle B values: others                1178     3.795     2.121
Long range B values: refined atoms             1858     6.902    16.538
Long range B values: others                    1762     6.550    15.188
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =    0.3108
Partial structure    1: scale =     0.3754, B  =   49.7341
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2191 100.00   479.6   485.4  0.16  0.17     120   483.5   471.8  0.20  0.20
 0.104    3733 100.00   384.0   367.9  0.15  0.14     191   409.0   383.7  0.17  0.17
 0.173    4713  99.96   247.6   242.3  0.15  0.13     229   248.5   241.1  0.22  0.19
 0.242    5503 100.00   188.3   188.9  0.19  0.15     301   186.6   191.4  0.25  0.20
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1510   0.913    681   0.825   2191   0.885  0.958  0.9591  0.9695  0.9023  0.9418
  0.1042   3032   0.900    701   0.794   3733   0.880  1.002  0.9661  0.9669  0.9360  0.9470
  0.1733   4027   0.878    686   0.779   4713   0.864  0.984  0.9443  0.9627  0.8693  0.9454
  0.2425   4811   0.854    695   0.741   5506   0.840  0.943  0.9354  0.9452  0.8713  0.9114
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16143
Percentage observed                  =    99.9823
Percentage of free reflections       =     4.9517
Overall R factor                     =     0.1628
Free R factor                        =     0.2063
Average Fourier shell correlation    =     0.9586
AverageFree Fourier shell correlation=     0.9482
Overall weighted R factor            =     0.1493
Free weighted R factor               =     0.1867
Overall weighted R2 factor           =     0.1811
Free weighted R2 factor              =     0.2211
Average correlation coefficient      =     0.9337
Overall correlation coefficient      =     0.9543
Free correlation coefficient         =     0.9286
Cruickshanks DPI for coordinate error=     0.1437
DPI based on free R factor           =     0.1345
Overall figure of merit              =     0.8623
ML based su of positional parameters =     0.0866
ML based su of thermal parameters    =     2.9339
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    88113.617       26618.086       665403.88      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.24129716    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    646517.63    

-------------------------------------------------------------------------------
             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  =   -0.1299
Partial structure    1: scale =     0.3752, B  =   49.9254
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                     =     0.1606
Free R factor                        =     0.2036
Average Fourier shell correlation    =     0.9611
AverageFree Fourier shell correlation=     0.9504
Average correlation coefficient      =     0.9376
Overall figure of merit              =     0.8679
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    87716.734       10608.975       646517.63       665403.88    


     CGMAT cycle number =      3

 Weight matrix   0.24483050    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    644188.50    

-------------------------------------------------------------------------------
             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  =   -0.0650
Partial structure    1: scale =     0.3748, B  =   48.0933
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1594
Free R factor                        =     0.2028
Average Fourier shell correlation    =     0.9617
AverageFree Fourier shell correlation=     0.9509
Average correlation coefficient      =     0.9392
Overall figure of merit              =     0.8689
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    87575.305       9305.1621       644188.50       646517.63    


     CGMAT cycle number =      4

 Weight matrix   0.24569814    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    643395.31    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =   -0.1151
Partial structure    1: scale =     0.3751, B  =   48.3424
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1589
Free R factor                        =     0.2024
Average Fourier shell correlation    =     0.9620
AverageFree Fourier shell correlation=     0.9511
Average correlation coefficient      =     0.9398
Overall figure of merit              =     0.8692
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    87530.719       8835.2480       643395.31       644188.50    


     CGMAT cycle number =      5

 Weight matrix   0.24583669    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    643168.38    

-------------------------------------------------------------------------------
             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  =   -0.1013
Partial structure    1: scale =     0.3752, B  =   48.5705
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1587
Free R factor                        =     0.2025
Average Fourier shell correlation    =     0.9621
AverageFree Fourier shell correlation=     0.9511
Average correlation coefficient      =     0.9402
Overall figure of merit              =     0.8693
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    87508.836       8766.9121       643168.38       643395.31    


     CGMAT cycle number =      6

 Weight matrix   0.24541467    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    643134.13    

-------------------------------------------------------------------------------
             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 =     0.0403, B  =   -0.0951
Partial structure    1: scale =     0.3756, B  =   48.7046
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1585
Free R factor                        =     0.2024
Average Fourier shell correlation    =     0.9621
AverageFree Fourier shell correlation=     0.9511
Average correlation coefficient      =     0.9404
Overall figure of merit              =     0.8693
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    87503.500       8771.3848       643134.13       643168.38    


     CGMAT cycle number =      7

 Weight matrix   0.24516179    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    643103.06    

-------------------------------------------------------------------------------
             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  =   -0.0962
Partial structure    1: scale =     0.3764, B  =   48.7555
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1584
Free R factor                        =     0.2023
Average Fourier shell correlation    =     0.9621
AverageFree Fourier shell correlation=     0.9510
Average correlation coefficient      =     0.9405
Overall figure of merit              =     0.8692
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    87499.195       8771.4697       643103.06       643134.13    


     CGMAT cycle number =      8

 Weight matrix   0.24476941    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    643124.44    

-------------------------------------------------------------------------------
             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 =     0.0403, B  =   -0.1076
Partial structure    1: scale =     0.3768, B  =   48.8250
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1584
Free R factor                        =     0.2023
Average Fourier shell correlation    =     0.9620
AverageFree Fourier shell correlation=     0.9509
Average correlation coefficient      =     0.9405
Overall figure of merit              =     0.8690
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    87503.078       8773.5586       643165.75       643103.06    

 fvalues    87503.078       8773.5586       643156.44       643133.25    
 fvalues    87503.078       8773.5586       643156.44       643133.25    


     CGMAT cycle number =      9

 Weight matrix   0.24428661    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    643173.63    

-------------------------------------------------------------------------------
             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  =   -0.1038
Partial structure    1: scale =     0.3768, B  =   48.8260
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1584
Free R factor                        =     0.2025
Average Fourier shell correlation    =     0.9620
AverageFree Fourier shell correlation=     0.9509
Average correlation coefficient      =     0.9405
Overall figure of merit              =     0.8688
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    87509.883       8769.7412       643167.19       643133.25    
 fvalues    87509.883       8769.7412       643167.19       643178.75    


     CGMAT cycle number =     10

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.919 id.= 3.000 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    31   31   65
 Minimum acceptable grid spacing:    73   73  154
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    31   31   65
 Minimum acceptable grid spacing:    73   73  154
 Weight matrix   0.24438767    
 Actual weight    7.2495699      is applied to the X-ray term
Norm of X_ray positional gradient                34.1
Norm of Geom. positional gradient                34.1
Norm of X_ray B-factor gradient                  111.
Norm of Geom. B-factor gradient                  116.
Product of X_ray and Geom posit. gradients     -0.112E+08
 Cosine of angle between them                      -0.998
Product of X_ray and Geom B-fact gradients     -0.412E+08
 Cosine of angle between them                      -0.988


Residuals: XRAY=     0.6344E+06 GEOM=      8766.     TOTAL=     0.6431E+06
 function value    643133.94    

-------------------------------------------------------------------------------
             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     1.787     1.644
Bond angles  : others                          3242     1.445     1.582
Torsion angles, period  1. refined              184     6.991     5.000
Torsion angles, period  2. refined               90    37.021    22.778
Torsion angles, period  3. refined              268    14.221    15.000
Torsion angles, period  4. refined                9    10.848    15.000
Chiral centres: refined atoms                   196     0.083     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   303     0.263     0.200
VDW repulsions.others                          1368     0.205     0.200
VDW; torsion: refined_atoms                     722     0.171     0.200
VDW; torsion.others                             787     0.083     0.200
HBOND: refined_atoms                            228     0.210     0.200
HBOND.others                                      1     0.091     0.200
VDW repulsions: symmetry: refined_atoms           9     0.221     0.200
VDW repulsions: symmetry: others                 24     0.171     0.200
HBOND: symmetry: refined_atoms                   23     0.202     0.200
HBOND: symmetry: others                           1     0.036     0.200
M. chain bond B values: refined atoms           745     1.548     1.209
M. chain bond B values: others                  745     1.547     1.210
M. chain angle B values: refined atoms          926     2.472     1.796
M. chain angle B values: others                 927     2.471     1.796
S. chain bond B values: refined atoms           811     2.608     1.557
S. chain bond B values: others                  810     2.605     1.557
S. chain angle B values: refined atoms         1177     4.100     2.187
S. chain angle B values: others                1178     4.098     2.186
Long range B values: refined atoms             1854     7.031    17.109
Long range B values: others                    1759     6.705    15.718
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =   -0.1010
Partial structure    1: scale =     0.3769, B  =   48.7662
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10.  v. resln :N:1,6,7,11,12:
:Cycle   10.  and  v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2191 100.00   480.3   486.5  0.16  0.17     120   484.3   473.4  0.19  0.20
 0.104    3733 100.00   384.7   367.8  0.16  0.15     191   409.6   384.3  0.17  0.17
 0.173    4713  99.96   248.0   242.5  0.15  0.13     229   249.0   241.1  0.22  0.19
 0.242    5503 100.00   188.6   189.5  0.17  0.13     301   186.9   191.7  0.24  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1510   0.924    681   0.843   2191   0.899  0.958  0.9633  0.9718  0.9056  0.9413
  0.1042   3032   0.902    701   0.798   3733   0.882  1.002  0.9664  0.9673  0.9358  0.9459
  0.1733   4027   0.881    686   0.781   4713   0.866  0.984  0.9455  0.9629  0.8739  0.9442
  0.2425   4811   0.865    695   0.750   5506   0.850  0.947  0.9400  0.9538  0.8769  0.9335
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16143
Percentage observed                  =    99.9823
Percentage of free reflections       =     4.9517
Overall R factor                     =     0.1584
Free R factor                        =     0.2025
Average Fourier shell correlation    =     0.9620
AverageFree Fourier shell correlation=     0.9509
Overall weighted R factor            =     0.1478
Free weighted R factor               =     0.1838
Overall weighted R2 factor           =     0.1811
Free weighted R2 factor              =     0.2196
Average correlation coefficient      =     0.9406
Overall correlation coefficient      =     0.9556
Free correlation coefficient         =     0.9302
Cruickshanks DPI for coordinate error=     0.1398
DPI based on free R factor           =     0.1320
Overall figure of merit              =     0.8689
ML based su of positional parameters =     0.0834
ML based su of thermal parameters    =     2.8145
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    87504.180       8766.2510       643133.94       643178.75    

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.919 id.= 3.000 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

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

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R17_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     1.787     1.644
Bond angles  : others                          3242     1.445     1.582
Torsion angles, period  1. refined              184     6.991     5.000
Torsion angles, period  2. refined               90    37.017    22.778
Torsion angles, period  3. refined              268    14.223    15.000
Torsion angles, period  4. refined                9    10.850    15.000
Chiral centres: refined atoms                   196     0.083     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   304     0.262     0.200
VDW repulsions.others                          1367     0.205     0.200
VDW; torsion: refined_atoms                     722     0.171     0.200
VDW; torsion.others                             789     0.083     0.200
HBOND: refined_atoms                            228     0.210     0.200
HBOND.others                                      1     0.092     0.200
VDW repulsions: symmetry: refined_atoms           9     0.221     0.200
VDW repulsions: symmetry: others                 24     0.171     0.200
HBOND: symmetry: refined_atoms                   23     0.203     0.200
HBOND: symmetry: others                           1     0.037     0.200
M. chain bond B values: refined atoms           745     1.549     1.209
M. chain bond B values: others                  745     1.548     1.209
M. chain angle B values: refined atoms          926     2.473     1.796
M. chain angle B values: others                 927     2.472     1.795
S. chain bond B values: refined atoms           811     2.608     1.557
S. chain bond B values: others                  810     2.606     1.557
S. chain angle B values: refined atoms         1177     4.100     2.187
S. chain angle B values: others                1178     4.099     2.186
Long range B values: refined atoms             1855     7.043    17.119
Long range B values: others                    1760     6.717    15.736
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =   -0.1032
Partial structure    1: scale =     0.3769, B  =   48.6603
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle   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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2191 100.00   480.4   486.5  0.16  0.17     120   484.3   473.5  0.19  0.20
 0.104    3733 100.00   384.7   367.8  0.16  0.15     191   409.7   384.3  0.17  0.17
 0.173    4713  99.96   248.0   242.5  0.15  0.13     229   249.0   241.1  0.22  0.19
 0.242    5503 100.00   188.6   189.5  0.17  0.13     301   186.9   191.8  0.24  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1510   0.924    681   0.843   2191   0.899  0.958  0.9633  0.9718  0.9056  0.9413
  0.1042   3032   0.901    701   0.798   3733   0.882  1.002  0.9664  0.9673  0.9358  0.9459
  0.1733   4027   0.881    686   0.782   4713   0.866  0.984  0.9455  0.9629  0.8737  0.9442
  0.2425   4811   0.864    695   0.750   5506   0.850  0.947  0.9400  0.9538  0.8767  0.9335
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16143
Percentage observed                  =    99.9823
Percentage of free reflections       =     4.9517
Overall R factor                     =     0.1584
Free R factor                        =     0.2026
Average Fourier shell correlation    =     0.9620
AverageFree Fourier shell correlation=     0.9508
Overall weighted R factor            =     0.1478
Free weighted R factor               =     0.1838
Overall weighted R2 factor           =     0.1811
Free weighted R2 factor              =     0.2195
Average correlation coefficient      =     0.9406
Overall correlation coefficient      =     0.9556
Free correlation coefficient         =     0.9302
Cruickshanks DPI for coordinate error=     0.1398
DPI based on free R factor           =     0.1320
Overall figure of merit              =     0.8688
ML based su of positional parameters =     0.0834
ML based su of thermal parameters    =     2.8145
-----------------------------------------------------------------------------
  Time in seconds: CPU =        15.46
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1628   0.2063   0.862       88114.    4731.0   0.0137  1.064   1.857  1.071   0.082
       1   0.1606   0.2036   0.868       87717.    4721.7   0.0117  0.858   1.769  1.014   0.083
       2   0.1594   0.2028   0.869       87575.    4718.5   0.0120  0.886   1.779  1.020   0.083
       3   0.1589   0.2024   0.869       87531.    4717.8   0.0121  0.893   1.783  1.023   0.083
       4   0.1587   0.2025   0.869       87509.    4717.4   0.0121  0.896   1.785  1.025   0.083
       5   0.1585   0.2024   0.869       87504.    4717.4   0.0122  0.897   1.786  1.026   0.083
       6   0.1584   0.2023   0.869       87499.    4717.4   0.0122  0.898   1.787  1.027   0.083
       7   0.1584   0.2023   0.869       87502.    4718.0   0.0122  0.898   1.787  1.027   0.083
       8   0.1584   0.2025   0.869       87509.    4718.8   0.0122  0.898   1.787  1.027   0.083
       9   0.1584   0.2025   0.869       87504.    4718.5   0.0122  0.898   1.787  1.027   0.083
      10   0.1584   0.2026   0.869       87509.    4718.8   0.0121  0.898   1.787  1.027   0.083
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1628   0.1584
             R free    0.2063   0.2026
     Rms BondLength    0.0137   0.0121
      Rms BondAngle    1.8570   1.7871
     Rms ChirVolume    0.0818   0.0832
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      47.6s System:    0.2s Elapsed:     0:47