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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: 15:53:31 


 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 1.80     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- bins 4
  Data line--- ncyc 10
  Data line--- monitor MEDIum
  Data line--- free 15
  Data line--- END

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN   Filename: CDO_R.mtz 

 LABIN FP=FP SIGFP=SIGFP FREE=FreeR_flag

    ****                     Input and Default parameters#                      ****


Input coordinate file.  Logical name - XYZIN actual file name  - CDO_complete_R15_1-90A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R15_1-80A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R15_1-80A.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       0.0772
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.8000
  Estimated number of reflections :      25918
  Free R exclusion - flag equals:    15
  Auto weighting. An attempt
  Refinement cycles       :    10
  Scaling type                           :
          Wilson scaling type with Guassians

  Estimation of D/Sigma in resolution bins
  using  free set of reflns with experimental sigmas
  using  free set of reflns with experimental sigmas

  Scaling and SigmaA resln:    41.9635  1.8000

  Damping factors:     1.0000  1.0000  1.0000


    ****                    Geometry restraints and weights                     ****


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

 Planar groups (all and main chain)
          WEIGHT= 1.00 1.00

 Chiral centers
          Weight= 1.00

 NON-BONDED CONTACTS
          Overall weight                          =  1.00
          Sigma for simple VDW                    =  0.20
          Sigma for VDW trhough torsion angle     =  0.20
          Sigma for HBOND                         =  0.20
          Sigma for metal-ion                     =  0.20
          Sigma for DUMMY and other atom          =  0.30
          Distance for donor-accepetor = vdw1+vdw2+(-0.30)
          Distance for acceptor - H    = vdw1+     ( 0.10)
          VDW distance through torsion = vdw1+vdw2+(-0.30)
          Distance for DUMMY-others    = vdw1+vdw2+(-0.70)

 TORSION ANGLES
          Weight= 1.00

 THERMAL FACTORS
          Weight= 1.00
     Main chain bond (1-2 neighbour)          1.5A**2
     Main chain angle (1-3 neighbour)         2.0A**2
     Side chain bond                          3.0A**2
     Side chain angle                         4.5A**2

 RESTRAINTS AGAINST EXCESSIVE SHIFTS
     Positional parameters                   0.00A
     Thermal parameters                      0.00A
     Occupancy parameters                    0.00

 RADIUS OF CONFIDENCE
     Positional parameters 0.00A
     Thermal parameters    0.00A**2
     Occupancy parameters  0.00

Monitoring style is "MEDIUM". Complete information will be printed out in the
first and last cycle. In all other cycles minimum information will be printed out
Sigma cutoffs for printing out outliers
If deviation of restraint parameter > alpha*sigma then information will be printed out
Distance outliers      10.000
Angle outliers         10.000
Torsion outliers       10.000
Chiral volume outliers 10.000
Plane outliers         10.000
Non-bonding outliers   10.000
B value  outliers      10.000
Rigid bond outliers    10.000
Sphericity outliers    10.000
---------------------------------------------------------------

 Input file :CDO_complete_R15_1-90A.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=   2.019 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=   2.209 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=   1.834 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=   2.201 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=   2.392 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=   2.429 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=   2.028 ideal_dist=   1.870
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:OD  .
  --------------------------------
  --- title of input coord file ---

  PDB_code:xxxx
  PDB_name:----
  PDB_date:26-MAY-20
  --------------------------------
  ATTENTION: atom:OXT  THR               171  AAA  is missing in the structure
  ATTENTION: atom:OXT  PRO               190  AAA  is missing in the structure
  Number of chains                  :       4
  Total number of monomers          :     502
  Number of atoms                   :    3948
  Number of missing atoms           :       0
  Number of rebuilt atoms           :    1482
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0

_ccp4_form_factor.scat_method    'Sum of Gaussians'
_ccp4_form_factor.scat_data_source  X-ray


 loop_
     _atom_type_symbol
     _atom_type_scat_Cromer_Mann_a1
     _atom_type_scat_Cromer_Mann_b1
     _atom_type_scat_Cromer_Mann_a2
     _atom_type_scat_Cromer_Mann_b2
     _atom_type_scat_Cromer_Mann_a3
     _atom_type_scat_Cromer_Mann_b3
     _atom_type_scat_Cromer_Mann_a4
     _atom_type_scat_Cromer_Mann_b4
     _atom_type_scat_Cromer_Mann_c


  N     12.2220   0.0057   3.1346   9.8933   2.0141  28.9975   1.1672   0.5826 -11.5379
  H      0.4930  10.5109   0.3229  26.1257   0.1402   3.1424   0.0408  57.7997   0.0030
  C      2.3103  20.8439   1.0201  10.2075   1.5888   0.5687   0.8651  51.6512   0.2156
  O      3.0487  13.2771   2.2870   5.7011   1.5464   0.3239   0.8671  32.9089   0.2508
  S      6.9054   1.4679   5.2035  22.2151   1.4379   0.2536   1.5863  56.1720   1.0490
  FE    11.7738   4.7611   7.3600   0.3072   3.5235  15.3535   2.3054  76.8805   1.2805


 Number of distances         :           0
 Number of angles            :           0
 Number of torsions          :           0
 Number of planes            :           0
 Number of chirals           :           0
 Number of intervals         :           0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
                        Standard  External       All
                Bonds:      2950         0      2950
               Angles:      5345         0      5345
              Chirals:       196         0       196
               Planes:       451         0       451
             Torsions:      1553         0      1553
            Intervals:         0         0         0
--------------------------------------------------------------------------------


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


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

FreeR flag                           15
Number of "free" reflections       1026
Number of   all  reflections      19877
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          19877

   Current auto weighting coefficient =    6.9995613    

 mode : HKRF


######  TLS Group Definitions ######



     CGMAT cycle number =      1

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.906 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Weight matrix   0.26506197    
 Actual weight    6.9995613      is applied to the X-ray term
Norm of X_ray positional gradient                40.2
Norm of Geom. positional gradient                78.8
Norm of X_ray B-factor gradient                  133.
Norm of Geom. B-factor gradient                 0.220E+05
Product of X_ray and Geom posit. gradients     -0.106E+08
 Cosine of angle between them                      -0.345
Product of X_ray and Geom B-fact gradients     -0.422E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.7058E+06 GEOM=     0.2646E+05 TOTAL=     0.7323E+06
 function value    732292.50    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.773     1.644
Bond angles  : others                          3242     2.339     1.582
Torsion angles, period  1. refined              184     6.988     5.000
Torsion angles, period  2. refined               90    36.738    22.778
Torsion angles, period  3. refined              268    14.091    15.000
Torsion angles, period  4. refined                9    10.869    15.000
Chiral centres: refined atoms                   196     0.086     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.018     0.020
VDW repulsions: refined_atoms                   303     0.266     0.200
VDW repulsions.others                          1341     0.231     0.200
VDW; torsion: refined_atoms                     723     0.171     0.200
VDW; torsion.others                             712     0.081     0.200
HBOND: refined_atoms                            236     0.205     0.200
HBOND.others                                      2     0.084     0.200
VDW repulsions: symmetry: refined_atoms           9     0.255     0.200
VDW repulsions: symmetry: others                 26     0.196     0.200
HBOND: symmetry: refined_atoms                   22     0.223     0.200
HBOND: symmetry: others                           1     0.023     0.200
M. chain bond B values: refined atoms           745     1.578     1.209
M. chain bond B values: others                  745     1.578     1.209
M. chain angle B values: refined atoms          926     2.542     1.794
M. chain angle B values: others                 927     2.541     1.793
S. chain bond B values: refined atoms           811     2.641     1.561
S. chain bond B values: others                  810     2.636     1.560
S. chain angle B values: refined atoms         1177     4.157     2.189
S. chain angle B values: others                1178     4.156     2.188
Long range B values: refined atoms             1865     7.026    17.154
Long range B values: others                    1768     6.602    15.773
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =    0.9166
Partial structure    1: scale =     0.3800, B  =   49.3718
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2563 100.00   470.9   478.4  0.15  0.16     130   514.7   529.9  0.18  0.20
 0.116    4341 100.00   340.9   326.5  0.16  0.15     238   355.2   336.5  0.20  0.18
 0.193    5515  99.97   226.7   215.3  0.16  0.14     293   215.9   208.5  0.22  0.19
 0.270    6424 100.00   147.9   154.8  0.21  0.16     363   148.3   154.3  0.25  0.20
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1796   0.919    767   0.821   2563   0.890  0.953  0.9721  0.9715  0.9343  0.9425
  0.1161   3564   0.887    777   0.787   4341   0.869  0.997  0.9539  0.9626  0.9034  0.9451
  0.1931   4731   0.873    784   0.759   5515   0.857  1.008  0.9374  0.9578  0.8747  0.9368
  0.2701   5646   0.824    784   0.744   6430   0.814  0.896  0.9330  0.9413  0.8798  0.9082
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18849
Percentage observed                  =    99.9849
Percentage of free reflections       =     5.1623
Overall R factor                     =     0.1698
Free R factor                        =     0.2086
Average Fourier shell correlation    =     0.9552
AverageFree Fourier shell correlation=     0.9441
Overall weighted R factor            =     0.1525
Free weighted R factor               =     0.1911
Overall weighted R2 factor           =     0.1827
Free weighted R2 factor              =     0.2268
Average correlation coefficient      =     0.9297
Overall correlation coefficient      =     0.9556
Free correlation coefficient         =     0.9380
Cruickshanks DPI for coordinate error=     0.1242
DPI based on free R factor           =     0.1193
Overall figure of merit              =     0.8498
ML based su of positional parameters =     0.0788
ML based su of thermal parameters    =     2.5398
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    100840.21       26455.264       732292.50      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.30115956    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    712119.00    

-------------------------------------------------------------------------------
             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 =     0.0413, B  =   -0.0758
Partial structure    1: scale =     0.3795, B  =   49.0480
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1685
Free R factor                        =     0.2076
Average Fourier shell correlation    =     0.9593
AverageFree Fourier shell correlation=     0.9479
Average correlation coefficient      =     0.9326
Overall figure of merit              =     0.8653
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    100303.53       10038.287       712119.00       732292.50    


     CGMAT cycle number =      3

 Weight matrix   0.30509570    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    709810.56    

-------------------------------------------------------------------------------
             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 =     0.0413, B  =   -0.0496
Partial structure    1: scale =     0.3793, B  =   46.1895
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1670
Free R factor                        =     0.2073
Average Fourier shell correlation    =     0.9601
AverageFree Fourier shell correlation=     0.9486
Average correlation coefficient      =     0.9347
Overall figure of merit              =     0.8662
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    100065.41       9396.6055       709810.56       712119.00    


     CGMAT cycle number =      4

 Weight matrix   0.30577844    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    708951.81    

-------------------------------------------------------------------------------
             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 =     0.0413, B  =   -0.0189
Partial structure    1: scale =     0.3796, B  =   45.8756
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1666
Free R factor                        =     0.2070
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9488
Average correlation coefficient      =     0.9354
Overall figure of merit              =     0.8664
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    99971.328       9196.3857       708951.81       709810.56    


     CGMAT cycle number =      5

 Weight matrix   0.30583474    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    708687.63    

-------------------------------------------------------------------------------
             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 =     0.0413, B  =   -0.0270
Partial structure    1: scale =     0.3796, B  =   45.8123
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1665
Free R factor                        =     0.2071
Average Fourier shell correlation    =     0.9604
AverageFree Fourier shell correlation=     0.9489
Average correlation coefficient      =     0.9357
Overall figure of merit              =     0.8664
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    99935.922       9180.0049       708687.63       708951.81    


     CGMAT cycle number =      6

 Weight matrix   0.30538309    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    708638.00    

-------------------------------------------------------------------------------
             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 =     0.0413, B  =   -0.0208
Partial structure    1: scale =     0.3797, B  =   45.8272
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1666
Free R factor                        =     0.2073
Average Fourier shell correlation    =     0.9605
AverageFree Fourier shell correlation=     0.9489
Average correlation coefficient      =     0.9359
Overall figure of merit              =     0.8662
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    99925.922       9200.3555       708638.00       708687.63    


     CGMAT cycle number =      7

 Weight matrix   0.30611414    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    708504.31    

-------------------------------------------------------------------------------
             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 =     0.0414, B  =   -0.0229
Partial structure    1: scale =     0.3796, B  =   45.8197
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1666
Free R factor                        =     0.2072
Average Fourier shell correlation    =     0.9605
AverageFree Fourier shell correlation=     0.9490
Average correlation coefficient      =     0.9360
Overall figure of merit              =     0.8664
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    99906.477       9202.8184       708504.31       708638.00    


     CGMAT cycle number =      8

 Weight matrix   0.30666879    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    708472.38    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0311
Partial structure    1: scale =     0.3798, B  =   46.2785
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1666
Free R factor                        =     0.2075
Average Fourier shell correlation    =     0.9606
AverageFree Fourier shell correlation=     0.9490
Average correlation coefficient      =     0.9361
Overall figure of merit              =     0.8665
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    99900.469       9212.9609       708472.38       708504.31    


     CGMAT cycle number =      9

 Weight matrix   0.30627042    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    708485.44    

-------------------------------------------------------------------------------
             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 =     0.0413, B  =   -0.0223
Partial structure    1: scale =     0.3799, B  =   46.2914
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1666
Free R factor                        =     0.2076
Average Fourier shell correlation    =     0.9606
AverageFree Fourier shell correlation=     0.9490
Average correlation coefficient      =     0.9361
Overall figure of merit              =     0.8664
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    99902.906       9214.5840       708461.19       708472.38    
 fvalues    99902.906       9214.5840       708461.19       708491.06    


     CGMAT cycle number =     10

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.918 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        :   120  120  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Weight matrix   0.30690929    
 Actual weight    6.9995613      is applied to the X-ray term
Norm of X_ray positional gradient                38.4
Norm of Geom. positional gradient                38.3
Norm of X_ray B-factor gradient                  125.
Norm of Geom. B-factor gradient                  127.
Product of X_ray and Geom posit. gradients     -0.143E+08
 Cosine of angle between them                      -0.998
Product of X_ray and Geom B-fact gradients     -0.512E+08
 Cosine of angle between them                      -0.995


Residuals: XRAY=     0.6993E+06 GEOM=      9216.     TOTAL=     0.7085E+06
 function value    708505.06    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2103     1.814     1.644
Bond angles  : others                          3242     1.481     1.582
Torsion angles, period  1. refined              184     7.024     5.000
Torsion angles, period  2. refined               90    36.463    22.778
Torsion angles, period  3. refined              268    14.011    15.000
Torsion angles, period  4. refined                9    11.882    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   304     0.267     0.200
VDW repulsions.others                          1366     0.203     0.200
VDW; torsion: refined_atoms                     723     0.171     0.200
VDW; torsion.others                             801     0.084     0.200
HBOND: refined_atoms                            230     0.200     0.200
HBOND.others                                      1     0.111     0.200
VDW repulsions: symmetry: refined_atoms           9     0.229     0.200
VDW repulsions: symmetry: others                 21     0.200     0.200
HBOND: symmetry: refined_atoms                   25     0.211     0.200
M. chain bond B values: refined atoms           745     1.651     1.291
M. chain bond B values: others                  745     1.650     1.291
M. chain angle B values: refined atoms          926     2.608     1.918
M. chain angle B values: others                 927     2.606     1.918
S. chain bond B values: refined atoms           811     2.866     1.673
S. chain bond B values: others                  810     2.862     1.673
S. chain angle B values: refined atoms         1177     4.497     2.346
S. chain angle B values: others                1178     4.495     2.346
Long range B values: refined atoms             1860     7.237    18.276
Long range B values: others                    1760     6.800    16.788
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0149
Partial structure    1: scale =     0.3799, B  =   46.4400
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2563 100.00   470.4   478.3  0.16  0.16     130   514.2   530.2  0.18  0.20
 0.116    4341 100.00   340.6   325.4  0.16  0.15     238   354.8   335.0  0.20  0.18
 0.193    5515  99.97   226.5   214.8  0.16  0.14     293   215.7   207.7  0.22  0.19
 0.270    6424 100.00   147.8   154.1  0.19  0.15     363   148.2   155.4  0.24  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1796   0.936    767   0.842   2563   0.908  0.956  0.9740  0.9744  0.9325  0.9420
  0.1161   3564   0.888    777   0.788   4341   0.870  0.997  0.9546  0.9631  0.9039  0.9447
  0.1931   4731   0.877    784   0.765   5515   0.861  1.008  0.9392  0.9587  0.8769  0.9372
  0.2701   5646   0.863    784   0.782   6430   0.853  0.913  0.9441  0.9549  0.8900  0.9270
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18849
Percentage observed                  =    99.9849
Percentage of free reflections       =     5.1623
Overall R factor                     =     0.1667
Free R factor                        =     0.2078
Average Fourier shell correlation    =     0.9606
AverageFree Fourier shell correlation=     0.9489
Overall weighted R factor            =     0.1522
Free weighted R factor               =     0.1913
Overall weighted R2 factor           =     0.1837
Free weighted R2 factor              =     0.2277
Average correlation coefficient      =     0.9361
Overall correlation coefficient      =     0.9567
Free correlation coefficient         =     0.9382
Cruickshanks DPI for coordinate error=     0.1220
DPI based on free R factor           =     0.1188
Overall figure of merit              =     0.8666
ML based su of positional parameters =     0.0731
ML based su of thermal parameters    =     2.3209
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    99904.188       9215.7910       708476.00       708491.06    
 fvalues    99904.188       9215.7910       708476.00       708501.31    

    ****                              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.= 0.918 id.= 3.000 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

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

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R15_1-80A.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     1.814     1.644
Bond angles  : others                          3242     1.480     1.582
Torsion angles, period  1. refined              184     7.021     5.000
Torsion angles, period  2. refined               90    36.457    22.778
Torsion angles, period  3. refined              268    14.014    15.000
Torsion angles, period  4. refined                9    11.919    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   304     0.266     0.200
VDW repulsions.others                          1366     0.203     0.200
VDW; torsion: refined_atoms                     722     0.171     0.200
VDW; torsion.others                             804     0.084     0.200
HBOND: refined_atoms                            232     0.199     0.200
HBOND.others                                      1     0.114     0.200
VDW repulsions: symmetry: refined_atoms           9     0.228     0.200
VDW repulsions: symmetry: others                 21     0.200     0.200
HBOND: symmetry: refined_atoms                   25     0.211     0.200
M. chain bond B values: refined atoms           745     1.651     1.293
M. chain bond B values: others                  745     1.650     1.293
M. chain angle B values: refined atoms          926     2.607     1.921
M. chain angle B values: others                 927     2.606     1.921
S. chain bond B values: refined atoms           811     2.867     1.675
S. chain bond B values: others                  810     2.863     1.675
S. chain angle B values: refined atoms         1177     4.496     2.350
S. chain angle B values: others                1178     4.494     2.349
Long range B values: refined atoms             1861     7.237    18.334
Long range B values: others                    1760     6.803    16.813
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0519
Partial structure    1: scale =     0.3797, B  =   46.5921
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2563 100.00   470.5   478.4  0.15  0.16     130   514.3   530.4  0.18  0.20
 0.116    4341 100.00   340.7   325.5  0.16  0.15     238   354.9   335.1  0.20  0.18
 0.193    5515  99.97   226.5   215.0  0.16  0.14     293   215.7   207.8  0.22  0.19
 0.270    6424 100.00   147.8   154.2  0.19  0.15     363   148.2   155.6  0.24  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1796   0.935    767   0.841   2563   0.907  0.956  0.9738  0.9743  0.9320  0.9420
  0.1161   3564   0.888    777   0.788   4341   0.870  0.997  0.9547  0.9631  0.9039  0.9446
  0.1931   4731   0.877    784   0.765   5515   0.861  1.008  0.9393  0.9587  0.8771  0.9372
  0.2701   5646   0.863    784   0.782   6430   0.853  0.913  0.9442  0.9549  0.8900  0.9273
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18849
Percentage observed                  =    99.9849
Percentage of free reflections       =     5.1623
Overall R factor                     =     0.1666
Free R factor                        =     0.2080
Average Fourier shell correlation    =     0.9606
AverageFree Fourier shell correlation=     0.9490
Overall weighted R factor            =     0.1522
Free weighted R factor               =     0.1916
Overall weighted R2 factor           =     0.1837
Free weighted R2 factor              =     0.2281
Average correlation coefficient      =     0.9362
Overall correlation coefficient      =     0.9567
Free correlation coefficient         =     0.9381
Cruickshanks DPI for coordinate error=     0.1220
DPI based on free R factor           =     0.1189
Overall figure of merit              =     0.8665
ML based su of positional parameters =     0.0731
ML based su of thermal parameters    =     2.3209
-----------------------------------------------------------------------------
  Time in seconds: CPU =        15.94
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1698   0.2086   0.850      100840.    5630.4   0.0124  0.909   1.773  1.027   0.086
       1   0.1685   0.2076   0.865      100304.    5614.7   0.0121  0.890   1.753  1.015   0.086
       2   0.1670   0.2073   0.866      100065.    5610.9   0.0130  0.950   1.789  1.036   0.088
       3   0.1666   0.2070   0.866       99971.    5608.7   0.0130  0.954   1.802  1.043   0.088
       4   0.1665   0.2071   0.866       99936.    5608.4   0.0130  0.953   1.808  1.046   0.088
       5   0.1666   0.2073   0.866       99926.    5608.9   0.0130  0.952   1.811  1.047   0.088
       6   0.1666   0.2072   0.866       99906.    5608.3   0.0129  0.951   1.812  1.048   0.088
       7   0.1666   0.2075   0.866       99900.    5608.6   0.0129  0.951   1.813  1.049   0.088
       8   0.1666   0.2076   0.866       99902.    5609.3   0.0129  0.951   1.814  1.049   0.088
       9   0.1667   0.2078   0.867       99905.    5610.0   0.0129  0.951   1.814  1.050   0.088
      10   0.1666   0.2080   0.867       99908.    5610.8   0.0129  0.951   1.814  1.050   0.088
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1698   0.1666
             R free    0.2086   0.2080
     Rms BondLength    0.0124   0.0129
      Rms BondAngle    1.7728   1.8144
     Rms ChirVolume    0.0861   0.0878
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      48.0s System:    0.1s Elapsed:     0:48