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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: 15:50:28 


 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 14
  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_R14_1-90A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R14_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_R14_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:    14
  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_R14_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=   2.010 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=   2.194 ideal_dist=   2.090
            ch:AAA  res:  88  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   1.826 ideal_dist=   1.720
            ch:AAA  res:  93  CYS              at:SG  .->ch:AAA  res: 157  TYR              at:CE1 .
  INFO:     link is found (not be used) dist=   2.193 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=   2.410 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=   2.413 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=   2.106 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                           14
Number of "free" reflections        950
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.= 0.891 id.= 3.000 dev= -2.11 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   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   0.30262122    
 Actual weight    6.9995613      is applied to the X-ray term
Norm of X_ray positional gradient                42.9
Norm of Geom. positional gradient                80.8
Norm of X_ray B-factor gradient                  141.
Norm of Geom. B-factor gradient                 0.220E+05
Product of X_ray and Geom posit. gradients     -0.126E+08
 Cosine of angle between them                      -0.375
Product of X_ray and Geom B-fact gradients     -0.473E+08
 Cosine of angle between them                      -0.005


Residuals: XRAY=     0.7047E+06 GEOM=     0.2719E+05 TOTAL=     0.7318E+06
 function value    731839.00    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.861     1.644
Bond angles  : others                          3242     2.359     1.582
Torsion angles, period  1. refined              184     6.940     5.000
Torsion angles, period  2. refined               90    36.830    22.778
Torsion angles, period  3. refined              268    14.370    15.000
Torsion angles, period  4. refined                9    11.777    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.019     0.020
VDW repulsions: refined_atoms                   309     0.267     0.200
VDW repulsions.others                          1341     0.234     0.200
VDW; torsion: refined_atoms                     718     0.173     0.200
VDW; torsion.others                             710     0.082     0.200
HBOND: refined_atoms                            233     0.210     0.200
HBOND.others                                      2     0.031     0.200
VDW repulsions: symmetry: refined_atoms          10     0.223     0.200
VDW repulsions: symmetry: others                 28     0.183     0.200
HBOND: symmetry: refined_atoms                   18     0.223     0.200
HBOND: symmetry: others                           1     0.008     0.200
M. chain bond B values: refined atoms           745     1.653     1.202
M. chain bond B values: others                  745     1.652     1.202
M. chain angle B values: refined atoms          926     2.611     1.783
M. chain angle B values: others                 927     2.609     1.783
S. chain bond B values: refined atoms           812     2.814     1.569
S. chain bond B values: others                  811     2.812     1.569
S. chain angle B values: refined atoms         1177     4.360     2.199
S. chain angle B values: others                1178     4.358     2.198
Long range B values: refined atoms             1863     7.056    17.152
Long range B values: others                    1766     6.796    15.746
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =    0.8963
Partial structure    1: scale =     0.3802, B  =   49.4483
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2562 100.00   471.6   480.3  0.16  0.17     131   500.0   496.7  0.18  0.20
 0.116    4357 100.00   341.1   326.9  0.16  0.15     222   351.9   334.0  0.19  0.18
 0.193    5531  99.97   225.5   215.0  0.15  0.13     277   239.7   227.5  0.18  0.16
 0.270    6467 100.00   148.2   155.3  0.21  0.16     320   142.4   152.3  0.26  0.19
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1803   0.934    759   0.839   2562   0.906  0.953  0.9736  0.9738  0.9404  0.9396
  0.1161   3581   0.889    776   0.783   4357   0.870  0.997  0.9579  0.9635  0.9206  0.9434
  0.1931   4751   0.895    780   0.787   5531   0.880  1.018  0.9632  0.9661  0.9252  0.9449
  0.2701   5695   0.833    780   0.751   6475   0.823  0.897  0.9320  0.9429  0.8815  0.9073
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18925
Percentage observed                  =    99.9849
Percentage of free reflections       =     4.7799
Overall R factor                     =     0.1689
Free R factor                        =     0.1956
Average Fourier shell correlation    =     0.9586
AverageFree Fourier shell correlation=     0.9529
Overall weighted R factor            =     0.1530
Free weighted R factor               =     0.1797
Overall weighted R2 factor           =     0.1860
Free weighted R2 factor              =     0.2112
Average correlation coefficient      =     0.9310
Overall correlation coefficient      =     0.9554
Free correlation coefficient         =     0.9462
Cruickshanks DPI for coordinate error=     0.1231
DPI based on free R factor           =     0.1115
Overall figure of merit              =     0.8616
ML based su of positional parameters =     0.0737
ML based su of thermal parameters    =     2.3886
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    100671.09       27185.551       731839.00      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.33682734    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    712395.31    

-------------------------------------------------------------------------------
             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  =   -0.0725
Partial structure    1: scale =     0.3804, B  =   48.7472
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                     =     0.1679
Free R factor                        =     0.1937
Average Fourier shell correlation    =     0.9619
AverageFree Fourier shell correlation=     0.9560
Average correlation coefficient      =     0.9334
Overall figure of merit              =     0.8734
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    100258.01       10633.250       712395.31       731839.00    


     CGMAT cycle number =      3

 Weight matrix   0.34210560    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    710061.88    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0305
Partial structure    1: scale =     0.3796, B  =   46.0486
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                        =     0.1921
Average Fourier shell correlation    =     0.9627
AverageFree Fourier shell correlation=     0.9566
Average correlation coefficient      =     0.9353
Overall figure of merit              =     0.8748
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    100026.78       9918.2881       710061.88       712395.31    


     CGMAT cycle number =      4

 Weight matrix   0.34330335    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    709335.00    

-------------------------------------------------------------------------------
             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  =   -0.0232
Partial structure    1: scale =     0.3800, B  =   45.9427
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                     =     0.1662
Free R factor                        =     0.1917
Average Fourier shell correlation    =     0.9629
AverageFree Fourier shell correlation=     0.9567
Average correlation coefficient      =     0.9359
Overall figure of merit              =     0.8752
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    99951.367       9719.2793       709335.00       710061.88    


     CGMAT cycle number =      5

 Weight matrix   0.34352106    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    709049.13    

-------------------------------------------------------------------------------
             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  =   -0.0127
Partial structure    1: scale =     0.3800, B  =   45.9379
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                     =     0.1661
Free R factor                        =     0.1916
Average Fourier shell correlation    =     0.9630
AverageFree Fourier shell correlation=     0.9568
Average correlation coefficient      =     0.9362
Overall figure of merit              =     0.8753
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    99910.156       9721.8945       709049.13       709335.00    


     CGMAT cycle number =      6

 Weight matrix   0.34460396    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    708878.94    

-------------------------------------------------------------------------------
             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  =   -0.0116
Partial structure    1: scale =     0.3798, B  =   45.8176
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                     =     0.1660
Free R factor                        =     0.1914
Average Fourier shell correlation    =     0.9630
AverageFree Fourier shell correlation=     0.9568
Average correlation coefficient      =     0.9363
Overall figure of merit              =     0.8756
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    99881.945       9749.1270       708878.94       709049.13    


     CGMAT cycle number =      7

 Weight matrix   0.34560782    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    708800.06    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0412
Partial structure    1: scale =     0.3805, B  =   45.9068
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                     =     0.1660
Free R factor                        =     0.1915
Average Fourier shell correlation    =     0.9631
AverageFree Fourier shell correlation=     0.9568
Average correlation coefficient      =     0.9365
Overall figure of merit              =     0.8757
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    99871.250       9745.1328       708800.06       708878.94    


     CGMAT cycle number =      8

 Weight matrix   0.34507588    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    708833.00    

-------------------------------------------------------------------------------
             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  =   -0.0588
Partial structure    1: scale =     0.3801, B  =   45.8782
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                     =     0.1660
Free R factor                        =     0.1920
Average Fourier shell correlation    =     0.9631
AverageFree Fourier shell correlation=     0.9567
Average correlation coefficient      =     0.9365
Overall figure of merit              =     0.8755
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    99875.727       9751.4063       708849.88       708800.06    

 fvalues    99875.727       9751.4063       708848.31       708837.63    
 fvalues    99875.727       9751.4063       708848.31       708837.63    


     CGMAT cycle number =      9

 Weight matrix   0.34483567    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    708835.88    

-------------------------------------------------------------------------------
             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  =   -0.0566
Partial structure    1: scale =     0.3799, B  =   45.8847
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                     =     0.1660
Free R factor                        =     0.1920
Average Fourier shell correlation    =     0.9631
AverageFree Fourier shell correlation=     0.9567
Average correlation coefficient      =     0.9365
Overall figure of merit              =     0.8755
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    99875.641       9750.1758       708835.88       708837.63    


     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.= 0.908 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   0.34461203    
 Actual weight    6.9995613      is applied to the X-ray term
Norm of X_ray positional gradient                41.8
Norm of Geom. positional gradient                41.8
Norm of X_ray B-factor gradient                  133.
Norm of Geom. B-factor gradient                  136.
Product of X_ray and Geom posit. gradients     -0.169E+08
 Cosine of angle between them                      -0.998
Product of X_ray and Geom B-fact gradients     -0.581E+08
 Cosine of angle between them                      -0.994


Residuals: XRAY=     0.6991E+06 GEOM=      9751.     TOTAL=     0.7089E+06
 function value    708852.63    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2103     1.889     1.644
Bond angles  : others                          3242     1.496     1.582
Torsion angles, period  1. refined              184     6.983     5.000
Torsion angles, period  2. refined               90    36.483    22.778
Torsion angles, period  3. refined              268    14.126    15.000
Torsion angles, period  4. refined                9    12.412    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   309     0.267     0.200
VDW repulsions.others                          1371     0.205     0.200
VDW; torsion: refined_atoms                     723     0.173     0.200
VDW; torsion.others                             803     0.084     0.200
HBOND: refined_atoms                            228     0.204     0.200
HBOND.others                                      1     0.079     0.200
VDW repulsions: symmetry: refined_atoms          11     0.200     0.200
VDW repulsions: symmetry: others                 23     0.184     0.200
HBOND: symmetry: refined_atoms                   21     0.204     0.200
M. chain bond B values: refined atoms           745     1.705     1.286
M. chain bond B values: others                  745     1.703     1.286
M. chain angle B values: refined atoms          926     2.658     1.909
M. chain angle B values: others                 927     2.656     1.909
S. chain bond B values: refined atoms           811     3.028     1.684
S. chain bond B values: others                  810     3.025     1.683
S. chain angle B values: refined atoms         1177     4.686     2.358
S. chain angle B values: others                1178     4.684     2.358
Long range B values: refined atoms             1861     7.308    18.291
Long range B values: others                    1764     7.011    16.785
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0550
Partial structure    1: scale =     0.3798, B  =   45.8714
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2562 100.00   471.4   480.6  0.16  0.17     131   499.7   499.8  0.17  0.19
 0.116    4357 100.00   341.0   325.9  0.16  0.15     222   351.7   332.9  0.19  0.18
 0.193    5531  99.97   225.4   214.4  0.16  0.13     277   239.6   227.5  0.18  0.16
 0.270    6467 100.00   148.1   154.6  0.20  0.15     320   142.3   151.1  0.25  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1803   0.940    759   0.848   2562   0.913  0.953  0.9763  0.9753  0.9457  0.9403
  0.1161   3581   0.894    776   0.789   4357   0.875  0.997  0.9589  0.9646  0.9212  0.9438
  0.1931   4751   0.899    780   0.790   5531   0.884  1.018  0.9641  0.9665  0.9261  0.9432
  0.2701   5695   0.864    780   0.785   6475   0.854  0.912  0.9406  0.9542  0.8876  0.9244
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18925
Percentage observed                  =    99.9849
Percentage of free reflections       =     4.7799
Overall R factor                     =     0.1661
Free R factor                        =     0.1920
Average Fourier shell correlation    =     0.9630
AverageFree Fourier shell correlation=     0.9567
Overall weighted R factor            =     0.1522
Free weighted R factor               =     0.1769
Overall weighted R2 factor           =     0.1857
Free weighted R2 factor              =     0.2091
Average correlation coefficient      =     0.9365
Overall correlation coefficient      =     0.9566
Free correlation coefficient         =     0.9485
Cruickshanks DPI for coordinate error=     0.1210
DPI based on free R factor           =     0.1094
Overall figure of merit              =     0.8755
ML based su of positional parameters =     0.0690
ML based su of thermal parameters    =     2.2061
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    99878.156       9750.7441       708840.38       708835.88    
 fvalues    99878.156       9750.7441       708840.38       708854.00    

    ****                              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.= 0.908 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

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

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R14_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     1.889     1.644
Bond angles  : others                          3242     1.496     1.582
Torsion angles, period  1. refined              184     6.981     5.000
Torsion angles, period  2. refined               90    36.475    22.778
Torsion angles, period  3. refined              268    14.122    15.000
Torsion angles, period  4. refined                9    12.421    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   309     0.266     0.200
VDW repulsions.others                          1373     0.204     0.200
VDW; torsion: refined_atoms                     722     0.173     0.200
VDW; torsion.others                             804     0.084     0.200
HBOND: refined_atoms                            227     0.204     0.200
HBOND.others                                      1     0.080     0.200
VDW repulsions: symmetry: refined_atoms          11     0.200     0.200
VDW repulsions: symmetry: others                 23     0.184     0.200
HBOND: symmetry: refined_atoms                   21     0.204     0.200
M. chain bond B values: refined atoms           745     1.704     1.286
M. chain bond B values: others                  745     1.703     1.286
M. chain angle B values: refined atoms          926     2.657     1.909
M. chain angle B values: others                 927     2.655     1.909
S. chain bond B values: refined atoms           811     3.029     1.684
S. chain bond B values: others                  810     3.026     1.683
S. chain angle B values: refined atoms         1177     4.688     2.358
S. chain angle B values: others                1178     4.686     2.358
Long range B values: refined atoms             1860     7.275    18.263
Long range B values: others                    1763     6.974    16.754
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0531
Partial structure    1: scale =     0.3797, B  =   45.7609
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2562 100.00   471.3   480.6  0.16  0.17     131   499.7   499.8  0.17  0.19
 0.116    4357 100.00   340.9   325.8  0.16  0.15     222   351.6   332.9  0.19  0.18
 0.193    5531  99.97   225.3   214.4  0.16  0.13     277   239.5   227.5  0.18  0.16
 0.270    6467 100.00   148.1   154.6  0.20  0.15     320   142.3   151.1  0.25  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1803   0.941    759   0.849   2562   0.913  0.953  0.9763  0.9753  0.9458  0.9403
  0.1161   3581   0.894    776   0.789   4357   0.875  0.997  0.9590  0.9646  0.9213  0.9438
  0.1931   4751   0.899    780   0.790   5531   0.883  1.018  0.9641  0.9665  0.9261  0.9431
  0.2701   5695   0.863    780   0.785   6475   0.854  0.912  0.9406  0.9542  0.8874  0.9245
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18925
Percentage observed                  =    99.9849
Percentage of free reflections       =     4.7799
Overall R factor                     =     0.1661
Free R factor                        =     0.1918
Average Fourier shell correlation    =     0.9631
AverageFree Fourier shell correlation=     0.9567
Overall weighted R factor            =     0.1522
Free weighted R factor               =     0.1768
Overall weighted R2 factor           =     0.1856
Free weighted R2 factor              =     0.2090
Average correlation coefficient      =     0.9365
Overall correlation coefficient      =     0.9566
Free correlation coefficient         =     0.9485
Cruickshanks DPI for coordinate error=     0.1210
DPI based on free R factor           =     0.1093
Overall figure of merit              =     0.8755
ML based su of positional parameters =     0.0690
ML based su of thermal parameters    =     2.2061
-----------------------------------------------------------------------------
  Time in seconds: CPU =        16.91
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1689   0.1956   0.862      100671.    5192.0   0.0128  0.951   1.861  1.073   0.090
       1   0.1679   0.1937   0.873      100258.    5181.1   0.0126  0.933   1.836  1.057   0.090
       2   0.1666   0.1921   0.875      100027.    5174.3   0.0133  0.983   1.862  1.071   0.091
       3   0.1662   0.1917   0.875       99951.    5171.7   0.0133  0.990   1.874  1.078   0.091
       4   0.1661   0.1916   0.875       99910.    5170.2   0.0134  0.992   1.880  1.081   0.091
       5   0.1660   0.1914   0.876       99882.    5169.6   0.0134  0.993   1.884  1.083   0.090
       6   0.1660   0.1915   0.876       99871.    5170.0   0.0134  0.994   1.887  1.084   0.090
       7   0.1660   0.1920   0.876       99875.    5170.3   0.0134  0.995   1.888  1.084   0.090
       8   0.1660   0.1920   0.875       99876.    5170.6   0.0134  0.995   1.888  1.085   0.090
       9   0.1661   0.1920   0.875       99878.    5170.8   0.0134  0.995   1.889  1.085   0.090
      10   0.1661   0.1918   0.875       99872.    5170.7   0.0134  0.995   1.889  1.085   0.090
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1689   0.1661
             R free    0.1956   0.1918
     Rms BondLength    0.0128   0.0134
      Rms BondAngle    1.8608   1.8887
     Rms ChirVolume    0.0904   0.0905
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      48.8s System:    0.2s Elapsed:     0:49