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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: 15:23:20 


 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 5
  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_R05_1-90A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R05_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_R05_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:     5
  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_R05_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=   2.035 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=   2.200 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=   1.841 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=   2.212 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=   2.377 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=   2.426 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=   2.065 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                            5
Number of "free" reflections        966
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.= 0.907 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   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   0.26204589    
 Actual weight    6.9995613      is applied to the X-ray term
Norm of X_ray positional gradient                40.1
Norm of Geom. positional gradient                79.2
Norm of X_ray B-factor gradient                  130.
Norm of Geom. B-factor gradient                 0.210E+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     -0.399E+08
 Cosine of angle between them                      -0.005


Residuals: XRAY=     0.7072E+06 GEOM=     0.2610E+05 TOTAL=     0.7333E+06
 function value    733297.63    

-------------------------------------------------------------------------------
             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     1.802     1.644
Bond angles  : others                          3242     2.344     1.582
Torsion angles, period  1. refined              184     6.999     5.000
Torsion angles, period  2. refined               90    36.616    22.778
Torsion angles, period  3. refined              268    14.277    15.000
Torsion angles, period  4. refined                9    12.823    15.000
Chiral centres: refined atoms                   196     0.085     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.015     0.020
VDW repulsions: refined_atoms                   314     0.264     0.200
VDW repulsions.others                          1367     0.230     0.200
VDW; torsion: refined_atoms                     720     0.173     0.200
VDW; torsion.others                             725     0.080     0.200
HBOND: refined_atoms                            235     0.207     0.200
HBOND.others                                      1     0.016     0.200
VDW repulsions: symmetry: refined_atoms           9     0.240     0.200
VDW repulsions: symmetry: others                 27     0.175     0.200
HBOND: symmetry: refined_atoms                   23     0.207     0.200
HBOND: symmetry: others                           1     0.085     0.200
M. chain bond B values: refined atoms           745     1.591     1.212
M. chain bond B values: others                  745     1.589     1.212
M. chain angle B values: refined atoms          926     2.552     1.798
M. chain angle B values: others                 927     2.550     1.797
S. chain bond B values: refined atoms           812     2.750     1.580
S. chain bond B values: others                  811     2.747     1.580
S. chain angle B values: refined atoms         1177     4.352     2.214
S. chain angle B values: others                1178     4.350     2.213
Long range B values: refined atoms             1871     7.139    17.271
Long range B values: others                    1771     6.797    15.853
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0414, B  =    0.8942
Partial structure    1: scale =     0.3801, B  =   50.2347
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2554 100.00   475.0   483.9  0.15  0.16     139   409.4   423.1  0.20  0.20
 0.116    4360 100.00   340.6   326.1  0.16  0.15     219   342.1   336.9  0.20  0.18
 0.193    5516  99.97   225.8   214.6  0.16  0.14     292   219.6   207.3  0.22  0.19
 0.270    6472 100.00   147.7   154.4  0.21  0.16     315   143.7   151.2  0.26  0.21
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1794   0.933    760   0.845   2554   0.907  0.952  0.9620  0.9755  0.9229  0.9449
  0.1161   3586   0.887    774   0.788   4360   0.870  0.997  0.9563  0.9641  0.9149  0.9449
  0.1931   4729   0.874    787   0.755   5516   0.857  1.010  0.9406  0.9582  0.8738  0.9382
  0.2701   5689   0.826    791   0.739   6480   0.815  0.897  0.9287  0.9400  0.8623  0.9079
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18910
Percentage observed                  =    99.9849
Percentage of free reflections       =     4.8553
Overall R factor                     =     0.1686
Free R factor                        =     0.2182
Average Fourier shell correlation    =     0.9557
AverageFree Fourier shell correlation=     0.9434
Overall weighted R factor            =     0.1514
Free weighted R factor               =     0.1942
Overall weighted R2 factor           =     0.1814
Free weighted R2 factor              =     0.2261
Average correlation coefficient      =     0.9303
Overall correlation coefficient      =     0.9566
Free correlation coefficient         =     0.9288
Cruickshanks DPI for coordinate error=     0.1229
DPI based on free R factor           =     0.1244
Overall figure of merit              =     0.8523
ML based su of positional parameters =     0.0792
ML based su of thermal parameters    =     2.5769
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    101035.22       26095.449       733297.63      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.30099070    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    713940.31    

-------------------------------------------------------------------------------
             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 =     0.0414, B  =   -0.0849
Partial structure    1: scale =     0.3798, B  =   49.8998
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1676
Free R factor                        =     0.2174
Average Fourier shell correlation    =     0.9596
AverageFree Fourier shell correlation=     0.9473
Average correlation coefficient      =     0.9329
Overall figure of merit              =     0.8670
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    100551.91       10120.982       713940.31       733297.63    


     CGMAT cycle number =      3

 Weight matrix   0.30371347    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    711631.88    

-------------------------------------------------------------------------------
             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 =     0.0414, B  =   -0.0424
Partial structure    1: scale =     0.3793, B  =   47.5420
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1663
Free R factor                        =     0.2167
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9478
Average correlation coefficient      =     0.9349
Overall figure of merit              =     0.8676
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    100305.54       9537.1533       711631.88       713940.31    


     CGMAT cycle number =      4

 Weight matrix   0.30461806    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    710860.31    

-------------------------------------------------------------------------------
             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  =   -0.0325
Partial structure    1: scale =     0.3795, B  =   46.9105
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1659
Free R factor                        =     0.2167
Average Fourier shell correlation    =     0.9606
AverageFree Fourier shell correlation=     0.9480
Average correlation coefficient      =     0.9355
Overall figure of merit              =     0.8678
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    100226.37       9319.6641       710860.31       711631.88    


     CGMAT cycle number =      5

 Weight matrix   0.30468994    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    710628.25    

-------------------------------------------------------------------------------
             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  =   -0.0301
Partial structure    1: scale =     0.3795, B  =   46.6823
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1658
Free R factor                        =     0.2167
Average Fourier shell correlation    =     0.9607
AverageFree Fourier shell correlation=     0.9480
Average correlation coefficient      =     0.9357
Overall figure of merit              =     0.8679
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    100195.66       9302.6143       710628.25       710860.31    


     CGMAT cycle number =      6

 Weight matrix   0.30432618    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    710555.25    

-------------------------------------------------------------------------------
             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  =   -0.0283
Partial structure    1: scale =     0.3797, B  =   46.6749
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1658
Free R factor                        =     0.2167
Average Fourier shell correlation    =     0.9607
AverageFree Fourier shell correlation=     0.9480
Average correlation coefficient      =     0.9359
Overall figure of merit              =     0.8677
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    100183.57       9314.1680       710555.25       710628.25    


     CGMAT cycle number =      7

 Weight matrix   0.30345982    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    710550.75    

-------------------------------------------------------------------------------
             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  =   -0.0282
Partial structure    1: scale =     0.3797, B  =   46.7503
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1658
Free R factor                        =     0.2170
Average Fourier shell correlation    =     0.9607
AverageFree Fourier shell correlation=     0.9479
Average correlation coefficient      =     0.9360
Overall figure of merit              =     0.8675
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    100183.33       9311.3584       710550.75       710555.25    


     CGMAT cycle number =      8

 Weight matrix   0.30265746    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    710561.75    

-------------------------------------------------------------------------------
             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 =     0.0414, B  =   -0.0252
Partial structure    1: scale =     0.3794, B  =   46.5528
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1659
Free R factor                        =     0.2174
Average Fourier shell correlation    =     0.9606
AverageFree Fourier shell correlation=     0.9477
Average correlation coefficient      =     0.9360
Overall figure of merit              =     0.8673
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    100187.70       9301.5137       710568.00       710550.75    
 fvalues    100187.70       9301.5137       710568.00       710571.44    


     CGMAT cycle number =      9

 Weight matrix   0.30222741    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    710560.00    

-------------------------------------------------------------------------------
             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 =     0.0414, B  =   -0.0281
Partial structure    1: scale =     0.3795, B  =   46.5917
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1659
Free R factor                        =     0.2175
Average Fourier shell correlation    =     0.9606
AverageFree Fourier shell correlation=     0.9477
Average correlation coefficient      =     0.9360
Overall figure of merit              =     0.8672
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    100188.59       9283.8447       710560.00       710571.44    


     CGMAT cycle number =     10

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.924 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   0.30191514    
 Actual weight    6.9995613      is applied to the X-ray term
Norm of X_ray positional gradient                38.7
Norm of Geom. positional gradient                38.7
Norm of X_ray B-factor gradient                  124.
Norm of Geom. B-factor gradient                  126.
Product of X_ray and Geom posit. gradients     -0.145E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.507E+08
 Cosine of angle between them                      -0.998


Residuals: XRAY=     0.7013E+06 GEOM=      9278.     TOTAL=     0.7106E+06
 function value    710552.94    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2103     1.828     1.644
Bond angles  : others                          3242     1.485     1.582
Torsion angles, period  1. refined              184     7.091     5.000
Torsion angles, period  2. refined               90    36.685    22.778
Torsion angles, period  3. refined              268    14.237    15.000
Torsion angles, period  4. refined                9    13.486    15.000
Chiral centres: refined atoms                   196     0.087     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                          1381     0.202     0.200
VDW; torsion: refined_atoms                     719     0.173     0.200
VDW; torsion.others                             784     0.085     0.200
HBOND: refined_atoms                            231     0.201     0.200
HBOND.others                                      2     0.064     0.200
VDW repulsions: symmetry: refined_atoms           9     0.207     0.200
VDW repulsions: symmetry: others                 26     0.165     0.200
HBOND: symmetry: refined_atoms                   25     0.202     0.200
HBOND: symmetry: others                           1     0.009     0.200
M. chain bond B values: refined atoms           745     1.642     1.292
M. chain bond B values: others                  745     1.639     1.292
M. chain angle B values: refined atoms          926     2.605     1.919
M. chain angle B values: others                 927     2.603     1.918
S. chain bond B values: refined atoms           811     2.927     1.682
S. chain bond B values: others                  810     2.923     1.682
S. chain angle B values: refined atoms         1177     4.615     2.358
S. chain angle B values: others                1178     4.613     2.358
Long range B values: refined atoms             1863     7.110    18.327
Long range B values: others                    1768     6.787    16.903
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0414, B  =   -0.0271
Partial structure    1: scale =     0.3796, B  =   46.5397
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.49 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2554 100.00   475.0   484.6  0.15  0.16     139   409.5   423.1  0.20  0.21
 0.116    4360 100.00   340.6   325.1  0.16  0.15     219   342.2   335.7  0.20  0.18
 0.193    5516  99.97   225.8   214.4  0.16  0.14     292   219.6   208.5  0.22  0.19
 0.270    6472 100.00   147.7   153.9  0.19  0.15     315   143.7   151.3  0.26  0.20
$$

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

 $TABLE: Cycle   10. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1794   0.943    760   0.855   2554   0.917  0.952  0.9648  0.9771  0.9237  0.9447
  0.1161   3586   0.889    774   0.791   4360   0.871  0.997  0.9571  0.9649  0.9156  0.9448
  0.1931   4729   0.879    787   0.760   5516   0.862  1.010  0.9428  0.9596  0.8765  0.9378
  0.2701   5689   0.859    791   0.776   6480   0.849  0.910  0.9379  0.9520  0.8687  0.9252
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18910
Percentage observed                  =    99.9849
Percentage of free reflections       =     4.8553
Overall R factor                     =     0.1659
Free R factor                        =     0.2175
Average Fourier shell correlation    =     0.9606
AverageFree Fourier shell correlation=     0.9476
Overall weighted R factor            =     0.1511
Free weighted R factor               =     0.1952
Overall weighted R2 factor           =     0.1818
Free weighted R2 factor              =     0.2262
Average correlation coefficient      =     0.9360
Overall correlation coefficient      =     0.9576
Free correlation coefficient         =     0.9300
Cruickshanks DPI for coordinate error=     0.1210
DPI based on free R factor           =     0.1241
Overall figure of merit              =     0.8671
ML based su of positional parameters =     0.0737
ML based su of thermal parameters    =     2.3610
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    100188.40       9278.1455       710552.94       710560.00    

    ****                              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.= 0.925 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_R05_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     1.828     1.644
Bond angles  : others                          3242     1.485     1.582
Torsion angles, period  1. refined              184     7.092     5.000
Torsion angles, period  2. refined               90    36.710    22.778
Torsion angles, period  3. refined              268    14.243    15.000
Torsion angles, period  4. refined                9    13.500    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   308     0.266     0.200
VDW repulsions.others                          1376     0.202     0.200
VDW; torsion: refined_atoms                     719     0.173     0.200
VDW; torsion.others                             788     0.085     0.200
HBOND: refined_atoms                            229     0.202     0.200
HBOND.others                                      2     0.066     0.200
VDW repulsions: symmetry: refined_atoms           9     0.206     0.200
VDW repulsions: symmetry: others                 26     0.166     0.200
HBOND: symmetry: refined_atoms                   24     0.206     0.200
HBOND: symmetry: others                           1     0.005     0.200
M. chain bond B values: refined atoms           745     1.640     1.292
M. chain bond B values: others                  745     1.638     1.292
M. chain angle B values: refined atoms          926     2.603     1.918
M. chain angle B values: others                 927     2.601     1.918
S. chain bond B values: refined atoms           811     2.926     1.682
S. chain bond B values: others                  810     2.923     1.681
S. chain angle B values: refined atoms         1177     4.614     2.358
S. chain angle B values: others                1178     4.612     2.357
Long range B values: refined atoms             1860     7.072    18.250
Long range B values: others                    1766     6.768    16.852
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0414, B  =   -0.0260
Partial structure    1: scale =     0.3796, B  =   46.5823
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.49 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2554 100.00   475.0   484.7  0.15  0.16     139   409.5   422.9  0.20  0.21
 0.116    4360 100.00   340.6   325.2  0.16  0.15     219   342.1   335.8  0.20  0.18
 0.193    5516  99.97   225.8   214.4  0.16  0.14     292   219.6   208.5  0.22  0.19
 0.270    6472 100.00   147.7   153.9  0.19  0.15     315   143.7   151.3  0.26  0.20
$$

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

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1794   0.943    760   0.855   2554   0.917  0.952  0.9649  0.9771  0.9239  0.9447
  0.1161   3586   0.889    774   0.791   4360   0.871  0.997  0.9571  0.9649  0.9155  0.9448
  0.1931   4729   0.879    787   0.760   5516   0.862  1.010  0.9427  0.9596  0.8763  0.9377
  0.2701   5689   0.859    791   0.776   6480   0.849  0.910  0.9378  0.9520  0.8685  0.9253
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18910
Percentage observed                  =    99.9849
Percentage of free reflections       =     4.8553
Overall R factor                     =     0.1660
Free R factor                        =     0.2176
Average Fourier shell correlation    =     0.9606
AverageFree Fourier shell correlation=     0.9476
Overall weighted R factor            =     0.1511
Free weighted R factor               =     0.1953
Overall weighted R2 factor           =     0.1819
Free weighted R2 factor              =     0.2261
Average correlation coefficient      =     0.9360
Overall correlation coefficient      =     0.9576
Free correlation coefficient         =     0.9300
Cruickshanks DPI for coordinate error=     0.1210
DPI based on free R factor           =     0.1241
Overall figure of merit              =     0.8670
ML based su of positional parameters =     0.0737
ML based su of thermal parameters    =     2.3610
-----------------------------------------------------------------------------
  Time in seconds: CPU =        15.27
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1686   0.2182   0.852      101035.    5305.5   0.0125  0.925   1.802  1.041   0.085
       1   0.1676   0.2174   0.867      100552.    5293.6   0.0120  0.890   1.774  1.023   0.085
       2   0.1663   0.2167   0.868      100306.    5288.4   0.0129  0.956   1.811  1.044   0.087
       3   0.1659   0.2167   0.868      100226.    5286.6   0.0129  0.958   1.822  1.050   0.087
       4   0.1658   0.2167   0.868      100196.    5286.0   0.0129  0.958   1.826  1.052   0.087
       5   0.1658   0.2167   0.868      100184.    5286.4   0.0129  0.958   1.828  1.053   0.087
       6   0.1658   0.2170   0.868      100183.    5287.5   0.0129  0.957   1.829  1.053   0.087
       7   0.1659   0.2174   0.867      100186.    5288.7   0.0129  0.956   1.829  1.053   0.087
       8   0.1659   0.2175   0.867      100189.    5289.4   0.0129  0.955   1.828  1.052   0.087
       9   0.1659   0.2175   0.867      100188.    5289.9   0.0129  0.955   1.828  1.052   0.087
      10   0.1660   0.2176   0.867      100191.    5290.3   0.0129  0.955   1.828  1.052   0.087
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1686   0.1660
             R free    0.2182   0.2176
     Rms BondLength    0.0125   0.0129
      Rms BondAngle    1.8016   1.8284
     Rms ChirVolume    0.0850   0.0869
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      48.1s System:    0.1s Elapsed:     0:48