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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: 15:35:26 


 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 9
  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_R09_1-90A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R09_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_R09_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:     9
  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_R09_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=   2.003 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=   2.224 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=   1.844 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=   2.210 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=   2.360 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=   2.432 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=   2.099 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                            9
Number of "free" reflections       1030
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.= 0.909 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   0.30175969    
 Actual weight    6.9995613      is applied to the X-ray term
Norm of X_ray positional gradient                44.7
Norm of Geom. positional gradient                80.2
Norm of X_ray B-factor gradient                  146.
Norm of Geom. B-factor gradient                 0.215E+05
Product of X_ray and Geom posit. gradients     -0.122E+08
 Cosine of angle between them                      -0.351
Product of X_ray and Geom B-fact gradients     -0.463E+08
 Cosine of angle between them                      -0.005


Residuals: XRAY=     0.7024E+06 GEOM=     0.2657E+05 TOTAL=     0.7289E+06
 function value    728929.38    

-------------------------------------------------------------------------------
             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     1.831     1.644
Bond angles  : others                          3242     2.350     1.582
Torsion angles, period  1. refined              184     6.950     5.000
Torsion angles, period  2. refined               90    36.872    22.778
Torsion angles, period  3. refined              268    14.392    15.000
Torsion angles, period  4. refined                9    10.568    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.018     0.020
VDW repulsions: refined_atoms                   302     0.265     0.200
VDW repulsions.others                          1335     0.231     0.200
VDW; torsion: refined_atoms                     708     0.172     0.200
VDW; torsion.others                             712     0.080     0.200
HBOND: refined_atoms                            236     0.210     0.200
HBOND.others                                      3     0.038     0.200
VDW repulsions: symmetry: refined_atoms           7     0.242     0.200
VDW repulsions: symmetry: others                 23     0.188     0.200
HBOND: symmetry: refined_atoms                   19     0.224     0.200
HBOND: symmetry: others                           1     0.026     0.200
M. chain bond B values: refined atoms           745     1.605     1.201
M. chain bond B values: others                  745     1.604     1.201
M. chain angle B values: refined atoms          926     2.555     1.783
M. chain angle B values: others                 927     2.553     1.783
S. chain bond B values: refined atoms           812     2.763     1.564
S. chain bond B values: others                  811     2.760     1.563
S. chain angle B values: refined atoms         1177     4.315     2.190
S. chain angle B values: others                1178     4.313     2.189
Long range B values: refined atoms             1851     7.022    17.072
Long range B values: others                    1754     6.708    15.613
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0414, B  =    0.9335
Partial structure    1: scale =     0.3789, B  =   50.5441
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2555 100.00   474.5   483.3  0.16  0.17     138   430.2   448.7  0.21  0.23
 0.116    4349 100.00   341.9   327.5  0.15  0.14     230   326.9   315.0  0.20  0.18
 0.193    5509  99.97   225.9   214.9  0.15  0.13     299   225.3   217.8  0.20  0.17
 0.270    6425 100.00   147.6   154.8  0.22  0.17     362   149.9   155.3  0.24  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1788   0.914    767   0.822   2555   0.886  0.948  0.9566  0.9691  0.9104  0.9390
  0.1161   3572   0.908    777   0.810   4349   0.890  1.004  0.9582  0.9699  0.9195  0.9496
  0.1931   4741   0.888    768   0.777   5509   0.873  1.015  0.9535  0.9643  0.8958  0.9447
  0.2701   5648   0.835    785   0.750   6433   0.825  0.897  0.9307  0.9409  0.8641  0.9024
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18846
Percentage observed                  =    99.9849
Percentage of free reflections       =     5.1774
Overall R factor                     =     0.1683
Free R factor                        =     0.2111
Average Fourier shell correlation    =     0.9583
AverageFree Fourier shell correlation=     0.9469
Overall weighted R factor            =     0.1514
Free weighted R factor               =     0.1977
Overall weighted R2 factor           =     0.1833
Free weighted R2 factor              =     0.2381
Average correlation coefficient      =     0.9306
Overall correlation coefficient      =     0.9564
Free correlation coefficient         =     0.9292
Cruickshanks DPI for coordinate error=     0.1232
DPI based on free R factor           =     0.1207
Overall figure of merit              =     0.8623
ML based su of positional parameters =     0.0739
ML based su of thermal parameters    =     2.3953
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    100343.55       26568.490       728929.38      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.32929444    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    709357.56    

-------------------------------------------------------------------------------
             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  =   -0.0927
Partial structure    1: scale =     0.3802, B  =   50.2231
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                     =     0.1673
Free R factor                        =     0.2091
Average Fourier shell correlation    =     0.9612
AverageFree Fourier shell correlation=     0.9501
Average correlation coefficient      =     0.9336
Overall figure of merit              =     0.8714
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    99856.117       10408.533       709357.56       728929.38    


     CGMAT cycle number =      3

 Weight matrix   0.33752394    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    707194.69    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0525
Partial structure    1: scale =     0.3787, B  =   47.5264
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                     =     0.1661
Free R factor                        =     0.2075
Average Fourier shell correlation    =     0.9621
AverageFree Fourier shell correlation=     0.9511
Average correlation coefficient      =     0.9353
Overall figure of merit              =     0.8734
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    99646.859       9710.3984       707194.69       709357.56    


     CGMAT cycle number =      4

 Weight matrix   0.34175366    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    706267.44    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.014     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0414, B  =   -0.0135
Partial structure    1: scale =     0.3804, B  =   47.2593
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                     =     0.1656
Free R factor                        =     0.2066
Average Fourier shell correlation    =     0.9625
AverageFree Fourier shell correlation=     0.9516
Average correlation coefficient      =     0.9360
Overall figure of merit              =     0.8742
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    99537.906       9545.7305       706267.44       707194.69    


     CGMAT cycle number =      5

 Weight matrix   0.34388047    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    705912.50    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.014     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0414, B  =   -0.0336
Partial structure    1: scale =     0.3804, B  =   47.0173
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                     =     0.1654
Free R factor                        =     0.2060
Average Fourier shell correlation    =     0.9627
AverageFree Fourier shell correlation=     0.9519
Average correlation coefficient      =     0.9364
Overall figure of merit              =     0.8746
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    99485.734       9556.0234       705912.50       706267.44    


     CGMAT cycle number =      6

 Weight matrix   0.31394136    
 Actual weight    6.3632374      is applied to the X-ray term


 function value    642422.31    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.014     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0414, B  =   -0.0263
Partial structure    1: scale =     0.3805, B  =   46.7901
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                     =     0.1653
Free R factor                        =     0.2056
Average Fourier shell correlation    =     0.9628
AverageFree Fourier shell correlation=     0.9521
Average correlation coefficient      =     0.9366
Overall figure of merit              =     0.8750
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    99447.633       9613.4258       642422.31       705912.50    


     CGMAT cycle number =      7

 Weight matrix   0.28546402    
 Actual weight    5.7847610      is applied to the X-ray term


 function value    584862.94    

-------------------------------------------------------------------------------
             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 =     0.0414, B  =   -0.0437
Partial structure    1: scale =     0.3785, B  =   46.5775
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                     =     0.1657
Free R factor                        =     0.2055
Average Fourier shell correlation    =     0.9628
AverageFree Fourier shell correlation=     0.9522
Average correlation coefficient      =     0.9363
Overall figure of merit              =     0.8751
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    99492.602       9321.9717       584862.94       642422.31    


     CGMAT cycle number =      8

 Weight matrix   0.28418025    
 Actual weight    5.7847610      is applied to the X-ray term


 function value    584954.56    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0598
Partial structure    1: scale =     0.3784, B  =   46.3608
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                     =     0.1664
Free R factor                        =     0.2059
Average Fourier shell correlation    =     0.9625
AverageFree Fourier shell correlation=     0.9520
Average correlation coefficient      =     0.9357
Overall figure of merit              =     0.8750
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    99572.922       8954.8584       584977.88       584862.94    

 fvalues    99572.922       8954.8584       584967.38       584960.44    
 fvalues    99572.922       8954.8584       584967.38       584960.44    


     CGMAT cycle number =      9

 Weight matrix   0.28446680    
 Actual weight    5.7847610      is applied to the X-ray term


 function value    584978.69    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0566
Partial structure    1: scale =     0.3783, B  =   46.3163
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                     =     0.1664
Free R factor                        =     0.2059
Average Fourier shell correlation    =     0.9625
AverageFree Fourier shell correlation=     0.9520
Average correlation coefficient      =     0.9357
Overall figure of merit              =     0.8751
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02

 fvalues    99574.281       8932.1943       584945.63       584960.44    


     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.= 0.923 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   0.28504267    
 Actual weight    5.7847610      is applied to the X-ray term
Norm of X_ray positional gradient                35.8
Norm of Geom. positional gradient                36.0
Norm of X_ray B-factor gradient                  115.
Norm of Geom. B-factor gradient                  119.
Product of X_ray and Geom posit. gradients     -0.125E+08
 Cosine of angle between them                      -0.998
Product of X_ray and Geom B-fact gradients     -0.440E+08
 Cosine of angle between them                      -0.993


Residuals: XRAY=     0.5760E+06 GEOM=      8898.     TOTAL=     0.5849E+06
 function value    584935.81    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.795     1.644
Bond angles  : others                          3242     1.463     1.582
Torsion angles, period  1. refined              184     6.992     5.000
Torsion angles, period  2. refined               90    36.528    22.778
Torsion angles, period  3. refined              268    14.208    15.000
Torsion angles, period  4. refined                9    10.926    15.000
Chiral centres: refined atoms                   196     0.084     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   298     0.266     0.200
VDW repulsions.others                          1357     0.204     0.200
VDW; torsion: refined_atoms                     715     0.171     0.200
VDW; torsion.others                             778     0.084     0.200
HBOND: refined_atoms                            236     0.198     0.200
HBOND.others                                      3     0.086     0.200
VDW repulsions: symmetry: refined_atoms           8     0.211     0.200
VDW repulsions: symmetry: others                 22     0.180     0.200
HBOND: symmetry: refined_atoms                   21     0.214     0.200
HBOND: symmetry: others                           1     0.007     0.200
M. chain bond B values: refined atoms           745     1.608     1.288
M. chain bond B values: others                  745     1.607     1.288
M. chain angle B values: refined atoms          926     2.533     1.915
M. chain angle B values: others                 927     2.532     1.915
S. chain bond B values: refined atoms           811     2.808     1.666
S. chain bond B values: others                  810     2.805     1.666
S. chain angle B values: refined atoms         1177     4.417     2.339
S. chain angle B values: others                1178     4.415     2.338
Long range B values: refined atoms             1854     6.999    18.136
Long range B values: others                    1753     6.659    16.583
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0591
Partial structure    1: scale =     0.3784, B  =   46.3439
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2555 100.00   474.9   483.8  0.16  0.17     138   430.5   447.8  0.21  0.23
 0.116    4349 100.00   342.2   327.1  0.16  0.14     230   327.1   313.5  0.19  0.18
 0.193    5509  99.97   226.0   214.9  0.16  0.13     299   225.4   216.6  0.19  0.17
 0.270    6425 100.00   147.7   154.4  0.20  0.15     362   150.1   155.6  0.24  0.19
$$

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

 $TABLE: Cycle   10. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1788   0.933    767   0.844   2555   0.907  0.951  0.9628  0.9732  0.9107  0.9387
  0.1161   3572   0.911    777   0.814   4349   0.894  1.004  0.9593  0.9703  0.9215  0.9483
  0.1931   4741   0.895    768   0.782   5509   0.879  1.015  0.9566  0.9652  0.9029  0.9412
  0.2701   5648   0.857    785   0.776   6433   0.847  0.908  0.9397  0.9509  0.8750  0.9210
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18846
Percentage observed                  =    99.9849
Percentage of free reflections       =     5.1774
Overall R factor                     =     0.1665
Free R factor                        =     0.2059
Average Fourier shell correlation    =     0.9626
AverageFree Fourier shell correlation=     0.9521
Overall weighted R factor            =     0.1518
Free weighted R factor               =     0.1937
Overall weighted R2 factor           =     0.1843
Free weighted R2 factor              =     0.2355
Average correlation coefficient      =     0.9356
Overall correlation coefficient      =     0.9569
Free correlation coefficient         =     0.9313
Cruickshanks DPI for coordinate error=     0.1219
DPI based on free R factor           =     0.1178
Overall figure of merit              =     0.8754
ML based su of positional parameters =     0.0690
ML based su of thermal parameters    =     2.2239
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    99578.461       8898.2197       584935.81       584945.63    

    ****                              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.= 0.923 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_R09_1-80A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.792     1.644
Bond angles  : others                          3242     1.462     1.582
Torsion angles, period  1. refined              184     6.991     5.000
Torsion angles, period  2. refined               90    36.523    22.778
Torsion angles, period  3. refined              268    14.201    15.000
Torsion angles, period  4. refined                9    10.923    15.000
Chiral centres: refined atoms                   196     0.084     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   299     0.266     0.200
VDW repulsions.others                          1356     0.204     0.200
VDW; torsion: refined_atoms                     715     0.171     0.200
VDW; torsion.others                             783     0.083     0.200
HBOND: refined_atoms                            236     0.198     0.200
HBOND.others                                      3     0.086     0.200
VDW repulsions: symmetry: refined_atoms           8     0.211     0.200
VDW repulsions: symmetry: others                 22     0.180     0.200
HBOND: symmetry: refined_atoms                   21     0.214     0.200
HBOND: symmetry: others                           1     0.007     0.200
M. chain bond B values: refined atoms           745     1.606     1.288
M. chain bond B values: others                  745     1.604     1.289
M. chain angle B values: refined atoms          926     2.529     1.916
M. chain angle B values: others                 927     2.528     1.915
S. chain bond B values: refined atoms           811     2.803     1.665
S. chain bond B values: others                  810     2.800     1.665
S. chain angle B values: refined atoms         1177     4.408     2.338
S. chain angle B values: others                1178     4.406     2.338
Long range B values: refined atoms             1855     7.002    18.127
Long range B values: others                    1754     6.663    16.575
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0562
Partial structure    1: scale =     0.3784, B  =   46.2488
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2555 100.00   475.0   483.8  0.16  0.17     138   430.6   447.7  0.21  0.23
 0.116    4349 100.00   342.2   327.1  0.16  0.14     230   327.2   313.4  0.19  0.18
 0.193    5509  99.97   226.1   214.9  0.16  0.13     299   225.5   216.6  0.19  0.17
 0.270    6425 100.00   147.7   154.4  0.20  0.15     362   150.1   155.6  0.24  0.19
$$

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

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1788   0.934    767   0.844   2555   0.907  0.951  0.9628  0.9732  0.9107  0.9387
  0.1161   3572   0.911    777   0.814   4349   0.894  1.004  0.9594  0.9702  0.9215  0.9483
  0.1931   4741   0.895    768   0.782   5509   0.879  1.015  0.9566  0.9652  0.9028  0.9411
  0.2701   5648   0.857    785   0.776   6433   0.847  0.908  0.9397  0.9509  0.8752  0.9211
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18846
Percentage observed                  =    99.9849
Percentage of free reflections       =     5.1774
Overall R factor                     =     0.1666
Free R factor                        =     0.2059
Average Fourier shell correlation    =     0.9626
AverageFree Fourier shell correlation=     0.9521
Overall weighted R factor            =     0.1519
Free weighted R factor               =     0.1937
Overall weighted R2 factor           =     0.1844
Free weighted R2 factor              =     0.2356
Average correlation coefficient      =     0.9356
Overall correlation coefficient      =     0.9568
Free correlation coefficient         =     0.9313
Cruickshanks DPI for coordinate error=     0.1219
DPI based on free R factor           =     0.1178
Overall figure of merit              =     0.8754
ML based su of positional parameters =     0.0690
ML based su of thermal parameters    =     2.2239
-----------------------------------------------------------------------------
  Time in seconds: CPU =        15.39
             Elapsed =         128.00

    ****           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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1683   0.2111   0.862      100344.    5618.4   0.0130  0.944   1.831  1.052   0.087
       1   0.1673   0.2091   0.871       99856.    5602.5   0.0129  0.942   1.814  1.042   0.088
       2   0.1661   0.2075   0.873       99647.    5593.5   0.0135  0.986   1.840  1.057   0.089
       3   0.1656   0.2066   0.874       99538.    5587.6   0.0136  0.997   1.854  1.064   0.089
       4   0.1654   0.2060   0.875       99486.    5584.7   0.0137  1.002   1.861  1.068   0.089
       5   0.1653   0.2056   0.875       99448.    5582.2   0.0137  1.005   1.866  1.071   0.089
       6   0.1657   0.2055   0.875       99493.    5582.4   0.0131  0.961   1.840  1.055   0.087
       7   0.1664   0.2059   0.875       99572.    5584.2   0.0125  0.916   1.802  1.034   0.084
       8   0.1664   0.2059   0.875       99580.    5584.0   0.0124  0.915   1.799  1.032   0.084
       9   0.1665   0.2059   0.875       99578.    5584.0   0.0124  0.914   1.795  1.030   0.084
      10   0.1666   0.2059   0.875       99585.    5584.0   0.0124  0.913   1.792  1.028   0.084
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1683   0.1666
             R free    0.2111   0.2059
     Rms BondLength    0.0130   0.0124
      Rms BondAngle    1.8311   1.7917
     Rms ChirVolume    0.0873   0.0840
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      47.4s System:    0.5s Elapsed:     0:48