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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: 17:25:00 


 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 1.60     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 1
  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_R01_1-70A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R01_1-60A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R01_1-60A.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       0.0977
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.6000
  Estimated number of reflections :      36894
  Free R exclusion - flag equals:     1
  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  1.6000

  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_R01_1-70A.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=   2.052 ideal_dist=   2.090
            ch:AAA  res:  86  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.209 ideal_dist=   2.090
            ch:AAA  res:  88  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   1.840 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=   2.206 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=   2.415 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=   2.394 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=   2.083 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                            1
Number of "free" reflections       1412
Number of   all  reflections      28041
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          28041

   Current auto weighting coefficient =    6.4996524    

 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        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Weight matrix   0.30034751    
 Actual weight    6.4996524      is applied to the X-ray term
Norm of X_ray positional gradient                39.3
Norm of Geom. positional gradient                81.3
Norm of X_ray B-factor gradient                  114.
Norm of Geom. B-factor gradient                 0.229E+05
Product of X_ray and Geom posit. gradients     -0.141E+08
 Cosine of angle between them                      -0.455
Product of X_ray and Geom B-fact gradients     -0.380E+08
 Cosine of angle between them                      -0.005


Residuals: XRAY=     0.8720E+06 GEOM=     0.2734E+05 TOTAL=     0.8993E+06
 function value    899335.00    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.818     1.644
Bond angles  : others                          3242     2.350     1.582
Torsion angles, period  1. refined              184     6.877     5.000
Torsion angles, period  2. refined               90    36.200    22.778
Torsion angles, period  3. refined              268    13.403    15.000
Torsion angles, period  4. refined                9    11.856    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.016     0.020
VDW repulsions: refined_atoms                   300     0.271     0.200
VDW repulsions.others                          1327     0.231     0.200
VDW; torsion: refined_atoms                     725     0.172     0.200
VDW; torsion.others                             718     0.081     0.200
HBOND: refined_atoms                            219     0.196     0.200
HBOND.others                                      1     0.067     0.200
VDW repulsions: symmetry: refined_atoms           8     0.202     0.200
VDW repulsions: symmetry: others                 24     0.184     0.200
HBOND: symmetry: refined_atoms                   23     0.185     0.200
M. chain bond B values: refined atoms           745     1.717     1.391
M. chain bond B values: others                  745     1.714     1.391
M. chain angle B values: refined atoms          926     2.674     2.071
M. chain angle B values: others                 927     2.673     2.071
S. chain bond B values: refined atoms           811     3.080     1.795
S. chain bond B values: others                  810     3.072     1.794
S. chain angle B values: refined atoms         1177     4.769     2.522
S. chain angle B values: others                1178     4.767     2.521
Long range B values: refined atoms             1843     7.071    19.297
Long range B values: others                    1752     6.836    17.883
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =    1.2588
Partial structure    1: scale =     0.3857, B  =   47.5864
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.42 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3586 100.00   432.7   442.9  0.17  0.18     196   419.8   426.1  0.20  0.20
 0.147    6119  99.97   257.9   242.5  0.16  0.15     325   269.9   260.1  0.20  0.18
 0.244    7814 100.00   166.8   150.9  0.19  0.17     404   174.4   160.7  0.23  0.20
 0.342    9103 100.00    71.2    85.7  0.33  0.27     487    72.0    85.4  0.35  0.29
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2628   0.907    958   0.791   3586   0.876  0.947  0.9567  0.9681  0.8871  0.9374
  0.1468   5150   0.883    969   0.788   6119   0.868  1.025  0.9571  0.9632  0.9133  0.9437
  0.2444   6814   0.862   1000   0.750   7814   0.848  1.050  0.9458  0.9536  0.9054  0.9362
  0.3419   8114   0.685    994   0.605   9108   0.676  0.711  0.8651  0.8703  0.8415  0.8509
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26626
Percentage observed                  =    99.9893
Percentage of free reflections       =     5.0360
Overall R factor                     =     0.1924
Free R factor                        =     0.2279
Average Fourier shell correlation    =     0.9292
AverageFree Fourier shell correlation=     0.9221
Overall weighted R factor            =     0.1667
Free weighted R factor               =     0.1957
Overall weighted R2 factor           =     0.1990
Free weighted R2 factor              =     0.2235
Average correlation coefficient      =     0.9089
Overall correlation coefficient      =     0.9586
Free correlation coefficient         =     0.9356
Cruickshanks DPI for coordinate error=     0.0966
DPI based on free R factor           =     0.0974
Overall figure of merit              =     0.7977
ML based su of positional parameters =     0.0713
ML based su of thermal parameters    =     2.1566
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    134160.81       27336.398       899335.00      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.36391482    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    875578.25    

-------------------------------------------------------------------------------
             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 =     0.0442, B  =   -0.0478
Partial structure    1: scale =     0.3856, B  =   47.2436
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1929
Free R factor                        =     0.2278
Average Fourier shell correlation    =     0.9402
AverageFree Fourier shell correlation=     0.9327
Average correlation coefficient      =     0.9099
Overall figure of merit              =     0.8292
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    133200.06       9824.1279       875578.25       899335.00    


     CGMAT cycle number =      3

 Weight matrix   0.37618756    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    873249.06    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =   -0.0272
Partial structure    1: scale =     0.3856, B  =   43.3008
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1919
Free R factor                        =     0.2267
Average Fourier shell correlation    =     0.9424
AverageFree Fourier shell correlation=     0.9347
Average correlation coefficient      =     0.9121
Overall figure of merit              =     0.8349
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    132943.48       9162.6406       873249.06       875578.25    


     CGMAT cycle number =      4

 Weight matrix   0.37921873    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    872542.50    

-------------------------------------------------------------------------------
             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 =     0.0442, B  =   -0.0006
Partial structure    1: scale =     0.3857, B  =   42.8479
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1917
Free R factor                        =     0.2263
Average Fourier shell correlation    =     0.9430
AverageFree Fourier shell correlation=     0.9351
Average correlation coefficient      =     0.9130
Overall figure of merit              =     0.8362
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    132858.28       9009.8906       872542.50       873249.06    


     CGMAT cycle number =      5

 Weight matrix   0.37989980    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    872345.56    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =   -0.0086
Partial structure    1: scale =     0.3863, B  =   42.7209
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1916
Free R factor                        =     0.2259
Average Fourier shell correlation    =     0.9431
AverageFree Fourier shell correlation=     0.9352
Average correlation coefficient      =     0.9135
Overall figure of merit              =     0.8364
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    132826.28       9020.9375       872345.56       872542.50    


     CGMAT cycle number =      6

 Weight matrix   0.37976158    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    872288.69    

-------------------------------------------------------------------------------
             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 =     0.0442, B  =   -0.0004
Partial structure    1: scale =     0.3863, B  =   42.7314
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1915
Free R factor                        =     0.2257
Average Fourier shell correlation    =     0.9432
AverageFree Fourier shell correlation=     0.9353
Average correlation coefficient      =     0.9137
Overall figure of merit              =     0.8364
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    132812.58       9053.1152       872288.69       872345.56    


     CGMAT cycle number =      7

 Weight matrix   0.37985200    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    872218.19    

-------------------------------------------------------------------------------
             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 =     0.0442, B  =   -0.0002
Partial structure    1: scale =     0.3864, B  =   42.7496
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1913
Free R factor                        =     0.2256
Average Fourier shell correlation    =     0.9432
AverageFree Fourier shell correlation=     0.9352
Average correlation coefficient      =     0.9139
Overall figure of merit              =     0.8364
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    132800.58       9060.5771       872218.19       872288.69    


     CGMAT cycle number =      8

 Weight matrix   0.37989578    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    872192.19    

-------------------------------------------------------------------------------
             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 =     0.0442, B  =    0.0004
Partial structure    1: scale =     0.3865, B  =   42.7870
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1913
Free R factor                        =     0.2256
Average Fourier shell correlation    =     0.9432
AverageFree Fourier shell correlation=     0.9353
Average correlation coefficient      =     0.9140
Overall figure of merit              =     0.8364
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    132796.05       9064.0889       872192.19       872218.19    


     CGMAT cycle number =      9

 Weight matrix   0.37964791    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    872203.69    

-------------------------------------------------------------------------------
             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 =     0.0442, B  =    0.0001
Partial structure    1: scale =     0.3865, B  =   42.7907
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1913
Free R factor                        =     0.2257
Average Fourier shell correlation    =     0.9432
AverageFree Fourier shell correlation=     0.9352
Average correlation coefficient      =     0.9140
Overall figure of merit              =     0.8364
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    132798.23       9056.8760       872196.31       872192.19    
 fvalues    132798.23       9056.8760       872196.31       872199.25    


     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.= 0.914 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        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Weight matrix   0.37959972    
 Actual weight    6.4996524      is applied to the X-ray term
Norm of X_ray positional gradient                43.5
Norm of Geom. positional gradient                43.5
Norm of X_ray B-factor gradient                  115.
Norm of Geom. B-factor gradient                  115.
Product of X_ray and Geom posit. gradients     -0.183E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.429E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.8631E+06 GEOM=      9059.     TOTAL=     0.8722E+06
 function value    872190.63    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.837     1.644
Bond angles  : others                          3242     1.506     1.582
Torsion angles, period  1. refined              184     6.801     5.000
Torsion angles, period  2. refined               90    35.636    22.778
Torsion angles, period  3. refined              268    12.879    15.000
Torsion angles, period  4. refined                9    11.883    15.000
Chiral centres: refined atoms                   196     0.089     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   297     0.273     0.200
VDW repulsions.others                          1363     0.204     0.200
VDW; torsion: refined_atoms                     720     0.173     0.200
VDW; torsion.others                             793     0.084     0.200
HBOND: refined_atoms                            214     0.203     0.200
HBOND.others                                      1     0.126     0.200
VDW repulsions: symmetry: refined_atoms           9     0.188     0.200
VDW repulsions: symmetry: others                 26     0.162     0.200
HBOND: symmetry: refined_atoms                   22     0.188     0.200
HBOND: symmetry: others                           1     0.013     0.200
M. chain bond B values: refined atoms           745     1.770     1.509
M. chain bond B values: others                  745     1.765     1.509
M. chain angle B values: refined atoms          926     2.740     2.250
M. chain angle B values: others                 927     2.739     2.250
S. chain bond B values: refined atoms           811     3.167     1.914
S. chain bond B values: others                  810     3.161     1.913
S. chain angle B values: refined atoms         1177     4.842     2.701
S. chain angle B values: others                1178     4.840     2.700
Long range B values: refined atoms             1835     7.106    20.829
Long range B values: others                    1747     6.879    19.435
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =    0.0013
Partial structure    1: scale =     0.3866, B  =   42.9091
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3586 100.00   433.1   443.1  0.17  0.18     196   420.2   426.8  0.20  0.20
 0.147    6119  99.97   258.1   242.5  0.16  0.15     325   270.1   259.5  0.20  0.18
 0.244    7814 100.00   166.9   151.1  0.19  0.17     404   174.5   160.5  0.23  0.20
 0.342    9103 100.00    71.3    85.4  0.32  0.26     487    72.1    85.4  0.35  0.28
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2628   0.924    958   0.817   3586   0.895  0.949  0.9608  0.9722  0.8870  0.9371
  0.1468   5150   0.891    969   0.797   6119   0.876  1.025  0.9591  0.9646  0.9162  0.9431
  0.2444   6814   0.872   1000   0.763   7814   0.858  1.050  0.9506  0.9571  0.9099  0.9360
  0.3419   8114   0.777    994   0.695   9108   0.768  0.754  0.8962  0.9054  0.8436  0.8665
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26626
Percentage observed                  =    99.9893
Percentage of free reflections       =     5.0360
Overall R factor                     =     0.1914
Free R factor                        =     0.2258
Average Fourier shell correlation    =     0.9432
AverageFree Fourier shell correlation=     0.9352
Overall weighted R factor            =     0.1669
Free weighted R factor               =     0.1940
Overall weighted R2 factor           =     0.1996
Free weighted R2 factor              =     0.2218
Average correlation coefficient      =     0.9140
Overall correlation coefficient      =     0.9588
Free correlation coefficient         =     0.9366
Cruickshanks DPI for coordinate error=     0.0961
DPI based on free R factor           =     0.0965
Overall figure of merit              =     0.8364
ML based su of positional parameters =     0.0634
ML based su of thermal parameters    =     1.8738
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    132796.55       9059.2422       872190.63       872199.25    

    ****                              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.= 0.914 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

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

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R01_1-60A.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     1.838     1.644
Bond angles  : others                          3242     1.506     1.582
Torsion angles, period  1. refined              184     6.800     5.000
Torsion angles, period  2. refined               90    35.597    22.778
Torsion angles, period  3. refined              268    12.846    15.000
Torsion angles, period  4. refined                9    11.892    15.000
Chiral centres: refined atoms                   196     0.089     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   298     0.272     0.200
VDW repulsions.others                          1364     0.204     0.200
VDW; torsion: refined_atoms                     721     0.173     0.200
VDW; torsion.others                             795     0.084     0.200
HBOND: refined_atoms                            215     0.203     0.200
HBOND.others                                      1     0.128     0.200
VDW repulsions: symmetry: refined_atoms           9     0.188     0.200
VDW repulsions: symmetry: others                 26     0.162     0.200
HBOND: symmetry: refined_atoms                   22     0.188     0.200
HBOND: symmetry: others                           1     0.013     0.200
M. chain bond B values: refined atoms           745     1.770     1.509
M. chain bond B values: others                  745     1.765     1.509
M. chain angle B values: refined atoms          926     2.740     2.250
M. chain angle B values: others                 927     2.739     2.250
S. chain bond B values: refined atoms           811     3.168     1.914
S. chain bond B values: others                  810     3.162     1.913
S. chain angle B values: refined atoms         1177     4.843     2.701
S. chain angle B values: others                1178     4.841     2.700
Long range B values: refined atoms             1838     7.112    20.891
Long range B values: others                    1749     6.886    19.465
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =    0.0008
Partial structure    1: scale =     0.3866, B  =   42.9726
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3586 100.00   433.1   443.1  0.17  0.18     196   420.2   426.9  0.20  0.20
 0.147    6119  99.97   258.1   242.5  0.16  0.15     325   270.1   259.5  0.20  0.18
 0.244    7814 100.00   166.9   151.1  0.19  0.17     404   174.5   160.4  0.23  0.20
 0.342    9103 100.00    71.3    85.4  0.32  0.26     487    72.1    85.4  0.35  0.28
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2628   0.924    958   0.817   3586   0.895  0.949  0.9608  0.9722  0.8869  0.9371
  0.1468   5150   0.891    969   0.797   6119   0.876  1.025  0.9591  0.9645  0.9162  0.9431
  0.2444   6814   0.872   1000   0.763   7814   0.858  1.050  0.9506  0.9571  0.9100  0.9360
  0.3419   8114   0.777    994   0.695   9108   0.768  0.754  0.8961  0.9054  0.8435  0.8666
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26626
Percentage observed                  =    99.9893
Percentage of free reflections       =     5.0360
Overall R factor                     =     0.1913
Free R factor                        =     0.2258
Average Fourier shell correlation    =     0.9432
AverageFree Fourier shell correlation=     0.9352
Overall weighted R factor            =     0.1669
Free weighted R factor               =     0.1941
Overall weighted R2 factor           =     0.1996
Free weighted R2 factor              =     0.2220
Average correlation coefficient      =     0.9141
Overall correlation coefficient      =     0.9589
Free correlation coefficient         =     0.9365
Cruickshanks DPI for coordinate error=     0.0961
DPI based on free R factor           =     0.0965
Overall figure of merit              =     0.8364
ML based su of positional parameters =     0.0634
ML based su of thermal parameters    =     1.8738
-----------------------------------------------------------------------------
  Time in seconds: CPU =        16.99
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1924   0.2279   0.798      134161.    7305.0   0.0131  0.977   1.818  1.054   0.090
       1   0.1929   0.2278   0.829      133200.    7268.3   0.0123  0.918   1.772  1.028   0.087
       2   0.1919   0.2267   0.835      132943.    7259.4   0.0130  0.974   1.798  1.046   0.088
       3   0.1917   0.2263   0.836      132858.    7257.0   0.0131  0.985   1.814  1.056   0.089
       4   0.1916   0.2259   0.836      132826.    7255.4   0.0132  0.989   1.823  1.062   0.089
       5   0.1915   0.2257   0.836      132813.    7254.9   0.0132  0.991   1.829  1.065   0.089
       6   0.1913   0.2256   0.836      132801.    7254.9   0.0132  0.991   1.832  1.066   0.089
       7   0.1913   0.2256   0.836      132796.    7254.6   0.0132  0.991   1.835  1.068   0.089
       8   0.1913   0.2257   0.836      132799.    7254.8   0.0132  0.992   1.836  1.069   0.089
       9   0.1914   0.2258   0.836      132797.    7254.7   0.0132  0.992   1.837  1.069   0.089
      10   0.1913   0.2258   0.836      132797.    7255.0   0.0132  0.992   1.838  1.070   0.089
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1924   0.1913
             R free    0.2279   0.2258
     Rms BondLength    0.0131   0.0132
      Rms BondAngle    1.8184   1.8381
     Rms ChirVolume    0.0898   0.0891
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      49.1s System:    0.1s Elapsed:     0:49