###############################################################
 ###############################################################
 ###############################################################
 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 26/ 5/2020 Run time: 19:28:58 


 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 1.50     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_1-60A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R09_1-50A.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_1-50A.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       0.1111
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.5000
  Estimated number of reflections :      43652
  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  1.5000

  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_1-60A.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=   2.042 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=   2.205 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=   1.825 ideal_dist=   1.720
            ch:AAA  res:  93  CYS              at:SG  .->ch:AAA  res: 157  TYR              at:CE1 .
  INFO:     link is found (not be used) dist=   2.212 ideal_dist=   2.090
            ch:AAA  res: 140  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.382 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=   2.389 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=   2.103 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       1737
Number of   all  reflections      33910
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          33910

   Current auto weighting coefficient =    6.2496691    

 mode : HKRF


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



     CGMAT cycle number =      1

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.891 id.= 3.000 dev= -2.11 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Weight matrix   0.31633893    
 Actual weight    6.2496691      is applied to the X-ray term
Norm of X_ray positional gradient                42.8
Norm of Geom. positional gradient                81.7
Norm of X_ray B-factor gradient                  116.
Norm of Geom. B-factor gradient                 0.228E+05
Product of X_ray and Geom posit. gradients     -0.164E+08
 Cosine of angle between them                      -0.485
Product of X_ray and Geom B-fact gradients     -0.375E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.9734E+06 GEOM=     0.2698E+05 TOTAL=     0.1000E+07
 function value    1000393.7    

-------------------------------------------------------------------------------
             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     1.814     1.644
Bond angles  : others                          3242     2.349     1.582
Torsion angles, period  1. refined              184     6.878     5.000
Torsion angles, period  2. refined               90    36.275    22.778
Torsion angles, period  3. refined              268    13.788    15.000
Torsion angles, period  4. refined                9    10.694    15.000
Chiral centres: refined atoms                   196     0.089     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.016     0.020
VDW repulsions: refined_atoms                   296     0.271     0.200
VDW repulsions.others                          1339     0.232     0.200
VDW; torsion: refined_atoms                     725     0.173     0.200
VDW; torsion.others                             727     0.081     0.200
HBOND: refined_atoms                            220     0.198     0.200
HBOND.others                                      4     0.082     0.200
VDW repulsions: symmetry: refined_atoms           8     0.203     0.200
VDW repulsions: symmetry: others                 20     0.194     0.200
HBOND: symmetry: refined_atoms                   21     0.193     0.200
M. chain bond B values: refined atoms           745     1.721     1.504
M. chain bond B values: others                  745     1.717     1.504
M. chain angle B values: refined atoms          926     2.681     2.245
M. chain angle B values: others                 927     2.680     2.244
S. chain bond B values: refined atoms           811     3.123     1.909
S. chain bond B values: others                  810     3.118     1.909
S. chain angle B values: refined atoms         1177     4.784     2.695
S. chain angle B values: others                1178     4.782     2.695
Long range B values: refined atoms             1844     7.160    20.846
Long range B values: others                    1752     6.868    19.366
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0457, B  =    1.1712
Partial structure    1: scale =     0.3920, B  =   45.9135
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4314 100.00   406.7   416.8  0.17  0.18     233   374.3   390.9  0.21  0.22
 0.167    7402  99.97   227.8   208.1  0.17  0.15     396   224.5   205.2  0.20  0.18
 0.278    9390 100.00   123.6   113.9  0.21  0.19     520   125.0   115.5  0.24  0.21
 0.389   11054 100.00    50.2    62.5  0.41  0.36     587    48.4    59.9  0.41  0.37
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3208   0.905   1106   0.801   4314   0.879  0.944  0.9569  0.9668  0.9165  0.9327
  0.1670   6279   0.894   1123   0.798   7402   0.880  1.067  0.9569  0.9656  0.9083  0.9403
  0.2780   8263   0.835   1127   0.753   9390   0.825  1.018  0.9346  0.9443  0.8838  0.9269
  0.3890   9937   0.575   1129   0.510  11066   0.569  0.569  0.7606  0.7816  0.7694  0.7733
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32172
Percentage observed                  =    99.9912
Percentage of free reflections       =     5.1197
Overall R factor                     =     0.2075
Free R factor                        =     0.2328
Average Fourier shell correlation    =     0.8963
AverageFree Fourier shell correlation=     0.8838
Overall weighted R factor            =     0.1758
Free weighted R factor               =     0.2081
Overall weighted R2 factor           =     0.2059
Free weighted R2 factor              =     0.2497
Average correlation coefficient      =     0.8780
Overall correlation coefficient      =     0.9588
Free correlation coefficient         =     0.9435
Cruickshanks DPI for coordinate error=     0.0861
DPI based on free R factor           =     0.0849
Overall figure of merit              =     0.7565
ML based su of positional parameters =     0.0681
ML based su of thermal parameters    =     2.0177
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    155754.52       26979.492       1000393.7      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.40180030    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    975963.75    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0457, B  =   -0.0687
Partial structure    1: scale =     0.3915, B  =   45.1958
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2074
Free R factor                        =     0.2331
Average Fourier shell correlation    =     0.9111
AverageFree Fourier shell correlation=     0.9003
Average correlation coefficient      =     0.8783
Overall figure of merit              =     0.7863
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    154538.86       10147.004       975963.75       1000393.7    


     CGMAT cycle number =      3

 Weight matrix   0.41142917    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    973774.19    

-------------------------------------------------------------------------------
             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 =     0.0457, B  =   -0.0181
Partial structure    1: scale =     0.3914, B  =   40.8914
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2062
Free R factor                        =     0.2325
Average Fourier shell correlation    =     0.9139
AverageFree Fourier shell correlation=     0.9033
Average correlation coefficient      =     0.8805
Overall figure of merit              =     0.7910
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    154272.44       9622.5117       973774.19       975963.75    


     CGMAT cycle number =      4

 Weight matrix   0.37582001    
 Actual weight    5.6815171      is applied to the X-ray term


 function value    885648.38    

-------------------------------------------------------------------------------
             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 =     0.0457, B  =   -0.0060
Partial structure    1: scale =     0.3921, B  =   39.0022
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2060
Free R factor                        =     0.2324
Average Fourier shell correlation    =     0.9147
AverageFree Fourier shell correlation=     0.9040
Average correlation coefficient      =     0.8814
Overall figure of merit              =     0.7924
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    154219.36       9448.4443       885648.38       973774.19    


     CGMAT cycle number =      5

 Weight matrix   0.34148428    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    805860.00    

-------------------------------------------------------------------------------
             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 =     0.0457, B  =   -0.0005
Partial structure    1: scale =     0.3921, B  =   38.9965
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2062
Free R factor                        =     0.2322
Average Fourier shell correlation    =     0.9147
AverageFree Fourier shell correlation=     0.9040
Average correlation coefficient      =     0.8813
Overall figure of merit              =     0.7928
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    154248.44       9164.5039       805860.00       885648.38    


     CGMAT cycle number =      6

 Weight matrix   0.34049216    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    805935.63    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0457, B  =   -0.0040
Partial structure    1: scale =     0.3922, B  =   38.9909
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2066
Free R factor                        =     0.2325
Average Fourier shell correlation    =     0.9146
AverageFree Fourier shell correlation=     0.9039
Average correlation coefficient      =     0.8810
Overall figure of merit              =     0.7926
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    154326.98       8838.6758       805984.31       805860.00    

 fvalues    154326.98       8838.6758       805946.63       805939.94    
 fvalues    154326.98       8838.6758       805946.63       805939.94    


     CGMAT cycle number =      7

 Weight matrix   0.34046715    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    805955.81    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0457, B  =   -0.0021
Partial structure    1: scale =     0.3922, B  =   38.9960
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2066
Free R factor                        =     0.2325
Average Fourier shell correlation    =     0.9145
AverageFree Fourier shell correlation=     0.9038
Average correlation coefficient      =     0.8809
Overall figure of merit              =     0.7926
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    154335.22       8818.1445       805976.94       805939.94    

 fvalues    154335.22       8818.1445       805966.19       805961.88    
 fvalues    154335.22       8818.1445       805966.19       805961.88    


     CGMAT cycle number =      8

 Weight matrix   0.34025332    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    805965.25    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0457, B  =   -0.0003
Partial structure    1: scale =     0.3922, B  =   38.9959
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2066
Free R factor                        =     0.2325
Average Fourier shell correlation    =     0.9145
AverageFree Fourier shell correlation=     0.9038
Average correlation coefficient      =     0.8809
Overall figure of merit              =     0.7925
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    154337.63       8809.5107       805989.63       805961.88    

 fvalues    154337.63       8809.5107       805965.56       805965.69    
 fvalues    154337.63       8809.5107       805965.56       805965.69    


     CGMAT cycle number =      9

 Weight matrix   0.34041777    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    806003.81    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0457, B  =   -0.0070
Partial structure    1: scale =     0.3923, B  =   39.0111
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2067
Free R factor                        =     0.2325
Average Fourier shell correlation    =     0.9145
AverageFree Fourier shell correlation=     0.9038
Average correlation coefficient      =     0.8809
Overall figure of merit              =     0.7926
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    154347.73       8804.4541       806018.00       805965.69    

 fvalues    154347.73       8804.4541       806018.69       806012.81    
 fvalues    154347.73       8804.4541       806018.69       806012.81    


     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.= 0.906 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Weight matrix   0.34032488    
 Actual weight    5.1650152      is applied to the X-ray term
Norm of X_ray positional gradient                41.4
Norm of Geom. positional gradient                41.7
Norm of X_ray B-factor gradient                  103.
Norm of Geom. B-factor gradient                  105.
Product of X_ray and Geom posit. gradients     -0.167E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.346E+08
 Cosine of angle between them                      -0.999


Residuals: XRAY=     0.7972E+06 GEOM=      8803.     TOTAL=     0.8060E+06
 function value    806015.13    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.819     1.644
Bond angles  : others                          3242     1.508     1.582
Torsion angles, period  1. refined              184     6.886     5.000
Torsion angles, period  2. refined               90    36.181    22.778
Torsion angles, period  3. refined              268    13.722    15.000
Torsion angles, period  4. refined                9    10.965    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   296     0.272     0.200
VDW repulsions.others                          1348     0.209     0.200
VDW; torsion: refined_atoms                     723     0.173     0.200
VDW; torsion.others                             758     0.086     0.200
HBOND: refined_atoms                            219     0.197     0.200
HBOND.others                                      2     0.122     0.200
VDW repulsions: symmetry: refined_atoms           8     0.199     0.200
VDW repulsions: symmetry: others                 23     0.167     0.200
HBOND: symmetry: refined_atoms                   21     0.194     0.200
M. chain bond B values: refined atoms           745     1.780     1.615
M. chain bond B values: others                  745     1.775     1.615
M. chain angle B values: refined atoms          926     2.752     2.412
M. chain angle B values: others                 927     2.751     2.412
S. chain bond B values: refined atoms           811     3.226     2.034
S. chain bond B values: others                  810     3.221     2.033
S. chain angle B values: refined atoms         1177     4.922     2.879
S. chain angle B values: others                1178     4.920     2.878
Long range B values: refined atoms             1838     7.249    22.153
Long range B values: others                    1746     6.973    20.654
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0457, B  =   -0.0063
Partial structure    1: scale =     0.3924, B  =   39.0128
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.35 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4314 100.00   407.2   417.3  0.17  0.18     233   374.8   390.8  0.21  0.22
 0.167    7402  99.97   228.1   208.3  0.17  0.15     396   224.8   205.5  0.20  0.18
 0.278    9390 100.00   123.7   114.2  0.21  0.19     520   125.2   115.6  0.24  0.21
 0.389   11054 100.00    50.2    62.6  0.41  0.36     587    48.5    59.8  0.41  0.37
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3208   0.927   1106   0.834   4314   0.903  0.948  0.9643  0.9725  0.9168  0.9326
  0.1670   6279   0.908   1123   0.813   7402   0.893  1.068  0.9599  0.9685  0.9086  0.9410
  0.2780   8263   0.853   1127   0.773   9390   0.843  1.021  0.9400  0.9505  0.8823  0.9278
  0.3890   9937   0.645   1129   0.583  11066   0.639  0.603  0.8100  0.8253  0.7700  0.7807
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32172
Percentage observed                  =    99.9912
Percentage of free reflections       =     5.1197
Overall R factor                     =     0.2067
Free R factor                        =     0.2325
Average Fourier shell correlation    =     0.9145
AverageFree Fourier shell correlation=     0.9038
Overall weighted R factor            =     0.1754
Free weighted R factor               =     0.2078
Overall weighted R2 factor           =     0.2057
Free weighted R2 factor              =     0.2486
Average correlation coefficient      =     0.8809
Overall correlation coefficient      =     0.9591
Free correlation coefficient         =     0.9437
Cruickshanks DPI for coordinate error=     0.0858
DPI based on free R factor           =     0.0848
Overall figure of merit              =     0.7925
ML based su of positional parameters =     0.0597
ML based su of thermal parameters    =     1.7388
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    154349.86       8802.9346       806013.75       806012.81    
 fvalues    154349.86       8802.9346       806013.75       806022.31    

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.906 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_R09_1-50A.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     1.819     1.644
Bond angles  : others                          3242     1.508     1.582
Torsion angles, period  1. refined              184     6.886     5.000
Torsion angles, period  2. refined               90    36.180    22.778
Torsion angles, period  3. refined              268    13.721    15.000
Torsion angles, period  4. refined                9    10.965    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   296     0.272     0.200
VDW repulsions.others                          1348     0.208     0.200
VDW; torsion: refined_atoms                     723     0.173     0.200
VDW; torsion.others                             758     0.086     0.200
HBOND: refined_atoms                            219     0.197     0.200
HBOND.others                                      2     0.122     0.200
VDW repulsions: symmetry: refined_atoms           8     0.199     0.200
VDW repulsions: symmetry: others                 23     0.167     0.200
HBOND: symmetry: refined_atoms                   21     0.194     0.200
M. chain bond B values: refined atoms           745     1.779     1.615
M. chain bond B values: others                  745     1.775     1.615
M. chain angle B values: refined atoms          926     2.752     2.412
M. chain angle B values: others                 927     2.751     2.412
S. chain bond B values: refined atoms           811     3.225     2.034
S. chain bond B values: others                  810     3.220     2.033
S. chain angle B values: refined atoms         1177     4.921     2.879
S. chain angle B values: others                1178     4.919     2.878
Long range B values: refined atoms             1838     7.248    22.153
Long range B values: others                    1746     6.973    20.654
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0457, B  =   -0.0066
Partial structure    1: scale =     0.3924, B  =   39.0205
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.35 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4314 100.00   407.3   417.3  0.17  0.18     233   374.8   390.8  0.21  0.22
 0.167    7402  99.97   228.1   208.3  0.17  0.15     396   224.8   205.5  0.20  0.18
 0.278    9390 100.00   123.7   114.2  0.21  0.19     520   125.2   115.6  0.24  0.21
 0.389   11054 100.00    50.2    62.6  0.41  0.36     587    48.5    59.8  0.41  0.37
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3208   0.927   1106   0.834   4314   0.903  0.948  0.9643  0.9725  0.9168  0.9326
  0.1670   6279   0.908   1123   0.813   7402   0.893  1.068  0.9599  0.9685  0.9086  0.9409
  0.2780   8263   0.853   1127   0.773   9390   0.843  1.021  0.9400  0.9505  0.8823  0.9278
  0.3890   9937   0.645   1129   0.583  11066   0.639  0.603  0.8100  0.8253  0.7700  0.7807
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32172
Percentage observed                  =    99.9912
Percentage of free reflections       =     5.1197
Overall R factor                     =     0.2067
Free R factor                        =     0.2325
Average Fourier shell correlation    =     0.9145
AverageFree Fourier shell correlation=     0.9038
Overall weighted R factor            =     0.1754
Free weighted R factor               =     0.2078
Overall weighted R2 factor           =     0.2057
Free weighted R2 factor              =     0.2486
Average correlation coefficient      =     0.8809
Overall correlation coefficient      =     0.9591
Free correlation coefficient         =     0.9437
Cruickshanks DPI for coordinate error=     0.0858
DPI based on free R factor           =     0.0848
Overall figure of merit              =     0.7925
ML based su of positional parameters =     0.0597
ML based su of thermal parameters    =     1.7388
-----------------------------------------------------------------------------
  Time in seconds: CPU =        31.26
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2075   0.2328   0.757      155755.    8506.5   0.0132  0.984   1.814  1.050   0.089
       1   0.2074   0.2331   0.786      154539.    8469.5   0.0130  0.973   1.794  1.038   0.089
       2   0.2062   0.2325   0.791      154272.    8461.2   0.0142  1.065   1.851  1.072   0.093
       3   0.2060   0.2324   0.792      154219.    8459.4   0.0143  1.074   1.876  1.086   0.094
       4   0.2062   0.2322   0.793      154248.    8458.9   0.0137  1.030   1.857  1.075   0.092
       5   0.2066   0.2325   0.793      154326.    8460.8   0.0130  0.981   1.823  1.055   0.090
       6   0.2066   0.2325   0.793      154334.    8461.2   0.0130  0.980   1.821  1.053   0.090
       7   0.2066   0.2325   0.792      154338.    8461.3   0.0130  0.980   1.820  1.053   0.090
       8   0.2067   0.2325   0.793      154346.    8461.8   0.0130  0.979   1.819  1.052   0.090
       9   0.2067   0.2325   0.793      154348.    8461.9   0.0130  0.979   1.819  1.052   0.090
      10   0.2067   0.2325   0.793      154351.    8462.0   0.0130  0.979   1.819  1.052   0.090
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2075   0.2067
             R free    0.2328   0.2325
     Rms BondLength    0.0132   0.0130
      Rms BondAngle    1.8137   1.8186
     Rms ChirVolume    0.0885   0.0903
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      63.4s System:    0.2s Elapsed:     1:03