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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: 17:13:31 


 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 1.70     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 18
  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_R18_1-80A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R18_1-70A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R18_1-70A.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       0.0865
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.7000
  Estimated number of reflections :      29131
  Free R exclusion - flag equals:    18
  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  1.7000

  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_R18_1-80A.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=   2.043 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=   2.196 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=   1.850 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=   2.179 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=   2.387 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=   2.398 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=   2.131 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                           18
Number of "free" reflections       1192
Number of   all  reflections      23491
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          23491

   Current auto weighting coefficient =    6.7496872    

 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.= 0.913 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    34   34   73
 Minimum acceptable grid spacing:    79   79  167
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    34   34   73
 Minimum acceptable grid spacing:    79   79  167
 Weight matrix   0.28997439    
 Actual weight    6.7496872      is applied to the X-ray term
Norm of X_ray positional gradient                39.4
Norm of Geom. positional gradient                79.1
Norm of X_ray B-factor gradient                  131.
Norm of Geom. B-factor gradient                 0.214E+05
Product of X_ray and Geom posit. gradients     -0.113E+08
 Cosine of angle between them                      -0.375
Product of X_ray and Geom B-fact gradients     -0.403E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.7833E+06 GEOM=     0.2611E+05 TOTAL=     0.8094E+06
 function value    809360.38    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.783     1.644
Bond angles  : others                          3242     2.345     1.582
Torsion angles, period  1. refined              184     7.043     5.000
Torsion angles, period  2. refined               90    36.602    22.778
Torsion angles, period  3. refined              268    14.060    15.000
Torsion angles, period  4. refined                9    11.788    15.000
Chiral centres: refined atoms                   196     0.086     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.016     0.020
VDW repulsions: refined_atoms                   309     0.263     0.200
VDW repulsions.others                          1337     0.229     0.200
VDW; torsion: refined_atoms                     721     0.171     0.200
VDW; torsion.others                             721     0.080     0.200
HBOND: refined_atoms                            236     0.200     0.200
HBOND.others                                      2     0.046     0.200
VDW repulsions: symmetry: refined_atoms          11     0.202     0.200
VDW repulsions: symmetry: others                 28     0.168     0.200
HBOND: symmetry: refined_atoms                   23     0.226     0.200
HBOND: symmetry: others                           1     0.035     0.200
M. chain bond B values: refined atoms           745     1.611     1.291
M. chain bond B values: others                  745     1.610     1.291
M. chain angle B values: refined atoms          926     2.551     1.919
M. chain angle B values: others                 927     2.550     1.918
S. chain bond B values: refined atoms           811     2.811     1.668
S. chain bond B values: others                  810     2.807     1.668
S. chain angle B values: refined atoms         1177     4.422     2.342
S. chain angle B values: others                1178     4.420     2.342
Long range B values: refined atoms             1870     7.095    18.227
Long range B values: others                    1770     6.783    16.777
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =    1.0871
Partial structure    1: scale =     0.3880, B  =   48.4231
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    2997 100.00   451.5   459.8  0.16  0.17     174   497.3   509.2  0.18  0.20
 0.130    5122 100.00   298.9   286.0  0.16  0.15     278   303.5   293.3  0.21  0.20
 0.216    6507  99.97   203.0   186.8  0.17  0.15     365   192.6   179.6  0.23  0.19
 0.303    7668 100.00   104.4   117.1  0.27  0.20     375   102.0   115.6  0.30  0.23
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2159   0.906    838   0.809   2997   0.879  0.944  0.9661  0.9689  0.9162  0.9390
  0.1301   4257   0.880    865   0.769   5122   0.861  0.999  0.9505  0.9608  0.8996  0.9448
  0.2165   5640   0.878    867   0.771   6507   0.864  1.044  0.9444  0.9595  0.8931  0.9408
  0.3028   6798   0.770    873   0.699   7671   0.762  0.818  0.9031  0.9190  0.8621  0.8898
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22297
Percentage observed                  =    99.9872
Percentage of free reflections       =     5.0747
Overall R factor                     =     0.1797
Free R factor                        =     0.2188
Average Fourier shell correlation    =     0.9471
AverageFree Fourier shell correlation=     0.9360
Overall weighted R factor            =     0.1584
Free weighted R factor               =     0.1971
Overall weighted R2 factor           =     0.1890
Free weighted R2 factor              =     0.2370
Average correlation coefficient      =     0.9239
Overall correlation coefficient      =     0.9572
Free correlation coefficient         =     0.9407
Cruickshanks DPI for coordinate error=     0.1089
DPI based on free R factor           =     0.1086
Overall figure of merit              =     0.8303
ML based su of positional parameters =     0.0740
ML based su of thermal parameters    =     2.2841
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    116043.10       26105.770       809360.38      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.33256543    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    788512.19    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =   -0.0721
Partial structure    1: scale =     0.3877, B  =   47.7112
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1793
Free R factor                        =     0.2176
Average Fourier shell correlation    =     0.9521
AverageFree Fourier shell correlation=     0.9409
Average correlation coefficient      =     0.9258
Overall figure of merit              =     0.8483
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    115370.03       9800.5840       788512.19       809360.38    


     CGMAT cycle number =      3

 Weight matrix   0.34004661    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    786273.38    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =   -0.0213
Partial structure    1: scale =     0.3878, B  =   44.2156
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1781
Free R factor                        =     0.2164
Average Fourier shell correlation    =     0.9532
AverageFree Fourier shell correlation=     0.9419
Average correlation coefficient      =     0.9277
Overall figure of merit              =     0.8509
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    115127.66       9197.6973       786273.38       788512.19    


     CGMAT cycle number =      4

 Weight matrix   0.34263718    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    785557.25    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =    0.0047
Partial structure    1: scale =     0.3882, B  =   44.1090
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1778
Free R factor                        =     0.2159
Average Fourier shell correlation    =     0.9535
AverageFree Fourier shell correlation=     0.9422
Average correlation coefficient      =     0.9283
Overall figure of merit              =     0.8517
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    115043.24       9051.3770       785557.25       786273.38    


     CGMAT cycle number =      5

 Weight matrix   0.34490845    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    785364.31    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =   -0.0111
Partial structure    1: scale =     0.3868, B  =   43.9686
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1780
Free R factor                        =     0.2158
Average Fourier shell correlation    =     0.9537
AverageFree Fourier shell correlation=     0.9424
Average correlation coefficient      =     0.9285
Overall figure of merit              =     0.8524
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    115013.35       9060.2109       785364.31       785557.25    


     CGMAT cycle number =      6

 Weight matrix   0.34555840    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    785241.06    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =   -0.0194
Partial structure    1: scale =     0.3867, B  =   43.9918
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1778
Free R factor                        =     0.2156
Average Fourier shell correlation    =     0.9538
AverageFree Fourier shell correlation=     0.9425
Average correlation coefficient      =     0.9287
Overall figure of merit              =     0.8526
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    114989.41       9098.5430       785241.06       785364.31    


     CGMAT cycle number =      7

 Weight matrix   0.34539995    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    785225.56    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =   -0.0144
Partial structure    1: scale =     0.3867, B  =   44.0207
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1777
Free R factor                        =     0.2157
Average Fourier shell correlation    =     0.9538
AverageFree Fourier shell correlation=     0.9425
Average correlation coefficient      =     0.9288
Overall figure of merit              =     0.8526
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    114983.93       9120.0088       785225.56       785241.06    


     CGMAT cycle number =      8

 Weight matrix   0.34490517    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    785236.25    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =   -0.0089
Partial structure    1: scale =     0.3868, B  =   44.2012
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1777
Free R factor                        =     0.2159
Average Fourier shell correlation    =     0.9537
AverageFree Fourier shell correlation=     0.9425
Average correlation coefficient      =     0.9289
Overall figure of merit              =     0.8525
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    114983.78       9125.6680       785226.19       785225.56    
 fvalues    114983.78       9125.6680       785226.19       785230.25    


     CGMAT cycle number =      9

 Weight matrix   0.34458989    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    785227.31    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =   -0.0077
Partial structure    1: scale =     0.3869, B  =   44.3095
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1777
Free R factor                        =     0.2159
Average Fourier shell correlation    =     0.9537
AverageFree Fourier shell correlation=     0.9425
Average correlation coefficient      =     0.9289
Overall figure of merit              =     0.8524
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    114984.40       9118.5420       785227.31       785230.25    


     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        :   120  120  256
 Maximuum H,K,L                 :    34   34   73
 Minimum acceptable grid spacing:    79   79  167
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    34   34   73
 Minimum acceptable grid spacing:    79   79  167
 Weight matrix   0.34466758    
 Actual weight    6.7496872      is applied to the X-ray term
Norm of X_ray positional gradient                40.4
Norm of Geom. positional gradient                40.4
Norm of X_ray B-factor gradient                  123.
Norm of Geom. B-factor gradient                  124.
Product of X_ray and Geom posit. gradients     -0.158E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.491E+08
 Cosine of angle between them                      -0.999


Residuals: XRAY=     0.7761E+06 GEOM=      9119.     TOTAL=     0.7852E+06
 function value    785207.44    

-------------------------------------------------------------------------------
             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     1.801     1.644
Bond angles  : others                          3242     1.501     1.582
Torsion angles, period  1. refined              184     6.911     5.000
Torsion angles, period  2. refined               90    36.134    22.778
Torsion angles, period  3. refined              268    13.376    15.000
Torsion angles, period  4. refined                9    11.972    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                   308     0.266     0.200
VDW repulsions.others                          1362     0.203     0.200
VDW; torsion: refined_atoms                     723     0.172     0.200
VDW; torsion.others                             784     0.083     0.200
HBOND: refined_atoms                            220     0.199     0.200
HBOND.others                                      2     0.103     0.200
VDW repulsions: symmetry: refined_atoms          10     0.202     0.200
VDW repulsions: symmetry: others                 25     0.175     0.200
HBOND: symmetry: refined_atoms                   22     0.226     0.200
HBOND: symmetry: others                           1     0.010     0.200
M. chain bond B values: refined atoms           745     1.683     1.386
M. chain bond B values: others                  745     1.681     1.386
M. chain angle B values: refined atoms          926     2.638     2.064
M. chain angle B values: others                 927     2.636     2.064
S. chain bond B values: refined atoms           811     3.014     1.788
S. chain bond B values: others                  810     3.008     1.788
S. chain angle B values: refined atoms         1177     4.685     2.513
S. chain angle B values: others                1178     4.683     2.513
Long range B values: refined atoms             1852     7.242    19.474
Long range B values: others                    1761     6.941    18.087
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =   -0.0106
Partial structure    1: scale =     0.3869, B  =   44.3211
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    2997 100.00   451.8   461.0  0.16  0.17     174   497.6   510.7  0.18  0.20
 0.130    5122 100.00   299.1   285.4  0.16  0.15     278   303.7   291.9  0.21  0.19
 0.216    6507  99.97   203.2   186.9  0.17  0.15     365   192.7   178.7  0.23  0.19
 0.303    7668 100.00   104.4   116.4  0.25  0.19     375   102.1   115.2  0.30  0.23
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2159   0.925    838   0.841   2997   0.901  0.946  0.9695  0.9728  0.9171  0.9385
  0.1301   4257   0.887    865   0.776   5122   0.868  0.999  0.9528  0.9623  0.9020  0.9446
  0.2165   5640   0.886    867   0.784   6507   0.873  1.044  0.9477  0.9617  0.8963  0.9406
  0.3028   6798   0.814    873   0.738   7671   0.806  0.836  0.9171  0.9338  0.8659  0.9049
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22297
Percentage observed                  =    99.9872
Percentage of free reflections       =     5.0747
Overall R factor                     =     0.1777
Free R factor                        =     0.2159
Average Fourier shell correlation    =     0.9537
AverageFree Fourier shell correlation=     0.9425
Overall weighted R factor            =     0.1584
Free weighted R factor               =     0.1954
Overall weighted R2 factor           =     0.1902
Free weighted R2 factor              =     0.2355
Average correlation coefficient      =     0.9290
Overall correlation coefficient      =     0.9577
Free correlation coefficient         =     0.9418
Cruickshanks DPI for coordinate error=     0.1077
DPI based on free R factor           =     0.1072
Overall figure of merit              =     0.8524
ML based su of positional parameters =     0.0678
ML based su of thermal parameters    =     2.0699
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    114981.36       9119.2744       785207.44       785227.31    

    ****                              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.= 0.913 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_R18_1-70A.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     1.801     1.644
Bond angles  : others                          3242     1.501     1.582
Torsion angles, period  1. refined              184     6.910     5.000
Torsion angles, period  2. refined               90    36.115    22.778
Torsion angles, period  3. refined              268    13.333    15.000
Torsion angles, period  4. refined                9    11.964    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                   307     0.266     0.200
VDW repulsions.others                          1364     0.202     0.200
VDW; torsion: refined_atoms                     722     0.173     0.200
VDW; torsion.others                             786     0.083     0.200
HBOND: refined_atoms                            220     0.199     0.200
HBOND.others                                      2     0.102     0.200
VDW repulsions: symmetry: refined_atoms          10     0.202     0.200
VDW repulsions: symmetry: others                 25     0.176     0.200
HBOND: symmetry: refined_atoms                   22     0.225     0.200
HBOND: symmetry: others                           1     0.009     0.200
M. chain bond B values: refined atoms           745     1.683     1.386
M. chain bond B values: others                  745     1.681     1.386
M. chain angle B values: refined atoms          926     2.638     2.063
M. chain angle B values: others                 927     2.636     2.063
S. chain bond B values: refined atoms           811     3.016     1.788
S. chain bond B values: others                  810     3.010     1.787
S. chain angle B values: refined atoms         1177     4.687     2.513
S. chain angle B values: others                1178     4.685     2.513
Long range B values: refined atoms             1851     7.246    19.444
Long range B values: others                    1760     6.943    18.054
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =   -0.0075
Partial structure    1: scale =     0.3868, B  =   44.3354
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    2997 100.00   451.8   461.0  0.16  0.17     174   497.6   510.7  0.18  0.20
 0.130    5122 100.00   299.1   285.4  0.16  0.15     278   303.7   291.8  0.21  0.19
 0.216    6507  99.97   203.2   186.9  0.17  0.15     365   192.7   178.6  0.23  0.19
 0.303    7668 100.00   104.4   116.4  0.25  0.19     375   102.1   115.1  0.30  0.23
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2159   0.925    838   0.841   2997   0.902  0.946  0.9696  0.9728  0.9173  0.9385
  0.1301   4257   0.887    865   0.776   5122   0.868  0.999  0.9528  0.9623  0.9020  0.9446
  0.2165   5640   0.886    867   0.784   6507   0.873  1.044  0.9477  0.9617  0.8963  0.9406
  0.3028   6798   0.814    873   0.738   7671   0.805  0.836  0.9171  0.9337  0.8660  0.9050
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22297
Percentage observed                  =    99.9872
Percentage of free reflections       =     5.0747
Overall R factor                     =     0.1777
Free R factor                        =     0.2159
Average Fourier shell correlation    =     0.9537
AverageFree Fourier shell correlation=     0.9424
Overall weighted R factor            =     0.1584
Free weighted R factor               =     0.1954
Overall weighted R2 factor           =     0.1901
Free weighted R2 factor              =     0.2352
Average correlation coefficient      =     0.9290
Overall correlation coefficient      =     0.9577
Free correlation coefficient         =     0.9418
Cruickshanks DPI for coordinate error=     0.1077
DPI based on free R factor           =     0.1072
Overall figure of merit              =     0.8524
ML based su of positional parameters =     0.0678
ML based su of thermal parameters    =     2.0699
-----------------------------------------------------------------------------
  Time in seconds: CPU =        15.41
             Elapsed =         128.00

    ****           Things for loggraph, R factor and others vs cycle            ****


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS: vs cycle :N:1,2,3:
:FOM vs cycle :N:1,4:
:-LL vs cycle :N:1,5:
:-LLfree vs cycle :N:1,6:
:Geometry vs cycle:N:1,7,8,9,10,11:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1797   0.2188   0.830      116043.    6417.0   0.0123  0.909   1.783  1.031   0.086
       1   0.1793   0.2176   0.848      115370.    6399.1   0.0119  0.886   1.749  1.014   0.086
       2   0.1781   0.2164   0.851      115128.    6391.2   0.0127  0.943   1.773  1.031   0.088
       3   0.1778   0.2159   0.852      115043.    6387.3   0.0128  0.953   1.785  1.040   0.089
       4   0.1780   0.2158   0.852      115013.    6385.4   0.0128  0.955   1.792  1.044   0.089
       5   0.1778   0.2156   0.853      114989.    6384.2   0.0128  0.958   1.797  1.047   0.090
       6   0.1777   0.2157   0.853      114984.    6384.1   0.0128  0.958   1.800  1.049   0.090
       7   0.1777   0.2159   0.852      114985.    6384.4   0.0128  0.958   1.801  1.050   0.090
       8   0.1777   0.2159   0.852      114984.    6384.8   0.0128  0.957   1.801  1.050   0.090
       9   0.1777   0.2159   0.852      114981.    6384.8   0.0128  0.957   1.801  1.050   0.090
      10   0.1777   0.2159   0.852      114981.    6384.8   0.0128  0.957   1.801  1.051   0.090
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1797   0.1777
             R free    0.2188   0.2159
     Rms BondLength    0.0123   0.0128
      Rms BondAngle    1.7828   1.8015
     Rms ChirVolume    0.0864   0.0901
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      47.5s System:    0.1s Elapsed:     0:48