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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
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 User: maly  Run date: 26/ 5/2020 Run time: 16:51:50 


 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 12
  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_R12_1-80A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R12_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_R12_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:    12
  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_R12_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=   2.034 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=   2.225 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=   1.812 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=   2.171 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=   2.358 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=   2.413 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=   2.100 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                           12
Number of "free" reflections       1187
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.= 0.875 id.= 3.000 dev= -2.13 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   0.29069248    
 Actual weight    6.7496872      is applied to the X-ray term
Norm of X_ray positional gradient                39.5
Norm of Geom. positional gradient                80.4
Norm of X_ray B-factor gradient                  126.
Norm of Geom. B-factor gradient                 0.205E+05
Product of X_ray and Geom posit. gradients     -0.131E+08
 Cosine of angle between them                      -0.426
Product of X_ray and Geom B-fact gradients     -0.442E+08
 Cosine of angle between them                      -0.005


Residuals: XRAY=     0.7840E+06 GEOM=     0.2596E+05 TOTAL=     0.8100E+06
 function value    809999.50    

-------------------------------------------------------------------------------
             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     1.853     1.644
Bond angles  : others                          3242     2.352     1.582
Torsion angles, period  1. refined              184     6.941     5.000
Torsion angles, period  2. refined               90    37.022    22.778
Torsion angles, period  3. refined              268    14.214    15.000
Torsion angles, period  4. refined                9    11.025    15.000
Chiral centres: refined atoms                   196     0.085     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.013     0.020
VDW repulsions: refined_atoms                   299     0.268     0.200
VDW repulsions.others                          1336     0.232     0.200
VDW; torsion: refined_atoms                     711     0.173     0.200
VDW; torsion.others                             709     0.083     0.200
HBOND: refined_atoms                            238     0.202     0.200
VDW repulsions: symmetry: refined_atoms          11     0.214     0.200
VDW repulsions: symmetry: others                 26     0.166     0.200
HBOND: symmetry: refined_atoms                   25     0.189     0.200
M. chain bond B values: refined atoms           745     1.674     1.287
M. chain bond B values: others                  745     1.672     1.287
M. chain angle B values: refined atoms          926     2.596     1.913
M. chain angle B values: others                 927     2.594     1.912
S. chain bond B values: refined atoms           811     2.929     1.671
S. chain bond B values: others                  810     2.926     1.671
S. chain angle B values: refined atoms         1177     4.567     2.344
S. chain angle B values: others                1178     4.565     2.343
Long range B values: refined atoms             1855     8.136    18.264
Long range B values: others                    1754     7.524    16.650
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =    1.0805
Partial structure    1: scale =     0.3877, B  =   49.4948
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3014 100.00   454.9   463.6  0.16  0.17     157   444.7   454.8  0.20  0.21
 0.130    5138 100.00   299.2   285.5  0.16  0.14     262   303.4   287.4  0.21  0.18
 0.216    6533  99.97   202.4   186.2  0.17  0.15     339   207.2   191.8  0.22  0.19
 0.303    7615 100.00   104.4   117.1  0.26  0.20     428   103.2   118.0  0.31  0.24
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2169   0.905    845   0.828   3014   0.883  0.944  0.9573  0.9678  0.9030  0.9375
  0.1301   4280   0.891    858   0.787   5138   0.873  1.006  0.9541  0.9650  0.9132  0.9488
  0.2165   5652   0.877    881   0.766   6533   0.862  1.044  0.9476  0.9586  0.8806  0.9381
  0.3028   6758   0.749    859   0.682   7617   0.741  0.805  0.9001  0.9144  0.8522  0.8920
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22302
Percentage observed                  =    99.9872
Percentage of free reflections       =     5.0534
Overall R factor                     =     0.1794
Free R factor                        =     0.2259
Average Fourier shell correlation    =     0.9462
AverageFree Fourier shell correlation=     0.9332
Overall weighted R factor            =     0.1577
Free weighted R factor               =     0.1959
Overall weighted R2 factor           =     0.1875
Free weighted R2 factor              =     0.2241
Average correlation coefficient      =     0.9247
Overall correlation coefficient      =     0.9575
Free correlation coefficient         =     0.9318
Cruickshanks DPI for coordinate error=     0.1087
DPI based on free R factor           =     0.1121
Overall figure of merit              =     0.8262
ML based su of positional parameters =     0.0739
ML based su of thermal parameters    =     2.3135
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    116159.10       25961.898       809999.50      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.35048717    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    788962.13    

-------------------------------------------------------------------------------
             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 =     0.0425, B  =   -0.0788
Partial structure    1: scale =     0.3875, B  =   48.8937
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                     =     0.1791
Free R factor                        =     0.2250
Average Fourier shell correlation    =     0.9535
AverageFree Fourier shell correlation=     0.9411
Average correlation coefficient      =     0.9261
Overall figure of merit              =     0.8524
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    115398.11       10061.026       788962.13       809999.50    


     CGMAT cycle number =      3

 Weight matrix   0.36273620    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    786564.19    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0425, B  =   -0.0228
Partial structure    1: scale =     0.3884, B  =   45.5736
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                        =     0.2241
Average Fourier shell correlation    =     0.9549
AverageFree Fourier shell correlation=     0.9426
Average correlation coefficient      =     0.9282
Overall figure of merit              =     0.8564
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    115121.55       9529.6904       786564.19       788962.13    


     CGMAT cycle number =      4

 Weight matrix   0.36655205    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    785761.75    

-------------------------------------------------------------------------------
             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 =     0.0425, B  =   -0.0000
Partial structure    1: scale =     0.3888, B  =   45.7782
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                        =     0.2235
Average Fourier shell correlation    =     0.9554
AverageFree Fourier shell correlation=     0.9431
Average correlation coefficient      =     0.9290
Overall figure of merit              =     0.8574
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    115020.37       9410.2520       785761.75       786564.19    


     CGMAT cycle number =      5

 Weight matrix   0.33531216    
 Actual weight    6.1360793      is applied to the X-ray term


 function value    714963.00    

-------------------------------------------------------------------------------
             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 =     0.0425, B  =    0.0108
Partial structure    1: scale =     0.3887, B  =   45.7281
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                        =     0.2234
Average Fourier shell correlation    =     0.9556
AverageFree Fourier shell correlation=     0.9433
Average correlation coefficient      =     0.9293
Overall figure of merit              =     0.8578
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    114977.13       9454.2432       714963.00       785761.75    


     CGMAT cycle number =      6

 Weight matrix   0.30584973    
 Actual weight    5.5782537      is applied to the X-ray term


 function value    650746.69    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0425, B  =   -0.0002
Partial structure    1: scale =     0.3888, B  =   45.7106
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                        =     0.2235
Average Fourier shell correlation    =     0.9555
AverageFree Fourier shell correlation=     0.9433
Average correlation coefficient      =     0.9291
Overall figure of merit              =     0.8580
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    115011.55       9183.0449       650746.69       714963.00    


     CGMAT cycle number =      7

 Weight matrix   0.30558643    
 Actual weight    5.5782537      is applied to the X-ray term


 function value    650713.63    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0425, B  =   -0.0328
Partial structure    1: scale =     0.3897, B  =   45.9915
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                     =     0.1788
Free R factor                        =     0.2237
Average Fourier shell correlation    =     0.9554
AverageFree Fourier shell correlation=     0.9432
Average correlation coefficient      =     0.9286
Overall figure of merit              =     0.8579
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    115069.75       8825.3828       650713.63       650746.69    


     CGMAT cycle number =      8

 Weight matrix   0.30508894    
 Actual weight    5.5782537      is applied to the X-ray term


 function value    650722.56    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0425, B  =   -0.0154
Partial structure    1: scale =     0.3901, B  =   46.0368
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                     =     0.1790
Free R factor                        =     0.2239
Average Fourier shell correlation    =     0.9553
AverageFree Fourier shell correlation=     0.9431
Average correlation coefficient      =     0.9285
Overall figure of merit              =     0.8576
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    115086.34       8735.7969       650732.44       650713.63    

 fvalues    115086.34       8735.7969       650726.06       650716.63    
 fvalues    115086.34       8735.7969       650726.06       650716.63    


     CGMAT cycle number =      9

 Weight matrix   0.30486840    
 Actual weight    5.5782537      is applied to the X-ray term


 function value    650727.06    

-------------------------------------------------------------------------------
             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 =     0.0425, B  =   -0.0120
Partial structure    1: scale =     0.3904, B  =   45.9863
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                     =     0.1790
Free R factor                        =     0.2240
Average Fourier shell correlation    =     0.9553
AverageFree Fourier shell correlation=     0.9431
Average correlation coefficient      =     0.9285
Overall figure of merit              =     0.8576
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    115091.03       8719.4082       650736.56       650716.63    

 fvalues    115091.03       8719.4082       650722.38       650726.44    
 fvalues    115091.03       8719.4082       650722.38       650726.44    


     CGMAT cycle number =     10

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.883 id.= 3.000 dev= -2.12 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   0.30498818    
 Actual weight    5.5782537      is applied to the X-ray term
Norm of X_ray positional gradient                37.0
Norm of Geom. positional gradient                37.2
Norm of X_ray B-factor gradient                  115.
Norm of Geom. B-factor gradient                  117.
Product of X_ray and Geom posit. gradients     -0.133E+08
 Cosine of angle between them                      -0.997
Product of X_ray and Geom B-fact gradients     -0.433E+08
 Cosine of angle between them                      -0.999


Residuals: XRAY=     0.6420E+06 GEOM=      8708.     TOTAL=     0.6507E+06
 function value    650722.00    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2103     1.764     1.644
Bond angles  : others                          3242     1.499     1.582
Torsion angles, period  1. refined              184     6.819     5.000
Torsion angles, period  2. refined               90    36.456    22.778
Torsion angles, period  3. refined              268    13.483    15.000
Torsion angles, period  4. refined                9    10.825    15.000
Chiral centres: refined atoms                   196     0.085     0.200
Planar groups: refined atoms                   1736     0.009     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   302     0.266     0.200
VDW repulsions.others                          1343     0.205     0.200
VDW; torsion: refined_atoms                     719     0.172     0.200
VDW; torsion.others                             779     0.084     0.200
HBOND: refined_atoms                            231     0.192     0.200
HBOND.others                                      1     0.001     0.200
VDW repulsions: symmetry: refined_atoms          10     0.192     0.200
VDW repulsions: symmetry: others                 25     0.169     0.200
HBOND: symmetry: refined_atoms                   24     0.208     0.200
M. chain bond B values: refined atoms           745     1.654     1.385
M. chain bond B values: others                  745     1.652     1.386
M. chain angle B values: refined atoms          926     2.593     2.063
M. chain angle B values: others                 927     2.592     2.063
S. chain bond B values: refined atoms           811     2.852     1.770
S. chain bond B values: others                  810     2.845     1.770
S. chain angle B values: refined atoms         1177     4.445     2.495
S. chain angle B values: others                1178     4.443     2.494
Long range B values: refined atoms             1855     7.994    19.543
Long range B values: others                    1754     7.457    17.900
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0425, B  =   -0.0141
Partial structure    1: scale =     0.3903, B  =   45.9573
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3014 100.00   455.9   464.3  0.17  0.17     157   445.6   455.9  0.20  0.21
 0.130    5138 100.00   299.8   285.4  0.16  0.15     262   304.1   287.9  0.21  0.18
 0.216    6533  99.97   202.8   186.6  0.17  0.15     339   207.7   192.1  0.21  0.18
 0.303    7615 100.00   104.6   116.7  0.25  0.19     428   103.4   118.0  0.31  0.24
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2169   0.913    845   0.839   3014   0.892  0.945  0.9583  0.9688  0.9010  0.9353
  0.1301   4280   0.890    858   0.785   5138   0.873  1.006  0.9530  0.9637  0.9099  0.9450
  0.2165   5652   0.891    881   0.781   6533   0.876  1.045  0.9530  0.9626  0.8891  0.9397
  0.3028   6758   0.827    859   0.750   7617   0.818  0.837  0.9235  0.9380  0.8594  0.9051
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22302
Percentage observed                  =    99.9872
Percentage of free reflections       =     5.0534
Overall R factor                     =     0.1790
Free R factor                        =     0.2240
Average Fourier shell correlation    =     0.9553
AverageFree Fourier shell correlation=     0.9431
Overall weighted R factor            =     0.1597
Free weighted R factor               =     0.1962
Overall weighted R2 factor           =     0.1911
Free weighted R2 factor              =     0.2263
Average correlation coefficient      =     0.9285
Overall correlation coefficient      =     0.9569
Free correlation coefficient         =     0.9318
Cruickshanks DPI for coordinate error=     0.1085
DPI based on free R factor           =     0.1112
Overall figure of merit              =     0.8576
ML based su of positional parameters =     0.0655
ML based su of thermal parameters    =     1.9919
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    115092.28       8708.0605       650722.00       650726.44    

    ****                              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.= 0.883 id.= 3.000 dev= -2.12 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_R12_1-70A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.763     1.644
Bond angles  : others                          3242     1.498     1.582
Torsion angles, period  1. refined              184     6.818     5.000
Torsion angles, period  2. refined               90    36.444    22.778
Torsion angles, period  3. refined              268    13.463    15.000
Torsion angles, period  4. refined                9    10.822    15.000
Chiral centres: refined atoms                   196     0.085     0.200
Planar groups: refined atoms                   1736     0.009     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   302     0.266     0.200
VDW repulsions.others                          1341     0.205     0.200
VDW; torsion: refined_atoms                     719     0.172     0.200
VDW; torsion.others                             778     0.084     0.200
HBOND: refined_atoms                            232     0.192     0.200
HBOND.others                                      1     0.001     0.200
VDW repulsions: symmetry: refined_atoms          10     0.192     0.200
VDW repulsions: symmetry: others                 25     0.169     0.200
HBOND: symmetry: refined_atoms                   24     0.209     0.200
M. chain bond B values: refined atoms           745     1.652     1.385
M. chain bond B values: others                  745     1.650     1.386
M. chain angle B values: refined atoms          926     2.591     2.063
M. chain angle B values: others                 927     2.590     2.063
S. chain bond B values: refined atoms           811     2.849     1.769
S. chain bond B values: others                  810     2.842     1.769
S. chain angle B values: refined atoms         1177     4.441     2.494
S. chain angle B values: others                1178     4.439     2.494
Long range B values: refined atoms             1856     7.991    19.552
Long range B values: others                    1755     7.457    17.912
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0425, B  =   -0.0109
Partial structure    1: scale =     0.3904, B  =   45.8640
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3014 100.00   455.9   464.3  0.17  0.17     157   445.6   456.0  0.20  0.21
 0.130    5138 100.00   299.8   285.4  0.16  0.15     262   304.0   287.9  0.21  0.18
 0.216    6533  99.97   202.8   186.6  0.17  0.15     339   207.7   192.1  0.21  0.18
 0.303    7615 100.00   104.6   116.7  0.25  0.19     428   103.4   118.0  0.31  0.24
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2169   0.913    845   0.839   3014   0.892  0.945  0.9584  0.9688  0.9011  0.9353
  0.1301   4280   0.890    858   0.785   5138   0.873  1.006  0.9530  0.9637  0.9098  0.9450
  0.2165   5652   0.891    881   0.780   6533   0.876  1.045  0.9530  0.9626  0.8892  0.9397
  0.3028   6758   0.827    859   0.750   7617   0.818  0.837  0.9235  0.9380  0.8594  0.9051
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22302
Percentage observed                  =    99.9872
Percentage of free reflections       =     5.0534
Overall R factor                     =     0.1790
Free R factor                        =     0.2240
Average Fourier shell correlation    =     0.9553
AverageFree Fourier shell correlation=     0.9431
Overall weighted R factor            =     0.1598
Free weighted R factor               =     0.1962
Overall weighted R2 factor           =     0.1912
Free weighted R2 factor              =     0.2262
Average correlation coefficient      =     0.9285
Overall correlation coefficient      =     0.9569
Free correlation coefficient         =     0.9318
Cruickshanks DPI for coordinate error=     0.1085
DPI based on free R factor           =     0.1112
Overall figure of merit              =     0.8576
ML based su of positional parameters =     0.0655
ML based su of thermal parameters    =     1.9919
-----------------------------------------------------------------------------
  Time in seconds: CPU =        17.71
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1794   0.2259   0.826      116159.    6340.0   0.0134  0.979   1.853  1.065   0.085
       1   0.1791   0.2250   0.852      115398.    6313.8   0.0126  0.929   1.798  1.035   0.084
       2   0.1781   0.2241   0.856      115122.    6304.4   0.0134  0.991   1.825  1.054   0.087
       3   0.1778   0.2235   0.857      115020.    6299.6   0.0135  1.001   1.837  1.063   0.088
       4   0.1778   0.2234   0.858      114977.    6299.0   0.0136  1.006   1.844  1.068   0.089
       5   0.1781   0.2235   0.858      115012.    6299.0   0.0130  0.963   1.818  1.053   0.087
       6   0.1788   0.2237   0.858      115070.    6301.7   0.0124  0.920   1.781  1.032   0.085
       7   0.1790   0.2239   0.858      115087.    6302.9   0.0123  0.912   1.767  1.025   0.085
       8   0.1790   0.2240   0.858      115091.    6303.1   0.0123  0.911   1.766  1.024   0.085
       9   0.1790   0.2240   0.858      115092.    6303.2   0.0123  0.910   1.764  1.023   0.085
      10   0.1790   0.2240   0.858      115093.    6303.1   0.0123  0.909   1.763  1.023   0.085
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1794   0.1790
             R free    0.2259   0.2240
     Rms BondLength    0.0134   0.0123
      Rms BondAngle    1.8528   1.7629
     Rms ChirVolume    0.0847   0.0847
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      50.0s System:    0.1s Elapsed:     0:50