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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: 18:54:50 


 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 1.50     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- bins 4
  Data line--- ncyc 10
  Data line--- monitor MEDIum
  Data line--- free 2
  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_R02_1-60A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R02_1-50A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R02_1-50A.mtz

Cell from mtz :    57.632    57.632   122.391    90.000    90.000    90.000
Space group from mtz: number -   96; name - P 43 21 2

  Refinement type                        : Restrained

    ****                           Makecif parameters                           ****

Dictionary files for restraints : /protein2/ccp4/ccp4-7.0/ccp4-7.0/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /protein2/ccp4/ccp4-7.0/ccp4-7.0/lib/data/monomers/ener_lib.cif
    Program will rely on residue and atom names. No checking
    If this option is used then monomers should be checked carefully before using
    Hydrogens will be restored in their riding positions
    Links between monomers will be checked. Only those links present in the coordinate file will be used
    Standard sugar links will be analysed and used
    For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
    Symmetry related links will be analysed and used
    Cis peptides will be found and used automatically


  Residual                               : Rice Maximum Likelihood for Fs

    ****                    Least-square scaling parameters                     ****

Overall scale
Overall B value
Overall anisotropic B with tr(B) = 0.0
Constant bulk solvent in non protein region
Probe radii for non-ions     1.200
Probe radii for ions         0.800
Shrinkage of the mask  by    0.800


    ****                 Map sharpening parameters and methods                  ****

No map sharpening will be performed

  Method of minimisation                 : Sparse Matrix
  Experimental sigmas used for weighting
  Number of Bins and width:     4       0.1111
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.5000
  Estimated number of reflections :      43652
  Free R exclusion - flag equals:     2
  Auto weighting. An attempt
  Refinement cycles       :    10
  Scaling type                           :
          Wilson scaling type with Guassians

  Estimation of D/Sigma in resolution bins
  using  free set of reflns with experimental sigmas
  using  free set of reflns with experimental sigmas

  Scaling and SigmaA resln:    41.9635  1.5000

  Damping factors:     1.0000  1.0000  1.0000


    ****                    Geometry restraints and weights                     ****


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

 Planar groups (all and main chain)
          WEIGHT= 1.00 1.00

 Chiral centers
          Weight= 1.00

 NON-BONDED CONTACTS
          Overall weight                          =  1.00
          Sigma for simple VDW                    =  0.20
          Sigma for VDW trhough torsion angle     =  0.20
          Sigma for HBOND                         =  0.20
          Sigma for metal-ion                     =  0.20
          Sigma for DUMMY and other atom          =  0.30
          Distance for donor-accepetor = vdw1+vdw2+(-0.30)
          Distance for acceptor - H    = vdw1+     ( 0.10)
          VDW distance through torsion = vdw1+vdw2+(-0.30)
          Distance for DUMMY-others    = vdw1+vdw2+(-0.70)

 TORSION ANGLES
          Weight= 1.00

 THERMAL FACTORS
          Weight= 1.00
     Main chain bond (1-2 neighbour)          1.5A**2
     Main chain angle (1-3 neighbour)         2.0A**2
     Side chain bond                          3.0A**2
     Side chain angle                         4.5A**2

 RESTRAINTS AGAINST EXCESSIVE SHIFTS
     Positional parameters                   0.00A
     Thermal parameters                      0.00A
     Occupancy parameters                    0.00

 RADIUS OF CONFIDENCE
     Positional parameters 0.00A
     Thermal parameters    0.00A**2
     Occupancy parameters  0.00

Monitoring style is "MEDIUM". Complete information will be printed out in the
first and last cycle. In all other cycles minimum information will be printed out
Sigma cutoffs for printing out outliers
If deviation of restraint parameter > alpha*sigma then information will be printed out
Distance outliers      10.000
Angle outliers         10.000
Torsion outliers       10.000
Chiral volume outliers 10.000
Plane outliers         10.000
Non-bonding outliers   10.000
B value  outliers      10.000
Rigid bond outliers    10.000
Sphericity outliers    10.000
---------------------------------------------------------------

 Input file :CDO_complete_R02_1-60A.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.51
 _lib_update       11/07/18
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 24624
                with complete description    : 24624
  NUMBER OF MODIFICATIONS                    :    70
  NUMBER OF LINKS                            :    77
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  Number of atoms    :    1836
  Number of residues :     502
  Number of chains   :       4
  I am reading library. Please wait.
                mon_lib.cif
  INFO:     link is found (not be used) dist=   2.063 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=   2.194 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=   1.827 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=   2.205 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=   2.395 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=   2.416 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=   2.106 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  PRO               190  AAA  is missing in the structure
  Number of chains                  :       4
  Total number of monomers          :     502
  Number of atoms                   :    3945
  Number of missing atoms           :       1
  Number of rebuilt atoms           :    1480
  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:      2949         0      2949
               Angles:      5344         0      5344
              Chirals:       196         0       196
               Planes:       453         0       453
             Torsions:      1556         0      1556
            Intervals:         0         0         0
--------------------------------------------------------------------------------


  Number of harmonic restraints       =            0
  Number of atoms in special position =            0
 -----------------------------------------------------


    ****                           Info from mtz file                           ****

FreeR flag                            2
Number of "free" reflections       1674
Number of   all  reflections      33910
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          33910

   Current auto weighting coefficient =    6.2496691    

 mode : HKRF


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



     CGMAT cycle number =      1

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.898 id.= 3.000 dev= -2.10 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Weight matrix   0.29621348    
 Actual weight    6.2496691      is applied to the X-ray term
Norm of X_ray positional gradient                39.9
Norm of Geom. positional gradient                79.8
Norm of X_ray B-factor gradient                  116.
Norm of Geom. B-factor gradient                  103.
Product of X_ray and Geom posit. gradients     -0.142E+08
 Cosine of angle between them                      -0.459
Product of X_ray and Geom B-fact gradients     -0.340E+08
 Cosine of angle between them                      -0.887


Residuals: XRAY=     0.9769E+06 GEOM=     0.1287E+05 TOTAL=     0.9898E+06
 function value    989791.44    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.035     0.017
Bond angles  : refined atoms                   2106     1.776     1.644
Bond angles  : others                          3238     2.349     1.580
Torsion angles, period  1. refined              185     6.830     5.000
Torsion angles, period  2. refined               90    35.759    22.778
Torsion angles, period  3. refined              268    13.275    15.000
Torsion angles, period  4. refined                9    11.579    15.000
Chiral centres: refined atoms                   196     0.086     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.015     0.020
VDW repulsions: refined_atoms                   299     0.248     0.200
VDW repulsions.others                          1337     0.221     0.200
VDW; torsion: refined_atoms                     733     0.172     0.200
VDW; torsion.others                             716     0.081     0.200
HBOND: refined_atoms                            211     0.188     0.200
HBOND.others                                      2     0.072     0.200
VDW repulsions: symmetry: refined_atoms           8     0.202     0.200
VDW repulsions: symmetry: others                 21     0.207     0.200
HBOND: symmetry: refined_atoms                   20     0.187     0.200
M. chain bond B values: refined atoms           746     1.678     1.513
M. chain bond B values: others                  746     1.674     1.514
M. chain angle B values: refined atoms          929     2.642     2.261
M. chain angle B values: others                 930     2.641     2.261
S. chain bond B values: refined atoms           811     3.046     1.911
S. chain bond B values: others                  810     3.042     1.910
S. chain angle B values: refined atoms         1177     4.744     2.697
S. chain angle B values: others                1178     4.742     2.696
Long range B values: refined atoms             1841     7.168    20.790
Long range B values: others                    1753     6.879    19.356
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    1.1581
Partial structure    1: scale =     0.3902, B  =   39.2732
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

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


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4317 100.00   407.0   416.5  0.17  0.18     230   393.1   406.0  0.20  0.21
 0.167    7404  99.97   228.4   208.5  0.18  0.16     394   226.9   209.5  0.23  0.20
 0.278    9431 100.00   123.9   113.9  0.21  0.19     479   127.0   120.1  0.23  0.20
 0.389   11071 100.00    50.2    62.5  0.41  0.36     570    50.8    62.8  0.41  0.36
$$

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

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3210   0.917   1107   0.817   4317   0.891  0.948  0.9648  0.9717  0.9108  0.9368
  0.1670   6302   0.872   1102   0.775   7404   0.858  1.058  0.9456  0.9572  0.8903  0.9327
  0.2780   8313   0.838   1118   0.756   9431   0.828  1.021  0.9379  0.9483  0.8853  0.9307
  0.3890   9956   0.562   1126   0.490  11082   0.555  0.566  0.7821  0.7710  0.7787  0.7704
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32234
Percentage observed                  =    99.9912
Percentage of free reflections       =     4.9369
Overall R factor                     =     0.2080
Free R factor                        =     0.2394
Average Fourier shell correlation    =     0.8925
AverageFree Fourier shell correlation=     0.8903
Overall weighted R factor            =     0.1760
Free weighted R factor               =     0.2062
Overall weighted R2 factor           =     0.2046
Free weighted R2 factor              =     0.2382
Average correlation coefficient      =     0.8769
Overall correlation coefficient      =     0.9592
Free correlation coefficient         =     0.9434
Cruickshanks DPI for coordinate error=     0.0862
DPI based on free R factor           =     0.0872
Overall figure of merit              =     0.7494
ML based su of positional parameters =     0.0704
ML based su of thermal parameters    =     2.0695
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    156316.19       12866.985       989791.44      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.36165646    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    978453.69    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =   -0.0651
Partial structure    1: scale =     0.3914, B  =   39.6707
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2074
Free R factor                        =     0.2386
Average Fourier shell correlation    =     0.9065
AverageFree Fourier shell correlation=     0.9035
Average correlation coefficient      =     0.8777
Overall figure of merit              =     0.7758
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    155265.52       8095.6421       978453.69       989791.44    


     CGMAT cycle number =      3

 Weight matrix   0.37223607    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    977481.94    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =   -0.0047
Partial structure    1: scale =     0.3910, B  =   39.5928
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2064
Free R factor                        =     0.2386
Average Fourier shell correlation    =     0.9097
AverageFree Fourier shell correlation=     0.9061
Average correlation coefficient      =     0.8795
Overall figure of merit              =     0.7808
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    155017.52       8673.7363       977481.94       978453.69    


     CGMAT cycle number =      4

 Weight matrix   0.34239474    
 Actual weight    5.6815171      is applied to the X-ray term


 function value    889230.00    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.014     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    0.0041
Partial structure    1: scale =     0.3909, B  =   39.5865
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2062
Free R factor                        =     0.2386
Average Fourier shell correlation    =     0.9107
AverageFree Fourier shell correlation=     0.9069
Average correlation coefficient      =     0.8803
Overall figure of merit              =     0.7826
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    154952.05       8867.3145       889230.00       977481.94    


     CGMAT cycle number =      5

 Weight matrix   0.31156084    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    809105.31    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    0.0131
Partial structure    1: scale =     0.3906, B  =   39.5480
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2064
Free R factor                        =     0.2388
Average Fourier shell correlation    =     0.9108
AverageFree Fourier shell correlation=     0.9070
Average correlation coefficient      =     0.8803
Overall figure of merit              =     0.7831
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    154971.14       8677.0020       809105.31       889230.00    


     CGMAT cycle number =      6

 Weight matrix   0.31081304    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    809178.31    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    0.0135
Partial structure    1: scale =     0.3901, B  =   39.3568
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2068
Free R factor                        =     0.2390
Average Fourier shell correlation    =     0.9106
AverageFree Fourier shell correlation=     0.9069
Average correlation coefficient      =     0.8799
Overall figure of merit              =     0.7830
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    155041.81       8378.5498       809166.31       809105.31    
 fvalues    155041.81       8378.5498       809166.31       809171.88    


     CGMAT cycle number =      7

 Weight matrix   0.31073737    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    809177.19    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    0.0171
Partial structure    1: scale =     0.3901, B  =   39.3488
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2069
Free R factor                        =     0.2391
Average Fourier shell correlation    =     0.9106
AverageFree Fourier shell correlation=     0.9069
Average correlation coefficient      =     0.8798
Overall figure of merit              =     0.7830
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    155057.61       8302.7803       809182.50       809171.88    

 fvalues    155057.61       8302.7803       809184.00       809177.69    
 fvalues    155057.61       8302.7803       809184.00       809177.69    


     CGMAT cycle number =      8

 Weight matrix   0.31050813    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    809207.88    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    0.0183
Partial structure    1: scale =     0.3901, B  =   39.3072
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2069
Free R factor                        =     0.2391
Average Fourier shell correlation    =     0.9105
AverageFree Fourier shell correlation=     0.9068
Average correlation coefficient      =     0.8798
Overall figure of merit              =     0.7829
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    155062.16       8291.2256       809197.44       809177.69    

 fvalues    155062.16       8291.2256       809182.81       809189.63    
 fvalues    155062.16       8291.2256       809182.81       809189.63    


     CGMAT cycle number =      9

 Weight matrix   0.31053048    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    809202.13    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    0.0189
Partial structure    1: scale =     0.3900, B  =   39.2766
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2069
Free R factor                        =     0.2391
Average Fourier shell correlation    =     0.9105
AverageFree Fourier shell correlation=     0.9068
Average correlation coefficient      =     0.8798
Overall figure of merit              =     0.7829
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    155065.94       8285.0635       809209.50       809189.63    

 fvalues    155065.94       8285.0635       809187.06       809203.00    
 fvalues    155065.94       8285.0635       809187.06       809203.00    


     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.= 0.913 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        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Weight matrix   0.31055075    
 Actual weight    5.1650152      is applied to the X-ray term
Norm of X_ray positional gradient                38.1
Norm of Geom. positional gradient                38.3
Norm of X_ray B-factor gradient                  101.
Norm of Geom. B-factor gradient                  100.
Product of X_ray and Geom posit. gradients     -0.141E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.325E+08
 Cosine of angle between them                      -0.997


Residuals: XRAY=     0.8009E+06 GEOM=      8282.     TOTAL=     0.8092E+06
 function value    809206.75    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.774     1.644
Bond angles  : others                          3238     1.499     1.580
Torsion angles, period  1. refined              185     6.827     5.000
Torsion angles, period  2. refined               90    35.713    22.778
Torsion angles, period  3. refined              268    13.208    15.000
Torsion angles, period  4. refined                9    11.947    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   299     0.248     0.200
VDW repulsions.others                          1336     0.196     0.200
VDW; torsion: refined_atoms                     726     0.173     0.200
VDW; torsion.others                             765     0.084     0.200
HBOND: refined_atoms                            209     0.186     0.200
HBOND.others                                      1     0.074     0.200
VDW repulsions: symmetry: refined_atoms           8     0.197     0.200
VDW repulsions: symmetry: others                 24     0.182     0.200
HBOND: symmetry: refined_atoms                   17     0.196     0.200
M. chain bond B values: refined atoms           746     1.731     1.623
M. chain bond B values: others                  746     1.726     1.623
M. chain angle B values: refined atoms          929     2.695     2.425
M. chain angle B values: others                 930     2.694     2.425
S. chain bond B values: refined atoms           811     3.155     2.033
S. chain bond B values: others                  810     3.151     2.033
S. chain angle B values: refined atoms         1177     4.894     2.877
S. chain angle B values: others                1178     4.892     2.876
Long range B values: refined atoms             1834     7.271    22.083
Long range B values: others                    1747     7.017    20.630
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    0.0189
Partial structure    1: scale =     0.3901, B  =   39.2697
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

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


$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10.  v. resln :N:1,6,7,11,12:
:Cycle   10.  and  v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4317 100.00   407.1   416.9  0.17  0.18     230   393.3   406.5  0.20  0.21
 0.167    7404  99.97   228.5   208.6  0.18  0.16     394   227.0   209.9  0.23  0.19
 0.278    9431 100.00   123.9   114.1  0.21  0.18     479   127.1   120.3  0.23  0.20
 0.389   11071 100.00    50.2    62.5  0.41  0.36     570    50.8    63.0  0.41  0.36
$$

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

 $TABLE: Cycle   10. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3210   0.930   1107   0.843   4317   0.908  0.950  0.9681  0.9747  0.9097  0.9369
  0.1670   6302   0.885   1102   0.787   7404   0.871  1.058  0.9490  0.9603  0.8925  0.9335
  0.2780   8313   0.853   1118   0.774   9431   0.843  1.021  0.9440  0.9537  0.8884  0.9314
  0.3890   9956   0.631   1126   0.562  11082   0.624  0.595  0.8219  0.8155  0.7804  0.7777
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32234
Percentage observed                  =    99.9912
Percentage of free reflections       =     4.9369
Overall R factor                     =     0.2069
Free R factor                        =     0.2390
Average Fourier shell correlation    =     0.9105
AverageFree Fourier shell correlation=     0.9068
Overall weighted R factor            =     0.1754
Free weighted R factor               =     0.2064
Overall weighted R2 factor           =     0.2040
Free weighted R2 factor              =     0.2386
Average correlation coefficient      =     0.8798
Overall correlation coefficient      =     0.9595
Free correlation coefficient         =     0.9436
Cruickshanks DPI for coordinate error=     0.0857
DPI based on free R factor           =     0.0870
Overall figure of merit              =     0.7829
ML based su of positional parameters =     0.0624
ML based su of thermal parameters    =     1.8120
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    155068.08       8281.5547       809212.31       809203.00    

 fvalues    155068.08       8281.5547       809180.56       809210.56    
 fvalues    155068.08       8281.5547       809180.56       809210.56    

    ****                              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_R02_1-50A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.774     1.644
Bond angles  : others                          3238     1.499     1.580
Torsion angles, period  1. refined              185     6.827     5.000
Torsion angles, period  2. refined               90    35.712    22.778
Torsion angles, period  3. refined              268    13.207    15.000
Torsion angles, period  4. refined                9    11.948    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   300     0.247     0.200
VDW repulsions.others                          1336     0.196     0.200
VDW; torsion: refined_atoms                     726     0.173     0.200
VDW; torsion.others                             765     0.084     0.200
HBOND: refined_atoms                            209     0.186     0.200
HBOND.others                                      1     0.073     0.200
VDW repulsions: symmetry: refined_atoms           8     0.197     0.200
VDW repulsions: symmetry: others                 24     0.182     0.200
HBOND: symmetry: refined_atoms                   17     0.196     0.200
M. chain bond B values: refined atoms           746     1.731     1.623
M. chain bond B values: others                  746     1.726     1.623
M. chain angle B values: refined atoms          929     2.695     2.425
M. chain angle B values: others                 930     2.693     2.425
S. chain bond B values: refined atoms           811     3.154     2.033
S. chain bond B values: others                  810     3.150     2.033
S. chain angle B values: refined atoms         1177     4.893     2.877
S. chain angle B values: others                1178     4.891     2.876
Long range B values: refined atoms             1835     7.270    22.103
Long range B values: others                    1748     7.016    20.652
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    0.0192
Partial structure    1: scale =     0.3901, B  =   39.2540
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

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


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4317 100.00   407.1   416.9  0.17  0.18     230   393.3   406.6  0.20  0.21
 0.167    7404  99.97   228.5   208.6  0.18  0.16     394   227.0   209.9  0.23  0.19
 0.278    9431 100.00   123.9   114.1  0.21  0.18     479   127.1   120.3  0.23  0.20
 0.389   11071 100.00    50.2    62.5  0.41  0.36     570    50.8    63.0  0.41  0.36
$$

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

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3210   0.930   1107   0.843   4317   0.908  0.950  0.9681  0.9747  0.9097  0.9369
  0.1670   6302   0.885   1102   0.787   7404   0.871  1.058  0.9491  0.9603  0.8926  0.9335
  0.2780   8313   0.853   1118   0.774   9431   0.843  1.021  0.9440  0.9537  0.8884  0.9314
  0.3890   9956   0.631   1126   0.562  11082   0.624  0.595  0.8219  0.8155  0.7804  0.7777
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32234
Percentage observed                  =    99.9912
Percentage of free reflections       =     4.9369
Overall R factor                     =     0.2069
Free R factor                        =     0.2390
Average Fourier shell correlation    =     0.9105
AverageFree Fourier shell correlation=     0.9068
Overall weighted R factor            =     0.1754
Free weighted R factor               =     0.2064
Overall weighted R2 factor           =     0.2040
Free weighted R2 factor              =     0.2385
Average correlation coefficient      =     0.8798
Overall correlation coefficient      =     0.9595
Free correlation coefficient         =     0.9436
Cruickshanks DPI for coordinate error=     0.0857
DPI based on free R factor           =     0.0870
Overall figure of merit              =     0.7829
ML based su of positional parameters =     0.0624
ML based su of thermal parameters    =     1.8120
-----------------------------------------------------------------------------
  Time in seconds: CPU =        31.36
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2080   0.2394   0.749      156316.    8299.4   0.0125  0.929   1.776  1.034   0.086
       1   0.2074   0.2386   0.776      155266.    8261.9   0.0125  0.934   1.760  1.024   0.088
       2   0.2064   0.2386   0.781      155018.    8253.5   0.0135  1.006   1.813  1.055   0.090
       3   0.2062   0.2386   0.783      154952.    8250.6   0.0136  1.017   1.837  1.069   0.091
       4   0.2064   0.2388   0.783      154971.    8249.8   0.0130  0.978   1.820  1.058   0.090
       5   0.2068   0.2390   0.783      155043.    8251.4   0.0124  0.934   1.787  1.039   0.088
       6   0.2069   0.2391   0.783      155058.    8251.9   0.0124  0.929   1.777  1.033   0.087
       7   0.2069   0.2391   0.783      155066.    8252.1   0.0124  0.929   1.776  1.032   0.087
       8   0.2069   0.2391   0.783      155066.    8252.1   0.0124  0.928   1.775  1.032   0.087
       9   0.2069   0.2390   0.783      155067.    8252.2   0.0124  0.928   1.774  1.032   0.087
      10   0.2069   0.2390   0.783      155067.    8252.0   0.0124  0.928   1.774  1.032   0.087
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2080   0.2069
             R free    0.2394   0.2390
     Rms BondLength    0.0125   0.0124
      Rms BondAngle    1.7756   1.7742
     Rms ChirVolume    0.0858   0.0871
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      63.4s System:    0.2s Elapsed:     1:04