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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: 15:47:29 


 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 1.80     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 13
  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_R13_1-90A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R13_1-80A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R13_1-80A.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       0.0772
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.8000
  Estimated number of reflections :      25918
  Free R exclusion - flag equals:    13
  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  1.8000

  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_R13_1-90A.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=   2.016 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=   2.211 ideal_dist=   2.090
            ch:AAA  res:  88  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   1.840 ideal_dist=   1.720
            ch:AAA  res:  93  CYS              at:SG  .->ch:AAA  res: 157  TYR              at:CE1 .
  INFO:     link is found (not be used) dist=   2.211 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=   2.372 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=   2.426 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=   2.085 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                           13
Number of "free" reflections        995
Number of   all  reflections      19877
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          19877

   Current auto weighting coefficient =    6.9995613    

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

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Weight matrix   0.29590425    
 Actual weight    6.9995613      is applied to the X-ray term
Norm of X_ray positional gradient                43.2
Norm of Geom. positional gradient                80.4
Norm of X_ray B-factor gradient                  140.
Norm of Geom. B-factor gradient                  123.
Product of X_ray and Geom posit. gradients     -0.119E+08
 Cosine of angle between them                      -0.353
Product of X_ray and Geom B-fact gradients     -0.438E+08
 Cosine of angle between them                      -0.789


Residuals: XRAY=     0.7035E+06 GEOM=     0.1390E+05 TOTAL=     0.7174E+06
 function value    717397.56    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.035     0.017
Bond angles  : refined atoms                   2106     1.840     1.644
Bond angles  : others                          3238     2.360     1.580
Torsion angles, period  1. refined              185     7.115     5.000
Torsion angles, period  2. refined               90    37.308    22.778
Torsion angles, period  3. refined              268    14.552    15.000
Torsion angles, period  4. refined                9    10.661    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.018     0.020
VDW repulsions: refined_atoms                   311     0.242     0.200
VDW repulsions.others                          1349     0.224     0.200
VDW; torsion: refined_atoms                     720     0.172     0.200
VDW; torsion.others                             717     0.082     0.200
HBOND: refined_atoms                            230     0.205     0.200
HBOND.others                                      1     0.040     0.200
VDW repulsions: symmetry: refined_atoms          10     0.222     0.200
VDW repulsions: symmetry: others                 30     0.178     0.200
HBOND: symmetry: refined_atoms                   21     0.204     0.200
HBOND: symmetry: others                           1     0.020     0.200
M. chain bond B values: refined atoms           746     1.660     1.210
M. chain bond B values: others                  746     1.659     1.211
M. chain angle B values: refined atoms          929     2.626     1.800
M. chain angle B values: others                 930     2.625     1.800
S. chain bond B values: refined atoms           811     2.857     1.588
S. chain bond B values: others                  810     2.853     1.588
S. chain angle B values: refined atoms         1177     4.477     2.220
S. chain angle B values: others                1178     4.475     2.220
Long range B values: refined atoms             1866     7.375    17.227
Long range B values: others                    1771     6.975    15.881
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0414, B  =    0.8588
Partial structure    1: scale =     0.3834, B  =   48.1554
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2572 100.00   471.6   480.0  0.15  0.16     121   478.1   487.6  0.16  0.16
 0.116    4332 100.00   340.9   327.2  0.16  0.15     247   341.1   321.3  0.20  0.19
 0.193    5510  99.97   225.5   214.8  0.16  0.13     298   228.3   213.7  0.20  0.17
 0.270    6458 100.00   148.1   155.0  0.22  0.16     329   137.8   148.6  0.26  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1809   0.944    763   0.861   2572   0.919  0.956  0.9754  0.9768  0.9314  0.9437
  0.1161   3556   0.893    776   0.794   4332   0.875  0.997  0.9577  0.9655  0.9235  0.9454
  0.1931   4736   0.889    774   0.781   5510   0.874  1.016  0.9530  0.9637  0.9044  0.9426
  0.2701   5683   0.833    783   0.749   6466   0.822  0.898  0.9285  0.9419  0.8794  0.9049
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18880
Percentage observed                  =    99.9849
Percentage of free reflections       =     5.0063
Overall R factor                     =     0.1682
Free R factor                        =     0.2002
Average Fourier shell correlation    =     0.9584
AverageFree Fourier shell correlation=     0.9488
Overall weighted R factor            =     0.1508
Free weighted R factor               =     0.1775
Overall weighted R2 factor           =     0.1808
Free weighted R2 factor              =     0.2054
Average correlation coefficient      =     0.9305
Overall correlation coefficient      =     0.9566
Free correlation coefficient         =     0.9407
Cruickshanks DPI for coordinate error=     0.1229
DPI based on free R factor           =     0.1143
Overall figure of merit              =     0.8628
ML based su of positional parameters =     0.0746
ML based su of thermal parameters    =     2.4320
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    100506.19       13898.316       717397.56      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.33343819    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    709423.69    

-------------------------------------------------------------------------------
             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 =     0.0414, B  =   -0.1015
Partial structure    1: scale =     0.3835, B  =   48.2787
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1671
Free R factor                        =     0.1987
Average Fourier shell correlation    =     0.9619
AverageFree Fourier shell correlation=     0.9527
Average correlation coefficient      =     0.9331
Overall figure of merit              =     0.8751
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    100085.87       8866.4893       709423.69       717397.56    


     CGMAT cycle number =      3

 Weight matrix   0.33952647    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    708430.44    

-------------------------------------------------------------------------------
             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 =     0.0413, B  =   -0.0633
Partial structure    1: scale =     0.3832, B  =   48.1331
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1659
Free R factor                        =     0.1976
Average Fourier shell correlation    =     0.9627
AverageFree Fourier shell correlation=     0.9534
Average correlation coefficient      =     0.9350
Overall figure of merit              =     0.8766
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    99867.102       9404.5605       708430.44       709423.69    


     CGMAT cycle number =      4

 Weight matrix   0.31037682    
 Actual weight    6.3632374      is applied to the X-ray term


 function value    644505.50    

-------------------------------------------------------------------------------
             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 =     0.0414, B  =   -0.0369
Partial structure    1: scale =     0.3831, B  =   47.7528
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1655
Free R factor                        =     0.1971
Average Fourier shell correlation    =     0.9629
AverageFree Fourier shell correlation=     0.9537
Average correlation coefficient      =     0.9355
Overall figure of merit              =     0.8770
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    99778.172       9593.3301       644505.50       708430.44    


     CGMAT cycle number =      5

 Weight matrix   0.28155625    
 Actual weight    5.7847610      is applied to the X-ray term


 function value    586667.88    

-------------------------------------------------------------------------------
             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 =     0.0414, B  =   -0.0442
Partial structure    1: scale =     0.3832, B  =   47.5945
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1659
Free R factor                        =     0.1973
Average Fourier shell correlation    =     0.9628
AverageFree Fourier shell correlation=     0.9536
Average correlation coefficient      =     0.9353
Overall figure of merit              =     0.8770
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    99798.320       9358.4541       586667.88       644505.50    


     CGMAT cycle number =      6

 Weight matrix   0.28093335    
 Actual weight    5.7847610      is applied to the X-ray term


 function value    586631.88    

-------------------------------------------------------------------------------
             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 =     0.0413, B  =   -0.0502
Partial structure    1: scale =     0.3830, B  =   47.3917
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1664
Free R factor                        =     0.1975
Average Fourier shell correlation    =     0.9626
AverageFree Fourier shell correlation=     0.9535
Average correlation coefficient      =     0.9349
Overall figure of merit              =     0.8769
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    99853.125       9005.4082       586631.88       586667.88    


     CGMAT cycle number =      7

 Weight matrix   0.28026867    
 Actual weight    5.7847610      is applied to the X-ray term


 function value    586613.56    

-------------------------------------------------------------------------------
             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 =     0.0413, B  =   -0.0691
Partial structure    1: scale =     0.3829, B  =   47.2540
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1666
Free R factor                        =     0.1981
Average Fourier shell correlation    =     0.9626
AverageFree Fourier shell correlation=     0.9534
Average correlation coefficient      =     0.9348
Overall figure of merit              =     0.8767
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    99870.188       8888.3564       586613.56       586631.88    


     CGMAT cycle number =      8

 Weight matrix   0.27972656    
 Actual weight    5.7847610      is applied to the X-ray term


 function value    586634.75    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0638
Partial structure    1: scale =     0.3829, B  =   47.1968
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1668
Free R factor                        =     0.1983
Average Fourier shell correlation    =     0.9625
AverageFree Fourier shell correlation=     0.9534
Average correlation coefficient      =     0.9348
Overall figure of merit              =     0.8766
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    99882.781       8836.7881       586612.88       586613.56    
 fvalues    99882.781       8836.7881       586612.88       586634.81    


     CGMAT cycle number =      9

 Weight matrix   0.27947506    
 Actual weight    5.7847610      is applied to the X-ray term


 function value    586591.75    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0563
Partial structure    1: scale =     0.3828, B  =   47.0231
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1668
Free R factor                        =     0.1984
Average Fourier shell correlation    =     0.9625
AverageFree Fourier shell correlation=     0.9533
Average correlation coefficient      =     0.9348
Overall figure of merit              =     0.8766
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    99881.188       8802.9297       586591.75       586634.81    


     CGMAT cycle number =     10

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.927 id.= 3.000 dev= -2.07 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  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Weight matrix   0.27935621    
 Actual weight    5.7847610      is applied to the X-ray term
Norm of X_ray positional gradient                35.3
Norm of Geom. positional gradient                35.3
Norm of X_ray B-factor gradient                  115.
Norm of Geom. B-factor gradient                  118.
Product of X_ray and Geom posit. gradients     -0.121E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.438E+08
 Cosine of angle between them                      -0.994


Residuals: XRAY=     0.5778E+06 GEOM=      8786.     TOTAL=     0.5866E+06
 function value    586580.38    

-------------------------------------------------------------------------------
             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     1.784     1.644
Bond angles  : others                          3238     1.470     1.580
Torsion angles, period  1. refined              185     7.096     5.000
Torsion angles, period  2. refined               90    37.040    22.778
Torsion angles, period  3. refined              268    14.319    15.000
Torsion angles, period  4. refined                9    10.851    15.000
Chiral centres: refined atoms                   196     0.085     0.200
Planar groups: refined atoms                   1743     0.009     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   312     0.240     0.200
VDW repulsions.others                          1368     0.194     0.200
VDW; torsion: refined_atoms                     721     0.172     0.200
VDW; torsion.others                             784     0.084     0.200
HBOND: refined_atoms                            230     0.196     0.200
HBOND.others                                      1     0.113     0.200
VDW repulsions: symmetry: refined_atoms           9     0.206     0.200
VDW repulsions: symmetry: others                 26     0.183     0.200
HBOND: symmetry: refined_atoms                   23     0.191     0.200
M. chain bond B values: refined atoms           746     1.637     1.295
M. chain bond B values: others                  746     1.636     1.295
M. chain angle B values: refined atoms          929     2.586     1.929
M. chain angle B values: others                 930     2.585     1.929
S. chain bond B values: refined atoms           811     2.843     1.679
S. chain bond B values: others                  810     2.839     1.679
S. chain angle B values: refined atoms         1177     4.501     2.356
S. chain angle B values: others                1178     4.499     2.355
Long range B values: refined atoms             1865     7.452    18.296
Long range B values: others                    1765     7.004    16.788
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0594
Partial structure    1: scale =     0.3829, B  =   47.1383
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2572 100.00   472.2   480.8  0.15  0.16     121   478.7   486.8  0.15  0.16
 0.116    4332 100.00   341.3   326.7  0.16  0.15     247   341.5   321.6  0.20  0.18
 0.193    5510  99.97   225.8   214.7  0.16  0.14     298   228.6   213.0  0.20  0.18
 0.270    6458 100.00   148.3   154.5  0.20  0.15     329   138.0   148.7  0.25  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1809   0.951    763   0.871   2572   0.927  0.956  0.9772  0.9782  0.9343  0.9446
  0.1161   3556   0.899    776   0.805   4332   0.882  0.997  0.9605  0.9665  0.9288  0.9436
  0.1931   4736   0.892    774   0.781   5510   0.876  1.016  0.9536  0.9632  0.9050  0.9382
  0.2701   5683   0.863    783   0.782   6466   0.853  0.911  0.9389  0.9530  0.8857  0.9220
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18880
Percentage observed                  =    99.9849
Percentage of free reflections       =     5.0063
Overall R factor                     =     0.1669
Free R factor                        =     0.1985
Average Fourier shell correlation    =     0.9625
AverageFree Fourier shell correlation=     0.9533
Overall weighted R factor            =     0.1513
Free weighted R factor               =     0.1758
Overall weighted R2 factor           =     0.1810
Free weighted R2 factor              =     0.2015
Average correlation coefficient      =     0.9348
Overall correlation coefficient      =     0.9570
Free correlation coefficient         =     0.9434
Cruickshanks DPI for coordinate error=     0.1219
DPI based on free R factor           =     0.1134
Overall figure of merit              =     0.8766
ML based su of positional parameters =     0.0697
ML based su of thermal parameters    =     2.2427
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    99882.164       8785.9170       586580.38       586591.75    

    ****                              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.= 0.928 id.= 3.000 dev= -2.07 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_R13_1-80A.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     1.784     1.644
Bond angles  : others                          3238     1.470     1.580
Torsion angles, period  1. refined              185     7.092     5.000
Torsion angles, period  2. refined               90    37.032    22.778
Torsion angles, period  3. refined              268    14.303    15.000
Torsion angles, period  4. refined                9    10.819    15.000
Chiral centres: refined atoms                   196     0.084     0.200
Planar groups: refined atoms                   1743     0.009     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   311     0.240     0.200
VDW repulsions.others                          1367     0.194     0.200
VDW; torsion: refined_atoms                     721     0.172     0.200
VDW; torsion.others                             789     0.084     0.200
HBOND: refined_atoms                            229     0.197     0.200
HBOND.others                                      1     0.116     0.200
VDW repulsions: symmetry: refined_atoms           9     0.205     0.200
VDW repulsions: symmetry: others                 26     0.183     0.200
HBOND: symmetry: refined_atoms                   23     0.192     0.200
M. chain bond B values: refined atoms           746     1.636     1.295
M. chain bond B values: others                  746     1.634     1.295
M. chain angle B values: refined atoms          929     2.583     1.929
M. chain angle B values: others                 930     2.581     1.928
S. chain bond B values: refined atoms           811     2.841     1.679
S. chain bond B values: others                  810     2.837     1.678
S. chain angle B values: refined atoms         1177     4.497     2.355
S. chain angle B values: others                1178     4.495     2.355
Long range B values: refined atoms             1863     7.444    18.267
Long range B values: others                    1764     7.011    16.789
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0575
Partial structure    1: scale =     0.3830, B  =   47.1375
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2572 100.00   472.2   480.8  0.15  0.16     121   478.7   486.8  0.16  0.16
 0.116    4332 100.00   341.3   326.7  0.16  0.15     247   341.5   321.6  0.19  0.18
 0.193    5510  99.97   225.8   214.7  0.16  0.14     298   228.6   212.9  0.20  0.18
 0.270    6458 100.00   148.3   154.5  0.20  0.15     329   138.0   148.8  0.25  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1809   0.950    763   0.870   2572   0.926  0.956  0.9770  0.9781  0.9337  0.9446
  0.1161   3556   0.899    776   0.805   4332   0.882  0.997  0.9606  0.9665  0.9291  0.9436
  0.1931   4736   0.892    774   0.781   5510   0.876  1.016  0.9535  0.9631  0.9047  0.9380
  0.2701   5683   0.863    783   0.782   6466   0.853  0.911  0.9390  0.9531  0.8859  0.9222
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18880
Percentage observed                  =    99.9849
Percentage of free reflections       =     5.0063
Overall R factor                     =     0.1669
Free R factor                        =     0.1987
Average Fourier shell correlation    =     0.9625
AverageFree Fourier shell correlation=     0.9533
Overall weighted R factor            =     0.1513
Free weighted R factor               =     0.1761
Overall weighted R2 factor           =     0.1811
Free weighted R2 factor              =     0.2018
Average correlation coefficient      =     0.9348
Overall correlation coefficient      =     0.9570
Free correlation coefficient         =     0.9433
Cruickshanks DPI for coordinate error=     0.1219
DPI based on free R factor           =     0.1134
Overall figure of merit              =     0.8765
ML based su of positional parameters =     0.0697
ML based su of thermal parameters    =     2.2427
-----------------------------------------------------------------------------
  Time in seconds: CPU =        14.65
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1682   0.2002   0.863      100506.    5410.8   0.0130  0.955   1.840  1.058   0.087
       1   0.1671   0.1987   0.875      100086.    5393.2   0.0129  0.943   1.819  1.045   0.088
       2   0.1659   0.1976   0.877       99867.    5385.8   0.0136  1.000   1.851  1.063   0.090
       3   0.1655   0.1971   0.877       99778.    5382.0   0.0137  1.009   1.865  1.071   0.090
       4   0.1659   0.1973   0.877       99798.    5382.6   0.0132  0.969   1.844  1.058   0.088
       5   0.1664   0.1975   0.877       99853.    5384.8   0.0125  0.922   1.808  1.038   0.086
       6   0.1666   0.1981   0.877       99870.    5386.0   0.0124  0.916   1.795  1.030   0.085
       7   0.1668   0.1983   0.877       99883.    5386.3   0.0123  0.911   1.788  1.027   0.085
       8   0.1668   0.1984   0.877       99881.    5386.3   0.0123  0.910   1.786  1.025   0.085
       9   0.1669   0.1985   0.877       99882.    5386.5   0.0123  0.909   1.784  1.025   0.085
      10   0.1669   0.1987   0.876       99887.    5386.9   0.0123  0.908   1.784  1.024   0.084
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1682   0.1669
             R free    0.2002   0.1987
     Rms BondLength    0.0130   0.0123
      Rms BondAngle    1.8402   1.7837
     Rms ChirVolume    0.0871   0.0844
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      46.7s System:    0.1s Elapsed:     0:47