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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: 14:53:30 


 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 1.90     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 14
  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_R14_2-00A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R14_1-90A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R14_1-90A.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       0.0693
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.9000
  Estimated number of reflections :      21862
  Free R exclusion - flag equals:    14
  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  1.9000

  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_R14_2-00A.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=   2.227 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=   1.837 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=   2.403 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=   2.439 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=   2.032 ideal_dist=   1.870
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:OD  .
  --------------------------------
  --- title of input coord file ---

  PDB_code:xxxx
  PDB_name:----
  PDB_date:26-MAY-20
  --------------------------------
  ATTENTION: atom:OXT  THR               171  AAA  is missing in the structure
  ATTENTION: atom:OXT  PRO               190  AAA  is missing in the structure
  Number of chains                  :       4
  Total number of monomers          :     502
  Number of atoms                   :    3948
  Number of missing atoms           :       0
  Number of rebuilt atoms           :    1482
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0

_ccp4_form_factor.scat_method    'Sum of Gaussians'
_ccp4_form_factor.scat_data_source  X-ray


 loop_
     _atom_type_symbol
     _atom_type_scat_Cromer_Mann_a1
     _atom_type_scat_Cromer_Mann_b1
     _atom_type_scat_Cromer_Mann_a2
     _atom_type_scat_Cromer_Mann_b2
     _atom_type_scat_Cromer_Mann_a3
     _atom_type_scat_Cromer_Mann_b3
     _atom_type_scat_Cromer_Mann_a4
     _atom_type_scat_Cromer_Mann_b4
     _atom_type_scat_Cromer_Mann_c


  N     12.2220   0.0057   3.1346   9.8933   2.0141  28.9975   1.1672   0.5826 -11.5379
  H      0.4930  10.5109   0.3229  26.1257   0.1402   3.1424   0.0408  57.7997   0.0030
  C      2.3103  20.8439   1.0201  10.2075   1.5888   0.5687   0.8651  51.6512   0.2156
  O      3.0487  13.2771   2.2870   5.7011   1.5464   0.3239   0.8671  32.9089   0.2508
  S      6.9054   1.4679   5.2035  22.2151   1.4379   0.2536   1.5863  56.1720   1.0490
  FE    11.7738   4.7611   7.3600   0.3072   3.5235  15.3535   2.3054  76.8805   1.2805


 Number of distances         :           0
 Number of angles            :           0
 Number of torsions          :           0
 Number of planes            :           0
 Number of chirals           :           0
 Number of intervals         :           0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
                        Standard  External       All
                Bonds:      2950         0      2950
               Angles:      5345         0      5345
              Chirals:       196         0       196
               Planes:       451         0       451
             Torsions:      1553         0      1553
            Intervals:         0         0         0
--------------------------------------------------------------------------------


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


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

FreeR flag                           14
Number of "free" reflections        811
Number of   all  reflections      16986
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          16986

   Current auto weighting coefficient =    7.2495699    

 mode : HKRF


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



     CGMAT cycle number =      1

    ****                         Bond distance outliers                         ****

Bond distance deviations from the ideal >10.000Sigma will be monitored

A    125 LEU C   . - A    126 ARG N   . mod.= 1.531 id.= 1.337 dev= -0.194 sig.= 0.011

    ****                              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.= 0.897 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        :   112  112  240
 Maximuum H,K,L                 :    31   31   65
 Minimum acceptable grid spacing:    73   73  154
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    31   31   65
 Minimum acceptable grid spacing:    73   73  154
 Weight matrix   0.26003316    
 Actual weight    7.2495699      is applied to the X-ray term
Norm of X_ray positional gradient                43.7
Norm of Geom. positional gradient                86.8
Norm of X_ray B-factor gradient                  144.
Norm of Geom. B-factor gradient                 0.214E+05
Product of X_ray and Geom posit. gradients     -0.873E+07
 Cosine of angle between them                      -0.237
Product of X_ray and Geom B-fact gradients     -0.424E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.6377E+06 GEOM=     0.2657E+05 TOTAL=     0.6643E+06
 function value    664296.31    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.014     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.876     1.644
Bond angles  : others                          3242     2.366     1.582
Torsion angles, period  1. refined              184     7.178     5.000
Torsion angles, period  2. refined               90    36.891    22.778
Torsion angles, period  3. refined              268    14.665    15.000
Torsion angles, period  4. refined                9    11.451    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.012     0.020
Planar groups: others                           331     0.018     0.020
VDW repulsions: refined_atoms                   327     0.255     0.200
VDW repulsions.others                          1338     0.232     0.200
VDW; torsion: refined_atoms                     711     0.171     0.200
VDW; torsion.others                             700     0.081     0.200
HBOND: refined_atoms                            234     0.219     0.200
HBOND.others                                      2     0.082     0.200
VDW repulsions: symmetry: refined_atoms           9     0.251     0.200
VDW repulsions: symmetry: others                 28     0.179     0.200
HBOND: symmetry: refined_atoms                   15     0.259     0.200
HBOND: symmetry: others                           1     0.084     0.200
M. chain bond B values: refined atoms           745     1.560     1.172
M. chain bond B values: others                  745     1.559     1.172
M. chain angle B values: refined atoms          926     2.521     1.738
M. chain angle B values: others                 927     2.520     1.738
S. chain bond B values: refined atoms           812     2.511     1.508
S. chain bond B values: others                  811     2.508     1.507
S. chain angle B values: refined atoms         1177     3.968     2.116
S. chain angle B values: others                1178     3.966     2.116
Long range B values: refined atoms             1880     6.919    16.580
Long range B values: others                    1783     6.666    15.266
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =    0.3552
Partial structure    1: scale =     0.3735, B  =   48.5303
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2196 100.00   480.1   484.5  0.16  0.17     115   507.9   500.7  0.18  0.20
 0.104    3736 100.00   385.7   369.0  0.16  0.15     188   404.2   378.9  0.19  0.18
 0.173    4708  99.96   247.6   242.4  0.15  0.13     234   266.0   259.0  0.19  0.16
 0.242    5530 100.00   189.2   189.9  0.18  0.14     274   181.9   187.5  0.22  0.16
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1517   0.929    679   0.833   2196   0.899  0.962  0.9724  0.9733  0.9370  0.9413
  0.1042   3035   0.888    701   0.781   3736   0.868  1.000  0.9587  0.9635  0.9234  0.9430
  0.1733   4012   0.885    696   0.784   4708   0.870  0.986  0.9588  0.9635  0.9102  0.9442
  0.2425   4829   0.877    704   0.769   5533   0.863  0.951  0.9464  0.9545  0.8907  0.9190
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16173
Percentage observed                  =    99.9823
Percentage of free reflections       =     4.7751
Overall R factor                     =     0.1633
Free R factor                        =     0.1925
Average Fourier shell correlation    =     0.9617
AverageFree Fourier shell correlation=     0.9565
Overall weighted R factor            =     0.1508
Free weighted R factor               =     0.1805
Overall weighted R2 factor           =     0.1834
Free weighted R2 factor              =     0.2138
Average correlation coefficient      =     0.9349
Overall correlation coefficient      =     0.9535
Free correlation coefficient         =     0.9409
Cruickshanks DPI for coordinate error=     0.1438
DPI based on free R factor           =     0.1252
Overall figure of merit              =     0.8711
ML based su of positional parameters =     0.0810
ML based su of thermal parameters    =     2.7028
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    87967.656       26568.602       664296.31      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.28734845    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    645305.00    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.1095
Partial structure    1: scale =     0.3734, B  =   48.1653
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1611
Free R factor                        =     0.1894
Average Fourier shell correlation    =     0.9646
AverageFree Fourier shell correlation=     0.9593
Average correlation coefficient      =     0.9384
Overall figure of merit              =     0.8787
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    87495.969       10996.873       645305.00       664296.31    


     CGMAT cycle number =      3

 Weight matrix   0.29460442    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    642565.75    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.0695
Partial structure    1: scale =     0.3746, B  =   46.2440
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1597
Free R factor                        =     0.1879
Average Fourier shell correlation    =     0.9655
AverageFree Fourier shell correlation=     0.9601
Average correlation coefficient      =     0.9401
Overall figure of merit              =     0.8803
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    87279.539       9826.6426       642565.75       645305.00    


     CGMAT cycle number =      4

 Weight matrix   0.29790837    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    641501.13    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.0632
Partial structure    1: scale =     0.3752, B  =   46.4841
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1590
Free R factor                        =     0.1874
Average Fourier shell correlation    =     0.9659
AverageFree Fourier shell correlation=     0.9605
Average correlation coefficient      =     0.9408
Overall figure of merit              =     0.8811
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    87182.633       9464.5469       641501.13       642565.75    


     CGMAT cycle number =      5

 Weight matrix   0.29913452    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    641119.88    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.0653
Partial structure    1: scale =     0.3749, B  =   46.5158
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1587
Free R factor                        =     0.1874
Average Fourier shell correlation    =     0.9660
AverageFree Fourier shell correlation=     0.9606
Average correlation coefficient      =     0.9412
Overall figure of merit              =     0.8813
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    87134.844       9429.7695       641119.88       641501.13    


     CGMAT cycle number =      6

 Weight matrix   0.30019692    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    640877.13    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.0638
Partial structure    1: scale =     0.3759, B  =   46.7356
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1585
Free R factor                        =     0.1873
Average Fourier shell correlation    =     0.9662
AverageFree Fourier shell correlation=     0.9607
Average correlation coefficient      =     0.9415
Overall figure of merit              =     0.8816
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    87096.523       9464.8379       640877.13       641119.88    


     CGMAT cycle number =      7

 Weight matrix   0.30076897    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    640747.69    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.0632
Partial structure    1: scale =     0.3762, B  =   46.7937
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1583
Free R factor                        =     0.1873
Average Fourier shell correlation    =     0.9662
AverageFree Fourier shell correlation=     0.9607
Average correlation coefficient      =     0.9416
Overall figure of merit              =     0.8818
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    87074.820       9492.6738       640747.69       640877.13    


     CGMAT cycle number =      8

 Weight matrix   0.30080280    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    640729.31    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.0688
Partial structure    1: scale =     0.3763, B  =   46.8729
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1582
Free R factor                        =     0.1875
Average Fourier shell correlation    =     0.9662
AverageFree Fourier shell correlation=     0.9607
Average correlation coefficient      =     0.9417
Overall figure of merit              =     0.8818
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    87069.016       9516.3770       640729.31       640747.69    


     CGMAT cycle number =      9

 Weight matrix   0.30072549    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    640692.44    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.0646
Partial structure    1: scale =     0.3765, B  =   47.0104
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1582
Free R factor                        =     0.1876
Average Fourier shell correlation    =     0.9662
AverageFree Fourier shell correlation=     0.9607
Average correlation coefficient      =     0.9417
Overall figure of merit              =     0.8817
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    87063.008       9523.0723       640692.44       640729.31    


     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.= 0.907 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        :   112  112  240
 Maximuum H,K,L                 :    31   31   65
 Minimum acceptable grid spacing:    73   73  154
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    31   31   65
 Minimum acceptable grid spacing:    73   73  154
 Weight matrix   0.30069900    
 Actual weight    7.2495699      is applied to the X-ray term
Norm of X_ray positional gradient                38.8
Norm of Geom. positional gradient                38.8
Norm of X_ray B-factor gradient                  128.
Norm of Geom. B-factor gradient                  132.
Product of X_ray and Geom posit. gradients     -0.146E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.544E+08
 Cosine of angle between them                      -0.993


Residuals: XRAY=     0.6311E+06 GEOM=      9531.     TOTAL=     0.6407E+06
 function value    640661.81    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.860     1.644
Bond angles  : others                          3242     1.468     1.582
Torsion angles, period  1. refined              184     6.940     5.000
Torsion angles, period  2. refined               90    36.848    22.778
Torsion angles, period  3. refined              268    14.373    15.000
Torsion angles, period  4. refined                9    11.768    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   308     0.267     0.200
VDW repulsions.others                          1378     0.206     0.200
VDW; torsion: refined_atoms                     717     0.173     0.200
VDW; torsion.others                             790     0.084     0.200
HBOND: refined_atoms                            235     0.209     0.200
HBOND.others                                      1     0.069     0.200
VDW repulsions: symmetry: refined_atoms          10     0.224     0.200
VDW repulsions: symmetry: others                 28     0.177     0.200
HBOND: symmetry: refined_atoms                   18     0.223     0.200
HBOND: symmetry: others                           1     0.026     0.200
M. chain bond B values: refined atoms           745     1.651     1.202
M. chain bond B values: others                  745     1.650     1.202
M. chain angle B values: refined atoms          926     2.607     1.783
M. chain angle B values: others                 927     2.606     1.783
S. chain bond B values: refined atoms           812     2.809     1.569
S. chain bond B values: others                  811     2.806     1.569
S. chain angle B values: refined atoms         1177     4.353     2.198
S. chain angle B values: others                1178     4.351     2.198
Long range B values: refined atoms             1863     7.054    17.155
Long range B values: others                    1766     6.792    15.748
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.0675
Partial structure    1: scale =     0.3765, B  =   47.0009
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2196 100.00   479.6   485.0  0.16  0.17     115   507.3   502.3  0.18  0.20
 0.104    3736 100.00   385.3   368.0  0.16  0.15     188   403.7   379.2  0.19  0.18
 0.173    4708  99.96   247.4   242.3  0.15  0.13     234   265.7   258.5  0.18  0.16
 0.242    5530 100.00   189.0   190.3  0.16  0.13     274   181.7   185.7  0.21  0.16
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1517   0.934    679   0.839   2196   0.905  0.962  0.9739  0.9742  0.9386  0.9404
  0.1042   3035   0.895    701   0.791   3736   0.876  1.000  0.9619  0.9658  0.9271  0.9430
  0.1733   4012   0.895    696   0.795   4708   0.880  0.986  0.9635  0.9658  0.9198  0.9435
  0.2425   4829   0.892    704   0.787   5533   0.878  0.956  0.9517  0.9637  0.8974  0.9399
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16173
Percentage observed                  =    99.9823
Percentage of free reflections       =     4.7751
Overall R factor                     =     0.1582
Free R factor                        =     0.1877
Average Fourier shell correlation    =     0.9663
AverageFree Fourier shell correlation=     0.9606
Overall weighted R factor            =     0.1487
Free weighted R factor               =     0.1768
Overall weighted R2 factor           =     0.1836
Free weighted R2 factor              =     0.2103
Average correlation coefficient      =     0.9418
Overall correlation coefficient      =     0.9551
Free correlation coefficient         =     0.9442
Cruickshanks DPI for coordinate error=     0.1393
DPI based on free R factor           =     0.1221
Overall figure of merit              =     0.8818
ML based su of positional parameters =     0.0752
ML based su of thermal parameters    =     2.4972
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    87057.648       9531.2852       640661.81       640692.44    

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.907 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_R14_1-90A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.861     1.644
Bond angles  : others                          3242     1.468     1.582
Torsion angles, period  1. refined              184     6.940     5.000
Torsion angles, period  2. refined               90    36.833    22.778
Torsion angles, period  3. refined              268    14.371    15.000
Torsion angles, period  4. refined                9    11.790    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   308     0.267     0.200
VDW repulsions.others                          1380     0.206     0.200
VDW; torsion: refined_atoms                     718     0.173     0.200
VDW; torsion.others                             791     0.084     0.200
HBOND: refined_atoms                            233     0.210     0.200
HBOND.others                                      1     0.074     0.200
VDW repulsions: symmetry: refined_atoms          10     0.223     0.200
VDW repulsions: symmetry: others                 28     0.177     0.200
HBOND: symmetry: refined_atoms                   18     0.223     0.200
HBOND: symmetry: others                           1     0.025     0.200
M. chain bond B values: refined atoms           745     1.653     1.202
M. chain bond B values: others                  745     1.652     1.202
M. chain angle B values: refined atoms          926     2.611     1.783
M. chain angle B values: others                 927     2.609     1.783
S. chain bond B values: refined atoms           812     2.814     1.569
S. chain bond B values: others                  811     2.811     1.569
S. chain angle B values: refined atoms         1177     4.360     2.199
S. chain angle B values: others                1178     4.358     2.198
Long range B values: refined atoms             1862     7.061    17.170
Long range B values: others                    1766     6.802    15.764
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =   -0.0649
Partial structure    1: scale =     0.3768, B  =   46.9461
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2196 100.00   479.5   484.9  0.16  0.17     115   507.2   502.5  0.18  0.20
 0.104    3736 100.00   385.2   368.0  0.16  0.15     188   403.6   379.2  0.19  0.18
 0.173    4708  99.96   247.3   242.3  0.15  0.13     234   265.6   258.4  0.18  0.16
 0.242    5530 100.00   188.9   190.2  0.16  0.13     274   181.7   185.6  0.21  0.16
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1517   0.934    679   0.838   2196   0.904  0.959  0.9739  0.9742  0.9388  0.9404
  0.1042   3035   0.895    701   0.791   3736   0.876  1.000  0.9618  0.9658  0.9268  0.9430
  0.1733   4012   0.895    696   0.795   4708   0.880  0.988  0.9636  0.9659  0.9198  0.9435
  0.2425   4829   0.891    704   0.787   5533   0.878  0.956  0.9516  0.9637  0.8973  0.9400
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16173
Percentage observed                  =    99.9823
Percentage of free reflections       =     4.7751
Overall R factor                     =     0.1582
Free R factor                        =     0.1879
Average Fourier shell correlation    =     0.9662
AverageFree Fourier shell correlation=     0.9606
Overall weighted R factor            =     0.1487
Free weighted R factor               =     0.1770
Overall weighted R2 factor           =     0.1835
Free weighted R2 factor              =     0.2103
Average correlation coefficient      =     0.9418
Overall correlation coefficient      =     0.9551
Free correlation coefficient         =     0.9442
Cruickshanks DPI for coordinate error=     0.1393
DPI based on free R factor           =     0.1223
Overall figure of merit              =     0.8817
ML based su of positional parameters =     0.0752
ML based su of thermal parameters    =     2.4972
-----------------------------------------------------------------------------
  Time in seconds: CPU =        12.54
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1633   0.1925   0.871       87968.    4545.2   0.0136  1.033   1.876  1.085   0.087
       1   0.1611   0.1894   0.879       87496.    4528.8   0.0121  0.889   1.810  1.042   0.089
       2   0.1597   0.1879   0.880       87280.    4520.4   0.0126  0.930   1.826  1.051   0.090
       3   0.1590   0.1874   0.881       87183.    4515.8   0.0127  0.940   1.836  1.058   0.090
       4   0.1587   0.1874   0.881       87135.    4514.5   0.0127  0.945   1.844  1.063   0.090
       5   0.1585   0.1873   0.882       87097.    4512.9   0.0128  0.947   1.849  1.066   0.091
       6   0.1583   0.1873   0.882       87075.    4512.0   0.0128  0.949   1.853  1.069   0.091
       7   0.1582   0.1875   0.882       87069.    4512.2   0.0128  0.949   1.856  1.070   0.091
       8   0.1582   0.1876   0.882       87063.    4512.3   0.0128  0.949   1.858  1.072   0.090
       9   0.1582   0.1877   0.882       87058.    4512.3   0.0128  0.950   1.860  1.073   0.090
      10   0.1582   0.1879   0.882       87055.    4512.5   0.0128  0.950   1.861  1.073   0.090
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1633   0.1582
             R free    0.1925   0.1879
     Rms BondLength    0.0136   0.0128
      Rms BondAngle    1.8756   1.8609
     Rms ChirVolume    0.0875   0.0905
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      44.4s System:    0.2s Elapsed:     0:45