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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: 14:38:53 


 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 8
  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_R08_2-00A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R08_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_R08_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:     8
  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_R08_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=   2.050 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=   2.228 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=   1.847 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=   2.210 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=   2.341 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=   2.457 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=   1.977 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                            8
Number of "free" reflections        860
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.= 1.556 id.= 1.337 dev= -0.219 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.= 0.911 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   0.23969014    
 Actual weight    7.2495699      is applied to the X-ray term
Norm of X_ray positional gradient                42.7
Norm of Geom. positional gradient                88.1
Norm of X_ray B-factor gradient                  142.
Norm of Geom. B-factor gradient                 0.219E+05
Product of X_ray and Geom posit. gradients     -0.724E+07
 Cosine of angle between them                      -0.199
Product of X_ray and Geom B-fact gradients     -0.379E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.6372E+06 GEOM=     0.2666E+05 TOTAL=     0.6639E+06
 function value    663866.00    

-------------------------------------------------------------------------------
             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     1.837     1.644
Bond angles  : others                          3242     2.358     1.582
Torsion angles, period  1. refined              184     7.328     5.000
Torsion angles, period  2. refined               90    36.527    22.778
Torsion angles, period  3. refined              268    14.694    15.000
Torsion angles, period  4. refined                9    11.248    15.000
Chiral centres: refined atoms                   196     0.086     0.200
Planar groups: refined atoms                   1736     0.012     0.020
Planar groups: others                           331     0.017     0.020
VDW repulsions: refined_atoms                   320     0.255     0.200
VDW repulsions.others                          1322     0.232     0.200
VDW; torsion: refined_atoms                     704     0.170     0.200
VDW; torsion.others                             701     0.080     0.200
HBOND: refined_atoms                            231     0.210     0.200
HBOND.others                                      3     0.035     0.200
VDW repulsions: symmetry: refined_atoms           6     0.314     0.200
VDW repulsions: symmetry: others                 26     0.174     0.200
HBOND: symmetry: refined_atoms                   18     0.222     0.200
HBOND: symmetry: others                           1     0.040     0.200
M. chain bond B values: refined atoms           745     1.565     1.180
M. chain bond B values: others                  745     1.564     1.180
M. chain angle B values: refined atoms          926     2.525     1.751
M. chain angle B values: others                 927     2.523     1.751
S. chain bond B values: refined atoms           812     2.485     1.510
S. chain bond B values: others                  811     2.480     1.509
S. chain angle B values: refined atoms         1177     3.944     2.121
S. chain angle B values: others                1178     3.943     2.120
Long range B values: refined atoms             1868     6.789    16.572
Long range B values: others                    1771     6.475    15.274
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =    0.3355
Partial structure    1: scale =     0.3725, B  =   48.7177
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.55 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2189 100.00   480.5   485.8  0.16  0.17     122   489.3   478.1  0.19  0.20
 0.104    3735 100.00   387.0   370.2  0.16  0.15     189   370.9   359.8  0.22  0.20
 0.173    4697  99.96   248.0   242.4  0.16  0.13     245   252.5   244.5  0.21  0.18
 0.242    5500 100.00   188.8   189.7  0.18  0.14     304   185.9   187.6  0.22  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1508   0.926    681   0.831   2189   0.896  0.961  0.9648  0.9720  0.9237  0.9429
  0.1042   3028   0.891    707   0.786   3735   0.871  0.999  0.9499  0.9653  0.8915  0.9455
  0.1733   3996   0.876    701   0.771   4697   0.860  0.984  0.9475  0.9608  0.8907  0.9418
  0.2425   4799   0.871    704   0.759   5503   0.857  0.951  0.9391  0.9522  0.8640  0.9189
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16124
Percentage observed                  =    99.9823
Percentage of free reflections       =     5.0636
Overall R factor                     =     0.1628
Free R factor                        =     0.2106
Average Fourier shell correlation    =     0.9604
AverageFree Fourier shell correlation=     0.9475
Overall weighted R factor            =     0.1500
Free weighted R factor               =     0.1941
Overall weighted R2 factor           =     0.1825
Free weighted R2 factor              =     0.2288
Average correlation coefficient      =     0.9350
Overall correlation coefficient      =     0.9544
Free correlation coefficient         =     0.9252
Cruickshanks DPI for coordinate error=     0.1439
DPI based on free R factor           =     0.1374
Overall figure of merit              =     0.8664
ML based su of positional parameters =     0.0843
ML based su of thermal parameters    =     2.8277
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    87895.789       26659.287       663866.00      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.25376818    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    644829.13    

-------------------------------------------------------------------------------
             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  =   -0.1111
Partial structure    1: scale =     0.3734, B  =   48.7475
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                     =     0.1607
Free R factor                        =     0.2078
Average Fourier shell correlation    =     0.9626
AverageFree Fourier shell correlation=     0.9498
Average correlation coefficient      =     0.9387
Overall figure of merit              =     0.8711
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    87467.711       10725.830       644829.13       663866.00    


     CGMAT cycle number =      3

 Weight matrix   0.25863737    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    642416.13    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.0576
Partial structure    1: scale =     0.3738, B  =   46.8920
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                     =     0.1595
Free R factor                        =     0.2065
Average Fourier shell correlation    =     0.9632
AverageFree Fourier shell correlation=     0.9506
Average correlation coefficient      =     0.9400
Overall figure of merit              =     0.8723
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    87312.984       9434.5908       642416.13       644829.13    


     CGMAT cycle number =      4

 Weight matrix   0.26226854    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    641331.56    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.0849
Partial structure    1: scale =     0.3747, B  =   46.8342
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                     =     0.1590
Free R factor                        =     0.2054
Average Fourier shell correlation    =     0.9636
AverageFree Fourier shell correlation=     0.9511
Average correlation coefficient      =     0.9405
Overall figure of merit              =     0.8733
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    87223.039       9002.0420       641331.56       642416.13    


     CGMAT cycle number =      5

 Weight matrix   0.26417023    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    640871.50    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =   -0.0888
Partial structure    1: scale =     0.3752, B  =   47.0021
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                     =     0.1587
Free R factor                        =     0.2050
Average Fourier shell correlation    =     0.9638
AverageFree Fourier shell correlation=     0.9514
Average correlation coefficient      =     0.9408
Overall figure of merit              =     0.8738
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    87166.266       8953.5840       640871.50       641331.56    


     CGMAT cycle number =      6

 Weight matrix   0.26526296    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    640618.63    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =   -0.0801
Partial structure    1: scale =     0.3753, B  =   46.9726
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                     =     0.1586
Free R factor                        =     0.2046
Average Fourier shell correlation    =     0.9639
AverageFree Fourier shell correlation=     0.9515
Average correlation coefficient      =     0.9410
Overall figure of merit              =     0.8740
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    87126.953       8985.6641       640618.63       640871.50    


     CGMAT cycle number =      7

 Weight matrix   0.26561981    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    640545.63    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =   -0.0870
Partial structure    1: scale =     0.3753, B  =   47.1476
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                     =     0.1585
Free R factor                        =     0.2045
Average Fourier shell correlation    =     0.9639
AverageFree Fourier shell correlation=     0.9516
Average correlation coefficient      =     0.9411
Overall figure of merit              =     0.8741
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    87114.117       9005.7559       640545.63       640618.63    


     CGMAT cycle number =      8

 Weight matrix   0.26612908    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    640438.81    

-------------------------------------------------------------------------------
             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 =     0.0403, B  =   -0.0739
Partial structure    1: scale =     0.3756, B  =   46.8740
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                     =     0.1584
Free R factor                        =     0.2045
Average Fourier shell correlation    =     0.9640
AverageFree Fourier shell correlation=     0.9517
Average correlation coefficient      =     0.9412
Overall figure of merit              =     0.8742
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    87096.945       9023.4355       640438.81       640545.63    


     CGMAT cycle number =      9

 Weight matrix   0.26596588    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    640355.19    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =   -0.0893
Partial structure    1: scale =     0.3758, B  =   47.0096
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                     =     0.1583
Free R factor                        =     0.2048
Average Fourier shell correlation    =     0.9640
AverageFree Fourier shell correlation=     0.9516
Average correlation coefficient      =     0.9413
Overall figure of merit              =     0.8741
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    87087.672       9007.0195       640355.19       640438.81    


     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.= 0.941 id.= 3.000 dev= -2.06 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   0.26618782    
 Actual weight    7.2495699      is applied to the X-ray term
Norm of X_ray positional gradient                36.1
Norm of Geom. positional gradient                36.0
Norm of X_ray B-factor gradient                  118.
Norm of Geom. B-factor gradient                  122.
Product of X_ray and Geom posit. gradients     -0.126E+08
 Cosine of angle between them                      -0.998
Product of X_ray and Geom B-fact gradients     -0.461E+08
 Cosine of angle between them                      -0.989


Residuals: XRAY=     0.6313E+06 GEOM=      9012.     TOTAL=     0.6403E+06
 function value    640272.50    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.803     1.644
Bond angles  : others                          3242     1.451     1.582
Torsion angles, period  1. refined              184     7.039     5.000
Torsion angles, period  2. refined               90    36.816    22.778
Torsion angles, period  3. refined              268    14.036    15.000
Torsion angles, period  4. refined                9    11.224    15.000
Chiral centres: refined atoms                   196     0.086     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   308     0.263     0.200
VDW repulsions.others                          1346     0.204     0.200
VDW; torsion: refined_atoms                     719     0.171     0.200
VDW; torsion.others                             783     0.084     0.200
HBOND: refined_atoms                            230     0.203     0.200
HBOND.others                                      1     0.042     0.200
VDW repulsions: symmetry: refined_atoms           9     0.253     0.200
VDW repulsions: symmetry: others                 23     0.192     0.200
HBOND: symmetry: refined_atoms                   22     0.185     0.200
HBOND: symmetry: others                           1     0.013     0.200
M. chain bond B values: refined atoms           745     1.614     1.213
M. chain bond B values: others                  745     1.613     1.213
M. chain angle B values: refined atoms          926     2.569     1.800
M. chain angle B values: others                 927     2.568     1.800
S. chain bond B values: refined atoms           812     2.739     1.572
S. chain bond B values: others                  811     2.735     1.572
S. chain angle B values: refined atoms         1177     4.278     2.204
S. chain angle B values: others                1178     4.276     2.204
Long range B values: refined atoms             1861     6.997    17.182
Long range B values: others                    1761     6.677    15.766
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =   -0.0868
Partial structure    1: scale =     0.3758, B  =   47.0965
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   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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2189 100.00   479.5   485.9  0.16  0.17     122   488.3   478.4  0.19  0.21
 0.104    3735 100.00   386.2   368.5  0.16  0.15     189   370.1   360.7  0.21  0.20
 0.173    4697  99.96   247.5   241.8  0.16  0.13     245   252.0   244.1  0.21  0.17
 0.242    5500 100.00   188.4   189.4  0.16  0.13     304   185.5   187.8  0.21  0.17
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1508   0.932    681   0.841   2189   0.903  0.960  0.9663  0.9736  0.9186  0.9431
  0.1042   3028   0.896    707   0.791   3735   0.876  1.001  0.9541  0.9666  0.9004  0.9446
  0.1733   3996   0.883    701   0.781   4697   0.868  0.986  0.9512  0.9628  0.8981  0.9419
  0.2425   4799   0.881    704   0.767   5503   0.867  0.955  0.9446  0.9595  0.8744  0.9381
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16124
Percentage observed                  =    99.9823
Percentage of free reflections       =     5.0636
Overall R factor                     =     0.1583
Free R factor                        =     0.2050
Average Fourier shell correlation    =     0.9640
AverageFree Fourier shell correlation=     0.9516
Overall weighted R factor            =     0.1480
Free weighted R factor               =     0.1911
Overall weighted R2 factor           =     0.1815
Free weighted R2 factor              =     0.2279
Average correlation coefficient      =     0.9414
Overall correlation coefficient      =     0.9559
Free correlation coefficient         =     0.9276
Cruickshanks DPI for coordinate error=     0.1400
DPI based on free R factor           =     0.1338
Overall figure of merit              =     0.8742
ML based su of positional parameters =     0.0799
ML based su of thermal parameters    =     2.6671
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    87075.594       9011.8770       640272.50       640355.19    

    ****                              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.= 0.941 id.= 3.000 dev= -2.06 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_R08_1-90A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.803     1.644
Bond angles  : others                          3242     1.451     1.582
Torsion angles, period  1. refined              184     7.036     5.000
Torsion angles, period  2. refined               90    36.827    22.778
Torsion angles, period  3. refined              268    14.016    15.000
Torsion angles, period  4. refined                9    11.229    15.000
Chiral centres: refined atoms                   196     0.086     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   305     0.264     0.200
VDW repulsions.others                          1349     0.204     0.200
VDW; torsion: refined_atoms                     717     0.171     0.200
VDW; torsion.others                             787     0.084     0.200
HBOND: refined_atoms                            233     0.202     0.200
HBOND.others                                      1     0.043     0.200
VDW repulsions: symmetry: refined_atoms           9     0.253     0.200
VDW repulsions: symmetry: others                 23     0.192     0.200
HBOND: symmetry: refined_atoms                   23     0.181     0.200
HBOND: symmetry: others                           1     0.013     0.200
M. chain bond B values: refined atoms           745     1.615     1.214
M. chain bond B values: others                  745     1.614     1.214
M. chain angle B values: refined atoms          926     2.570     1.802
M. chain angle B values: others                 927     2.569     1.801
S. chain bond B values: refined atoms           812     2.739     1.573
S. chain bond B values: others                  811     2.735     1.573
S. chain angle B values: refined atoms         1177     4.278     2.206
S. chain angle B values: others                1178     4.276     2.205
Long range B values: refined atoms             1860     7.000    17.199
Long range B values: others                    1760     6.682    15.783
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =   -0.0922
Partial structure    1: scale =     0.3756, B  =   47.1488
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   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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2189 100.00   479.6   486.0  0.16  0.17     122   488.4   478.5  0.20  0.21
 0.104    3735 100.00   386.3   368.5  0.16  0.15     189   370.2   360.7  0.21  0.20
 0.173    4697  99.96   247.6   241.8  0.16  0.13     245   252.1   244.1  0.21  0.17
 0.242    5500 100.00   188.4   189.3  0.16  0.13     304   185.5   187.8  0.21  0.17
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1508   0.931    681   0.840   2189   0.903  0.960  0.9659  0.9735  0.9180  0.9432
  0.1042   3028   0.896    707   0.791   3735   0.876  1.001  0.9542  0.9666  0.9006  0.9446
  0.1733   3996   0.883    701   0.781   4697   0.868  0.986  0.9511  0.9627  0.8982  0.9419
  0.2425   4799   0.881    704   0.767   5503   0.867  0.955  0.9446  0.9595  0.8741  0.9383
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16124
Percentage observed                  =    99.9823
Percentage of free reflections       =     5.0636
Overall R factor                     =     0.1583
Free R factor                        =     0.2053
Average Fourier shell correlation    =     0.9640
AverageFree Fourier shell correlation=     0.9516
Overall weighted R factor            =     0.1480
Free weighted R factor               =     0.1915
Overall weighted R2 factor           =     0.1815
Free weighted R2 factor              =     0.2285
Average correlation coefficient      =     0.9415
Overall correlation coefficient      =     0.9559
Free correlation coefficient         =     0.9274
Cruickshanks DPI for coordinate error=     0.1399
DPI based on free R factor           =     0.1339
Overall figure of merit              =     0.8741
ML based su of positional parameters =     0.0799
ML based su of thermal parameters    =     2.6671
-----------------------------------------------------------------------------
  Time in seconds: CPU =        12.05
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1628   0.2106   0.866       87896.    4823.7   0.0138  1.065   1.837  1.060   0.086
       1   0.1607   0.2078   0.871       87468.    4810.8   0.0118  0.862   1.779  1.020   0.087
       2   0.1595   0.2065   0.872       87313.    4804.5   0.0121  0.888   1.788  1.025   0.086
       3   0.1590   0.2054   0.873       87223.    4800.2   0.0122  0.897   1.793  1.027   0.086
       4   0.1587   0.2050   0.874       87166.    4798.3   0.0123  0.904   1.797  1.030   0.086
       5   0.1586   0.2046   0.874       87127.    4796.7   0.0123  0.908   1.800  1.032   0.086
       6   0.1585   0.2045   0.874       87114.    4796.7   0.0123  0.909   1.802  1.034   0.086
       7   0.1584   0.2045   0.874       87097.    4797.3   0.0123  0.910   1.804  1.035   0.086
       8   0.1583   0.2048   0.874       87088.    4797.7   0.0123  0.910   1.803  1.035   0.086
       9   0.1583   0.2050   0.874       87076.    4797.3   0.0123  0.910   1.803  1.035   0.086
      10   0.1583   0.2053   0.874       87079.    4798.3   0.0123  0.910   1.803  1.035   0.086
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1628   0.1583
             R free    0.2106   0.2053
     Rms BondLength    0.0138   0.0123
      Rms BondAngle    1.8369   1.8033
     Rms ChirVolume    0.0861   0.0856
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      44.4s System:    0.1s Elapsed:     0:44