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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 26/ 5/2020 Run time: 15:05:44 


 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 19
  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_R19_2-00A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R19_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_R19_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:    19
  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_R19_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=   2.043 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=   2.230 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=   1.848 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=   2.212 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=   2.386 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=   2.430 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=   2.035 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                           19
Number of "free" reflections        849
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     10 ARG C   . - A     11 THR N   . mod.= 1.451 id.= 1.337 dev= -0.114 sig.= 0.011
A    125 LEU C   . - A    126 ARG N   . mod.= 1.523 id.= 1.337 dev= -0.186 sig.= 0.011

    ****                Large deviation of atoms from planarity                 ****

Deviations from the planarity >10.000Sigma will be monitored
Atom: A     10 ARG C     deviation=  -0.21 sigma.=   0.02

    ****                              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.= 0.909 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   0.23723798    
 Actual weight    7.2495699      is applied to the X-ray term
Norm of X_ray positional gradient                37.9
Norm of Geom. positional gradient                87.3
Norm of X_ray B-factor gradient                  127.
Norm of Geom. B-factor gradient                 0.211E+05
Product of X_ray and Geom posit. gradients     -0.810E+07
 Cosine of angle between them                      -0.253
Product of X_ray and Geom B-fact gradients     -0.400E+08
 Cosine of angle between them                      -0.005


Residuals: XRAY=     0.6377E+06 GEOM=     0.2619E+05 TOTAL=     0.6639E+06
 function value    663935.38    

-------------------------------------------------------------------------------
             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     1.848     1.644
Bond angles  : others                          3242     2.350     1.582
Torsion angles, period  1. refined              184     7.246     5.000
Torsion angles, period  2. refined               90    37.091    22.778
Torsion angles, period  3. refined              268    14.419    15.000
Torsion angles, period  4. refined                9    11.126    15.000
Chiral centres: refined atoms                   196     0.085     0.200
Planar groups: refined atoms                   1736     0.013     0.020
Planar groups: others                           331     0.017     0.020
VDW repulsions: refined_atoms                   311     0.261     0.200
VDW repulsions.others                          1362     0.230     0.200
VDW; torsion: refined_atoms                     707     0.172     0.200
VDW; torsion.others                             717     0.080     0.200
HBOND: refined_atoms                            230     0.217     0.200
VDW repulsions: symmetry: refined_atoms           9     0.245     0.200
VDW repulsions: symmetry: others                 28     0.160     0.200
HBOND: symmetry: refined_atoms                   14     0.293     0.200
HBOND: symmetry: others                           1     0.103     0.200
M. chain bond B values: refined atoms           745     1.545     1.166
M. chain bond B values: others                  745     1.544     1.166
M. chain angle B values: refined atoms          926     2.467     1.728
M. chain angle B values: others                 927     2.465     1.728
S. chain bond B values: refined atoms           811     2.411     1.493
S. chain bond B values: others                  810     2.407     1.493
S. chain angle B values: refined atoms         1177     3.806     2.098
S. chain angle B values: others                1178     3.804     2.097
Long range B values: refined atoms             1853     6.744    16.245
Long range B values: others                    1758     6.448    14.949
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0401, B  =    0.3499
Partial structure    1: scale =     0.3745, B  =   48.4284
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2188 100.00   480.7   484.2  0.16  0.17     123   508.9   506.3  0.19  0.20
 0.104    3733 100.00   386.6   369.1  0.16  0.15     191   398.8   384.6  0.22  0.20
 0.173    4703  99.96   249.0   243.8  0.15  0.13     239   246.3   242.6  0.21  0.17
 0.242    5508 100.00   189.0   190.0  0.18  0.14     296   191.5   194.9  0.23  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1511   0.921    677   0.822   2188   0.890  0.960  0.9689  0.9715  0.9288  0.9410
  0.1042   3040   0.884    693   0.768   3733   0.863  0.998  0.9497  0.9611  0.8891  0.9416
  0.1733   4014   0.890    689   0.787   4703   0.875  0.986  0.9526  0.9646  0.9024  0.9449
  0.2425   4812   0.851    699   0.739   5511   0.837  0.943  0.9335  0.9482  0.8478  0.9212
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16135
Percentage observed                  =    99.9823
Percentage of free reflections       =     4.9988
Overall R factor                     =     0.1630
Free R factor                        =     0.2129
Average Fourier shell correlation    =     0.9591
AverageFree Fourier shell correlation=     0.9476
Overall weighted R factor            =     0.1513
Free weighted R factor               =     0.1914
Overall weighted R2 factor           =     0.1840
Free weighted R2 factor              =     0.2180
Average correlation coefficient      =     0.9355
Overall correlation coefficient      =     0.9534
Free correlation coefficient         =     0.9273
Cruickshanks DPI for coordinate error=     0.1440
DPI based on free R factor           =     0.1388
Overall figure of merit              =     0.8612
ML based su of positional parameters =     0.0848
ML based su of thermal parameters    =     2.8593
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    87969.563       26193.891       663935.38      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.25490412    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    645599.19    

-------------------------------------------------------------------------------
             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 =     0.0401, B  =   -0.1200
Partial structure    1: scale =     0.3741, B  =   48.4160
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                     =     0.1613
Free R factor                        =     0.2115
Average Fourier shell correlation    =     0.9616
AverageFree Fourier shell correlation=     0.9502
Average correlation coefficient      =     0.9383
Overall figure of merit              =     0.8679
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    87589.875       10610.232       645599.19       663935.38    


     CGMAT cycle number =      3

 Weight matrix   0.25922489    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    643396.13    

-------------------------------------------------------------------------------
             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 =     0.0401, B  =   -0.0509
Partial structure    1: scale =     0.3742, B  =   46.9768
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                     =     0.1599
Free R factor                        =     0.2107
Average Fourier shell correlation    =     0.9623
AverageFree Fourier shell correlation=     0.9509
Average correlation coefficient      =     0.9397
Overall figure of merit              =     0.8691
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    87452.898       9400.2705       643396.13       645599.19    


     CGMAT cycle number =      4

 Weight matrix   0.26129535    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    642429.19    

-------------------------------------------------------------------------------
             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 =     0.0401, B  =   -0.0770
Partial structure    1: scale =     0.3745, B  =   46.9690
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                     =     0.1594
Free R factor                        =     0.2101
Average Fourier shell correlation    =     0.9626
AverageFree Fourier shell correlation=     0.9513
Average correlation coefficient      =     0.9404
Overall figure of merit              =     0.8698
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    87378.016       8976.1230       642429.19       643396.13    


     CGMAT cycle number =      5

 Weight matrix   0.26264155    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    642031.13    

-------------------------------------------------------------------------------
             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 =     0.0401, B  =   -0.0768
Partial structure    1: scale =     0.3746, B  =   46.9845
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                        =     0.2096
Average Fourier shell correlation    =     0.9629
AverageFree Fourier shell correlation=     0.9515
Average correlation coefficient      =     0.9408
Overall figure of merit              =     0.8703
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    87330.594       8921.9014       642031.13       642429.19    


     CGMAT cycle number =      6

 Weight matrix   0.26305825    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    641896.38    

-------------------------------------------------------------------------------
             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 =     0.0401, B  =   -0.0802
Partial structure    1: scale =     0.3746, B  =   47.1045
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                     =     0.1588
Free R factor                        =     0.2094
Average Fourier shell correlation    =     0.9630
AverageFree Fourier shell correlation=     0.9516
Average correlation coefficient      =     0.9410
Overall figure of merit              =     0.8704
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    87308.914       8944.3438       641896.38       642031.13    


     CGMAT cycle number =      7

 Weight matrix   0.26321673    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    641803.69    

-------------------------------------------------------------------------------
             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 =     0.0401, B  =   -0.0780
Partial structure    1: scale =     0.3750, B  =   47.1957
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                        =     0.2093
Average Fourier shell correlation    =     0.9630
AverageFree Fourier shell correlation=     0.9516
Average correlation coefficient      =     0.9411
Overall figure of merit              =     0.8704
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    87293.961       8960.0039       641803.69       641896.38    


     CGMAT cycle number =      8

 Weight matrix   0.26341352    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    641686.75    

-------------------------------------------------------------------------------
             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  =   -0.0767
Partial structure    1: scale =     0.3749, B  =   47.1306
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                        =     0.2088
Average Fourier shell correlation    =     0.9631
AverageFree Fourier shell correlation=     0.9517
Average correlation coefficient      =     0.9412
Overall figure of merit              =     0.8705
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    87276.664       8968.4941       641686.75       641803.69    


     CGMAT cycle number =      9

 Weight matrix   0.26305750    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    641671.00    

-------------------------------------------------------------------------------
             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  =   -0.0768
Partial structure    1: scale =     0.3751, B  =   47.2008
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                        =     0.2088
Average Fourier shell correlation    =     0.9631
AverageFree Fourier shell correlation=     0.9517
Average correlation coefficient      =     0.9412
Overall figure of merit              =     0.8705
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    87275.023       8964.6055       641671.00       641686.75    


     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.= 0.944 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   0.26281077    
 Actual weight    7.2495699      is applied to the X-ray term
Norm of X_ray positional gradient                35.3
Norm of Geom. positional gradient                35.3
Norm of X_ray B-factor gradient                  118.
Norm of Geom. B-factor gradient                  122.
Product of X_ray and Geom posit. gradients     -0.121E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.462E+08
 Cosine of angle between them                      -0.992


Residuals: XRAY=     0.6327E+06 GEOM=      8969.     TOTAL=     0.6417E+06
 function value    641681.00    

-------------------------------------------------------------------------------
             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     1.785     1.644
Bond angles  : others                          3242     1.453     1.582
Torsion angles, period  1. refined              184     6.967     5.000
Torsion angles, period  2. refined               90    37.111    22.778
Torsion angles, period  3. refined              268    14.057    15.000
Torsion angles, period  4. refined                9    11.362    15.000
Chiral centres: refined atoms                   196     0.084     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   312     0.262     0.200
VDW repulsions.others                          1384     0.202     0.200
VDW; torsion: refined_atoms                     712     0.172     0.200
VDW; torsion.others                             786     0.084     0.200
HBOND: refined_atoms                            234     0.210     0.200
HBOND.others                                      1     0.036     0.200
VDW repulsions: symmetry: refined_atoms          10     0.244     0.200
VDW repulsions: symmetry: others                 27     0.175     0.200
HBOND: symmetry: refined_atoms                   18     0.257     0.200
HBOND: symmetry: others                           1     0.122     0.200
M. chain bond B values: refined atoms           745     1.603     1.201
M. chain bond B values: others                  745     1.602     1.201
M. chain angle B values: refined atoms          926     2.543     1.780
M. chain angle B values: others                 927     2.542     1.780
S. chain bond B values: refined atoms           811     2.626     1.554
S. chain bond B values: others                  810     2.623     1.554
S. chain angle B values: refined atoms         1177     4.117     2.180
S. chain angle B values: others                1178     4.115     2.180
Long range B values: refined atoms             1864     7.037    17.021
Long range B values: others                    1766     6.684    15.627
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.0776
Partial structure    1: scale =     0.3754, B  =   47.3015
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2188 100.00   480.2   485.0  0.16  0.17     123   508.4   508.1  0.19  0.20
 0.104    3733 100.00   386.2   368.3  0.16  0.15     191   398.4   382.4  0.22  0.20
 0.173    4703  99.96   248.8   243.5  0.15  0.13     239   246.0   243.0  0.20  0.17
 0.242    5508 100.00   188.8   190.1  0.17  0.13     296   191.3   195.2  0.22  0.17
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1511   0.934    677   0.840   2188   0.905  0.960  0.9717  0.9743  0.9304  0.9424
  0.1042   3040   0.887    693   0.772   3733   0.866  0.998  0.9512  0.9621  0.8912  0.9415
  0.1733   4014   0.896    689   0.797   4703   0.882  0.986  0.9554  0.9668  0.9062  0.9469
  0.2425   4812   0.865    699   0.751   5511   0.850  0.947  0.9405  0.9560  0.8604  0.9358
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16135
Percentage observed                  =    99.9823
Percentage of free reflections       =     4.9988
Overall R factor                     =     0.1585
Free R factor                        =     0.2088
Average Fourier shell correlation    =     0.9630
AverageFree Fourier shell correlation=     0.9516
Overall weighted R factor            =     0.1486
Free weighted R factor               =     0.1890
Overall weighted R2 factor           =     0.1824
Free weighted R2 factor              =     0.2159
Average correlation coefficient      =     0.9412
Overall correlation coefficient      =     0.9552
Free correlation coefficient         =     0.9295
Cruickshanks DPI for coordinate error=     0.1400
DPI based on free R factor           =     0.1362
Overall figure of merit              =     0.8704
ML based su of positional parameters =     0.0804
ML based su of thermal parameters    =     2.7065
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    87275.586       8969.3926       641681.13       641671.00    

 fvalues    87275.586       8969.3926       641686.25       641679.81    
 fvalues    87275.586       8969.3926       641686.25       641679.81    

    ****                              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.= 0.944 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_R19_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     1.786     1.644
Bond angles  : others                          3242     1.453     1.582
Torsion angles, period  1. refined              184     6.966     5.000
Torsion angles, period  2. refined               90    37.113    22.778
Torsion angles, period  3. refined              268    14.056    15.000
Torsion angles, period  4. refined                9    11.371    15.000
Chiral centres: refined atoms                   196     0.084     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   311     0.262     0.200
VDW repulsions.others                          1383     0.202     0.200
VDW; torsion: refined_atoms                     712     0.172     0.200
VDW; torsion.others                             790     0.084     0.200
HBOND: refined_atoms                            234     0.210     0.200
HBOND.others                                      1     0.037     0.200
VDW repulsions: symmetry: refined_atoms          10     0.244     0.200
VDW repulsions: symmetry: others                 27     0.175     0.200
HBOND: symmetry: refined_atoms                   18     0.257     0.200
HBOND: symmetry: others                           1     0.123     0.200
M. chain bond B values: refined atoms           745     1.603     1.201
M. chain bond B values: others                  745     1.602     1.201
M. chain angle B values: refined atoms          926     2.543     1.780
M. chain angle B values: others                 927     2.542     1.780
S. chain bond B values: refined atoms           811     2.627     1.555
S. chain bond B values: others                  810     2.623     1.554
S. chain angle B values: refined atoms         1177     4.117     2.180
S. chain angle B values: others                1178     4.116     2.180
Long range B values: refined atoms             1863     7.041    17.021
Long range B values: others                    1765     6.687    15.626
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.0797
Partial structure    1: scale =     0.3756, B  =   47.2826
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2188 100.00   480.2   485.0  0.16  0.17     123   508.4   508.3  0.19  0.20
 0.104    3733 100.00   386.2   368.3  0.16  0.15     191   398.3   382.4  0.22  0.20
 0.173    4703  99.96   248.8   243.5  0.15  0.13     239   246.0   243.1  0.20  0.17
 0.242    5508 100.00   188.8   190.1  0.17  0.13     296   191.3   195.2  0.22  0.17
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1511   0.934    677   0.840   2188   0.905  0.960  0.9716  0.9743  0.9302  0.9424
  0.1042   3040   0.887    693   0.772   3733   0.866  0.998  0.9512  0.9621  0.8912  0.9415
  0.1733   4014   0.896    689   0.797   4703   0.882  0.986  0.9554  0.9668  0.9061  0.9469
  0.2425   4812   0.865    699   0.751   5511   0.850  0.947  0.9405  0.9560  0.8603  0.9358
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16135
Percentage observed                  =    99.9823
Percentage of free reflections       =     4.9988
Overall R factor                     =     0.1585
Free R factor                        =     0.2090
Average Fourier shell correlation    =     0.9630
AverageFree Fourier shell correlation=     0.9516
Overall weighted R factor            =     0.1486
Free weighted R factor               =     0.1892
Overall weighted R2 factor           =     0.1824
Free weighted R2 factor              =     0.2160
Average correlation coefficient      =     0.9412
Overall correlation coefficient      =     0.9552
Free correlation coefficient         =     0.9294
Cruickshanks DPI for coordinate error=     0.1400
DPI based on free R factor           =     0.1363
Overall figure of merit              =     0.8704
ML based su of positional parameters =     0.0804
ML based su of thermal parameters    =     2.7065
-----------------------------------------------------------------------------
  Time in seconds: CPU =        13.65
             Elapsed =           0.00

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


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS: vs cycle :N:1,2,3:
:FOM vs cycle :N:1,4:
:-LL vs cycle :N:1,5:
:-LLfree vs cycle :N:1,6:
:Geometry vs cycle:N:1,7,8,9,10,11:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1630   0.2129   0.861       87970.    4802.4   0.0136  1.048   1.848  1.071   0.085
       1   0.1613   0.2115   0.868       87590.    4792.2   0.0118  0.864   1.764  1.017   0.086
       2   0.1599   0.2107   0.869       87453.    4787.4   0.0122  0.898   1.772  1.022   0.086
       3   0.1594   0.2101   0.870       87378.    4784.7   0.0123  0.906   1.774  1.024   0.085
       4   0.1590   0.2096   0.870       87331.    4782.6   0.0123  0.911   1.777  1.026   0.085
       5   0.1588   0.2094   0.870       87309.    4782.1   0.0123  0.914   1.780  1.027   0.085
       6   0.1586   0.2093   0.870       87294.    4781.8   0.0124  0.915   1.782  1.029   0.085
       7   0.1586   0.2088   0.870       87277.    4781.1   0.0124  0.916   1.784  1.029   0.085
       8   0.1585   0.2088   0.870       87275.    4781.3   0.0124  0.916   1.785  1.030   0.085
       9   0.1585   0.2088   0.870       87276.    4781.4   0.0124  0.916   1.785  1.030   0.084
      10   0.1585   0.2090   0.870       87276.    4781.6   0.0124  0.916   1.786  1.030   0.084
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1630   0.1585
             R free    0.2129   0.2090
     Rms BondLength    0.0136   0.0124
      Rms BondAngle    1.8479   1.7856
     Rms ChirVolume    0.0853   0.0845
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      45.8s System:    0.1s Elapsed:     0:46