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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: 14:24:19 


 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 2
  Data line--- END

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN   Filename: CDO_R.mtz 

 LABIN FP=FP SIGFP=SIGFP FREE=FreeR_flag

    ****                     Input and Default parameters#                      ****


Input coordinate file.  Logical name - XYZIN actual file name  - CDO_complete_R02_2-00A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R02_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_R02_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:     2
  Auto weighting. An attempt
  Refinement cycles       :    10
  Scaling type                           :
          Wilson scaling type with Guassians

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

  Scaling and SigmaA resln:    41.9635  1.9000

  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_R02_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=   2.023 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=   2.226 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=   1.842 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=   2.224 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=   2.358 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=   2.479 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=   2.046 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                            2
Number of "free" reflections        847
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.= 1.583 id.= 1.337 dev= -0.246 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.= 0.908 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   0.22998793    
 Actual weight    7.2495699      is applied to the X-ray term
Norm of X_ray positional gradient                41.9
Norm of Geom. positional gradient                88.6
Norm of X_ray B-factor gradient                  138.
Norm of Geom. B-factor gradient                 0.215E+05
Product of X_ray and Geom posit. gradients     -0.687E+07
 Cosine of angle between them                      -0.191
Product of X_ray and Geom B-fact gradients     -0.357E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.6387E+06 GEOM=     0.2627E+05 TOTAL=     0.6649E+06
 function value    664941.94    

-------------------------------------------------------------------------------
             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     1.845     1.644
Bond angles  : others                          3242     2.360     1.582
Torsion angles, period  1. refined              184     7.387     5.000
Torsion angles, period  2. refined               90    36.618    22.778
Torsion angles, period  3. refined              268    14.760    15.000
Torsion angles, period  4. refined                9    10.683    15.000
Chiral centres: refined atoms                   196     0.084     0.200
Planar groups: refined atoms                   1736     0.012     0.020
Planar groups: others                           331     0.016     0.020
VDW repulsions: refined_atoms                   325     0.257     0.200
VDW repulsions.others                          1348     0.231     0.200
VDW; torsion: refined_atoms                     720     0.170     0.200
VDW; torsion.others                             710     0.080     0.200
HBOND: refined_atoms                            226     0.211     0.200
HBOND.others                                      5     0.033     0.200
VDW repulsions: symmetry: refined_atoms          12     0.201     0.200
VDW repulsions: symmetry: others                 26     0.183     0.200
HBOND: symmetry: refined_atoms                   17     0.226     0.200
HBOND: symmetry: others                           1     0.031     0.200
M. chain bond B values: refined atoms           745     1.505     1.186
M. chain bond B values: others                  745     1.503     1.187
M. chain angle B values: refined atoms          926     2.444     1.761
M. chain angle B values: others                 927     2.443     1.761
S. chain bond B values: refined atoms           811     2.479     1.518
S. chain bond B values: others                  810     2.474     1.517
S. chain angle B values: refined atoms         1177     3.966     2.130
S. chain angle B values: others                1178     3.965     2.129
Long range B values: refined atoms             1875     6.913    16.703
Long range B values: others                    1781     6.593    15.473
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =    0.3440
Partial structure    1: scale =     0.3738, B  =   48.1242
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2185 100.00   481.3   486.4  0.15  0.17     126   451.0   464.9  0.21  0.22
 0.104    3732 100.00   385.3   368.8  0.15  0.15     192   381.4   371.5  0.21  0.19
 0.173    4681  99.96   248.2   242.6  0.16  0.14     261   236.0   236.3  0.24  0.20
 0.242    5536 100.00   188.0   188.2  0.19  0.15     268   191.5   198.3  0.23  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1511   0.928    674   0.830   2185   0.898  0.957  0.9655  0.9740  0.9093  0.9453
  0.1042   3037   0.894    695   0.795   3732   0.876  0.998  0.9561  0.9675  0.8981  0.9486
  0.1733   3988   0.861    693   0.764   4681   0.846  0.977  0.9323  0.9552  0.8513  0.9371
  0.2425   4840   0.868    699   0.760   5539   0.854  0.951  0.9430  0.9511  0.8825  0.9165
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16137
Percentage observed                  =    99.9823
Percentage of free reflections       =     4.9870
Overall R factor                     =     0.1631
Free R factor                        =     0.2228
Average Fourier shell correlation    =     0.9592
AverageFree Fourier shell correlation=     0.9460
Overall weighted R factor            =     0.1496
Free weighted R factor               =     0.2021
Overall weighted R2 factor           =     0.1795
Free weighted R2 factor              =     0.2365
Average correlation coefficient      =     0.9338
Overall correlation coefficient      =     0.9551
Free correlation coefficient         =     0.9166
Cruickshanks DPI for coordinate error=     0.1440
DPI based on free R factor           =     0.1453
Overall figure of merit              =     0.8629
ML based su of positional parameters =     0.0861
ML based su of thermal parameters    =     2.8962
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    88097.930       26269.787       664941.94      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.25521383    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    645387.56    

-------------------------------------------------------------------------------
             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  =   -0.0882
Partial structure    1: scale =     0.3740, B  =   47.7101
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                        =     0.2184
Average Fourier shell correlation    =     0.9623
AverageFree Fourier shell correlation=     0.9494
Average correlation coefficient      =     0.9379
Overall figure of merit              =     0.8715
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    87564.102       10585.502       645387.56       664941.94    


     CGMAT cycle number =      3

 Weight matrix   0.26000613    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    642775.94    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =   -0.0572
Partial structure    1: scale =     0.3741, B  =   45.8914
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1592
Free R factor                        =     0.2167
Average Fourier shell correlation    =     0.9631
AverageFree Fourier shell correlation=     0.9502
Average correlation coefficient      =     0.9396
Overall figure of merit              =     0.8729
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    87361.695       9441.2480       642775.94       645387.56    


     CGMAT cycle number =      4

 Weight matrix   0.26241818    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    641776.69    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =   -0.0492
Partial structure    1: scale =     0.3742, B  =   45.7636
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1586
Free R factor                        =     0.2157
Average Fourier shell correlation    =     0.9634
AverageFree Fourier shell correlation=     0.9506
Average correlation coefficient      =     0.9402
Overall figure of merit              =     0.8736
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    87275.750       9065.0830       641776.69       642775.94    


     CGMAT cycle number =      5

 Weight matrix   0.26411870    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    641382.25    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =   -0.0378
Partial structure    1: scale =     0.3742, B  =   45.8522
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1584
Free R factor                        =     0.2151
Average Fourier shell correlation    =     0.9636
AverageFree Fourier shell correlation=     0.9508
Average correlation coefficient      =     0.9405
Overall figure of merit              =     0.8740
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    87227.961       9017.0625       641382.25       641776.69    


     CGMAT cycle number =      6

 Weight matrix   0.26500809    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    641207.50    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =   -0.0436
Partial structure    1: scale =     0.3745, B  =   45.9009
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1583
Free R factor                        =     0.2147
Average Fourier shell correlation    =     0.9637
AverageFree Fourier shell correlation=     0.9509
Average correlation coefficient      =     0.9407
Overall figure of merit              =     0.8742
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    87201.031       9037.5273       641207.50       641382.25    


     CGMAT cycle number =      7

 Weight matrix   0.26599136    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    641076.25    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =   -0.0405
Partial structure    1: scale =     0.3746, B  =   45.8321
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1582
Free R factor                        =     0.2143
Average Fourier shell correlation    =     0.9638
AverageFree Fourier shell correlation=     0.9510
Average correlation coefficient      =     0.9407
Overall figure of merit              =     0.8745
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    87179.789       9060.2471       641076.25       641207.50    


     CGMAT cycle number =      8

 Weight matrix   0.26644540    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    641079.88    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =   -0.0432
Partial structure    1: scale =     0.3747, B  =   46.1992
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1583
Free R factor                        =     0.2144
Average Fourier shell correlation    =     0.9638
AverageFree Fourier shell correlation=     0.9511
Average correlation coefficient      =     0.9408
Overall figure of merit              =     0.8745
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    87178.164       9085.0547       641068.31       641076.25    
 fvalues    87178.164       9085.0547       641068.31       641089.25    


     CGMAT cycle number =      9

 Weight matrix   0.26635659    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    641024.50    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =   -0.0315
Partial structure    1: scale =     0.3751, B  =   46.1762
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1583
Free R factor                        =     0.2145
Average Fourier shell correlation    =     0.9638
AverageFree Fourier shell correlation=     0.9510
Average correlation coefficient      =     0.9408
Overall figure of merit              =     0.8745
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    87168.141       9093.0098       641024.50       641089.25    


     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.= 0.940 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   0.26625612    
 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                  119.
Norm of Geom. B-factor gradient                  121.
Product of X_ray and Geom posit. gradients     -0.126E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.467E+08
 Cosine of angle between them                      -0.999


Residuals: XRAY=     0.6319E+06 GEOM=      9096.     TOTAL=     0.6410E+06
 function value    640988.56    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.812     1.644
Bond angles  : others                          3242     1.462     1.582
Torsion angles, period  1. refined              184     7.027     5.000
Torsion angles, period  2. refined               90    36.748    22.778
Torsion angles, period  3. refined              268    14.424    15.000
Torsion angles, period  4. refined                9    10.971    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   300     0.271     0.200
VDW repulsions.others                          1368     0.206     0.200
VDW; torsion: refined_atoms                     723     0.172     0.200
VDW; torsion.others                             783     0.085     0.200
HBOND: refined_atoms                            221     0.205     0.200
HBOND.others                                      2     0.049     0.200
VDW repulsions: symmetry: refined_atoms          10     0.219     0.200
VDW repulsions: symmetry: others                 28     0.178     0.200
HBOND: symmetry: refined_atoms                   22     0.191     0.200
HBOND: symmetry: others                           1     0.051     0.200
M. chain bond B values: refined atoms           745     1.571     1.212
M. chain bond B values: others                  745     1.570     1.213
M. chain angle B values: refined atoms          926     2.499     1.800
M. chain angle B values: others                 927     2.498     1.800
S. chain bond B values: refined atoms           811     2.763     1.576
S. chain bond B values: others                  810     2.760     1.576
S. chain angle B values: refined atoms         1177     4.346     2.205
S. chain angle B values: others                1178     4.345     2.205
Long range B values: refined atoms             1844     7.096    16.868
Long range B values: others                    1755     6.818    15.640
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =   -0.0324
Partial structure    1: scale =     0.3751, B  =   46.1462
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10.  v. resln :N:1,6,7,11,12:
:Cycle   10.  and  v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2185 100.00   480.9   487.0  0.15  0.17     126   450.7   464.6  0.21  0.22
 0.104    3732 100.00   385.0   368.0  0.16  0.15     192   381.1   365.6  0.20  0.18
 0.173    4681  99.96   248.0   242.3  0.16  0.14     261   235.8   235.8  0.23  0.19
 0.242    5536 100.00   187.8   188.2  0.16  0.13     268   191.4   199.1  0.22  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1511   0.940    674   0.848   2185   0.912  0.959  0.9679  0.9759  0.9082  0.9446
  0.1042   3037   0.902    695   0.805   3732   0.884  0.998  0.9596  0.9693  0.9057  0.9478
  0.1733   3988   0.868    693   0.771   4681   0.853  0.979  0.9368  0.9570  0.8654  0.9361
  0.2425   4840   0.885    699   0.777   5539   0.871  0.955  0.9508  0.9611  0.8932  0.9388
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16137
Percentage observed                  =    99.9823
Percentage of free reflections       =     4.9870
Overall R factor                     =     0.1582
Free R factor                        =     0.2146
Average Fourier shell correlation    =     0.9638
AverageFree Fourier shell correlation=     0.9510
Overall weighted R factor            =     0.1476
Free weighted R factor               =     0.1949
Overall weighted R2 factor           =     0.1796
Free weighted R2 factor              =     0.2286
Average correlation coefficient      =     0.9409
Overall correlation coefficient      =     0.9565
Free correlation coefficient         =     0.9206
Cruickshanks DPI for coordinate error=     0.1397
DPI based on free R factor           =     0.1399
Overall figure of merit              =     0.8744
ML based su of positional parameters =     0.0799
ML based su of thermal parameters    =     2.6693
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    87162.828       9095.5693       640988.56       641024.50    

    ****                              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_R02_1-90A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.813     1.644
Bond angles  : others                          3242     1.463     1.582
Torsion angles, period  1. refined              184     7.021     5.000
Torsion angles, period  2. refined               90    36.721    22.778
Torsion angles, period  3. refined              268    14.384    15.000
Torsion angles, period  4. refined                9    10.985    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   302     0.271     0.200
VDW repulsions.others                          1368     0.206     0.200
VDW; torsion: refined_atoms                     722     0.173     0.200
VDW; torsion.others                             785     0.085     0.200
HBOND: refined_atoms                            221     0.205     0.200
HBOND.others                                      2     0.054     0.200
VDW repulsions: symmetry: refined_atoms          10     0.218     0.200
VDW repulsions: symmetry: others                 29     0.175     0.200
HBOND: symmetry: refined_atoms                   22     0.191     0.200
HBOND: symmetry: others                           1     0.053     0.200
M. chain bond B values: refined atoms           745     1.573     1.212
M. chain bond B values: others                  745     1.571     1.213
M. chain angle B values: refined atoms          926     2.502     1.800
M. chain angle B values: others                 927     2.501     1.800
S. chain bond B values: refined atoms           811     2.766     1.576
S. chain bond B values: others                  810     2.762     1.576
S. chain angle B values: refined atoms         1177     4.349     2.206
S. chain angle B values: others                1178     4.347     2.205
Long range B values: refined atoms             1845     7.099    16.823
Long range B values: others                    1755     6.809    15.579
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =   -0.0302
Partial structure    1: scale =     0.3749, B  =   46.0508
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2185 100.00   480.9   486.9  0.15  0.17     126   450.6   464.6  0.21  0.22
 0.104    3732 100.00   385.0   368.0  0.16  0.15     192   381.1   365.3  0.20  0.18
 0.173    4681  99.96   248.0   242.3  0.16  0.14     261   235.8   235.8  0.23  0.19
 0.242    5536 100.00   187.8   188.2  0.16  0.13     268   191.4   199.0  0.22  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1511   0.940    674   0.848   2185   0.912  0.959  0.9678  0.9760  0.9079  0.9447
  0.1042   3037   0.902    695   0.805   3732   0.884  0.998  0.9596  0.9693  0.9058  0.9478
  0.1733   3988   0.867    693   0.771   4681   0.853  0.979  0.9367  0.9569  0.8652  0.9361
  0.2425   4840   0.885    699   0.777   5539   0.872  0.955  0.9509  0.9612  0.8932  0.9389
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16137
Percentage observed                  =    99.9823
Percentage of free reflections       =     4.9870
Overall R factor                     =     0.1582
Free R factor                        =     0.2147
Average Fourier shell correlation    =     0.9638
AverageFree Fourier shell correlation=     0.9510
Overall weighted R factor            =     0.1476
Free weighted R factor               =     0.1950
Overall weighted R2 factor           =     0.1796
Free weighted R2 factor              =     0.2284
Average correlation coefficient      =     0.9409
Overall correlation coefficient      =     0.9565
Free correlation coefficient         =     0.9205
Cruickshanks DPI for coordinate error=     0.1397
DPI based on free R factor           =     0.1400
Overall figure of merit              =     0.8744
ML based su of positional parameters =     0.0799
ML based su of thermal parameters    =     2.6693
-----------------------------------------------------------------------------
  Time in seconds: CPU =        12.89
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1631   0.2228   0.863       88098.    4780.0   0.0141  1.085   1.845  1.070   0.084
       1   0.1607   0.2184   0.871       87564.    4762.5   0.0120  0.865   1.757  1.013   0.086
       2   0.1592   0.2167   0.873       87362.    4756.9   0.0126  0.913   1.778  1.024   0.087
       3   0.1586   0.2157   0.874       87276.    4753.8   0.0127  0.920   1.788  1.030   0.087
       4   0.1584   0.2151   0.874       87228.    4751.7   0.0127  0.925   1.795  1.034   0.087
       5   0.1583   0.2147   0.874       87201.    4750.2   0.0127  0.928   1.801  1.037   0.087
       6   0.1582   0.2143   0.875       87180.    4748.4   0.0127  0.929   1.805  1.040   0.087
       7   0.1583   0.2144   0.874       87177.    4748.5   0.0128  0.932   1.809  1.042   0.087
       8   0.1583   0.2145   0.874       87168.    4748.4   0.0128  0.932   1.811  1.044   0.087
       9   0.1582   0.2146   0.874       87163.    4748.4   0.0128  0.931   1.812  1.045   0.087
      10   0.1582   0.2147   0.874       87157.    4748.3   0.0127  0.931   1.813  1.045   0.087
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1631   0.1582
             R free    0.2228   0.2147
     Rms BondLength    0.0141   0.0127
      Rms BondAngle    1.8454   1.8129
     Rms ChirVolume    0.0842   0.0867
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      44.9s System:    0.1s Elapsed:     0:45