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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
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 User: maly  Run date: 26/ 5/2020 Run time: 14:29:08 


 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 4
  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_R04_2-00A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R04_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_R04_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:     4
  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_R04_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=   2.041 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=   2.232 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=   1.829 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=   2.234 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=   2.353 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=   2.441 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=   2.065 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                            4
Number of "free" reflections        854
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.= 1.480 id.= 1.337 dev= -0.143 sig.= 0.011
A    125 LEU C   . - A    126 ARG N   . mod.= 1.579 id.= 1.337 dev= -0.242 sig.= 0.011

    ****                          Bond angle outliers                           ****

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

A     10 ARG O     - A     11 THR N     mod.= 105.62 id.= 123.47 dev= 17.851 sig.=  1.500

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

Deviations from the planarity >10.000Sigma will be monitored
Atom: A     10 ARG C     deviation=   0.24 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.= 0.892 id.= 3.000 dev= -2.11 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   0.22417755    
 Actual weight    7.2495699      is applied to the X-ray term
Norm of X_ray positional gradient                41.3
Norm of Geom. positional gradient                90.1
Norm of X_ray B-factor gradient                  135.
Norm of Geom. B-factor gradient                 0.208E+05
Product of X_ray and Geom posit. gradients     -0.649E+07
 Cosine of angle between them                      -0.180
Product of X_ray and Geom B-fact gradients     -0.349E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.6388E+06 GEOM=     0.2593E+05 TOTAL=     0.6647E+06
 function value    664722.31    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.014     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.849     1.644
Bond angles  : others                          3242     2.354     1.582
Torsion angles, period  1. refined              184     7.367     5.000
Torsion angles, period  2. refined               90    37.235    22.778
Torsion angles, period  3. refined              268    14.879    15.000
Torsion angles, period  4. refined                9    10.426    15.000
Chiral centres: refined atoms                   196     0.085     0.200
Planar groups: refined atoms                   1736     0.013     0.020
Planar groups: others                           331     0.014     0.020
VDW repulsions: refined_atoms                   319     0.262     0.200
VDW repulsions.others                          1348     0.232     0.200
VDW; torsion: refined_atoms                     709     0.170     0.200
VDW; torsion.others                             702     0.080     0.200
HBOND: refined_atoms                            238     0.212     0.200
HBOND.others                                      3     0.068     0.200
VDW repulsions: symmetry: refined_atoms           8     0.256     0.200
VDW repulsions: symmetry: others                 25     0.179     0.200
HBOND: symmetry: refined_atoms                   17     0.241     0.200
HBOND: symmetry: others                           1     0.086     0.200
M. chain bond B values: refined atoms           745     1.544     1.194
M. chain bond B values: others                  745     1.543     1.195
M. chain angle B values: refined atoms          926     2.511     1.773
M. chain angle B values: others                 927     2.510     1.773
S. chain bond B values: refined atoms           811     2.498     1.532
S. chain bond B values: others                  810     2.495     1.532
S. chain angle B values: refined atoms         1177     3.991     2.151
S. chain angle B values: others                1178     3.989     2.150
Long range B values: refined atoms             1873     6.910    16.798
Long range B values: others                    1775     6.596    15.511
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =    0.3102
Partial structure    1: scale =     0.3752, B  =   49.0895
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2193 100.00   480.7   483.7  0.15  0.16     118   465.5   480.9  0.18  0.19
 0.104    3720 100.00   385.2   369.5  0.16  0.15     204   388.4   364.1  0.20  0.19
 0.173    4698  99.96   248.0   242.2  0.16  0.14     244   242.2   243.2  0.23  0.19
 0.242    5516 100.00   188.0   188.5  0.19  0.15     288   192.5   192.7  0.22  0.17
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1509   0.934    684   0.845   2193   0.906  0.972  0.9742  0.9745  0.9448  0.9454
  0.1042   3026   0.897    694   0.795   3720   0.878  0.998  0.9601  0.9668  0.9259  0.9462
  0.1733   4013   0.862    685   0.760   4698   0.847  0.976  0.9384  0.9557  0.8693  0.9382
  0.2425   4810   0.863    709   0.753   5519   0.849  0.950  0.9408  0.9492  0.8835  0.9150
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16130
Percentage observed                  =    99.9823
Percentage of free reflections       =     5.0283
Overall R factor                     =     0.1630
Free R factor                        =     0.2057
Average Fourier shell correlation    =     0.9586
AverageFree Fourier shell correlation=     0.9493
Overall weighted R factor            =     0.1487
Free weighted R factor               =     0.1888
Overall weighted R2 factor           =     0.1779
Free weighted R2 factor              =     0.2240
Average correlation coefficient      =     0.9331
Overall correlation coefficient      =     0.9546
Free correlation coefficient         =     0.9334
Cruickshanks DPI for coordinate error=     0.1440
DPI based on free R factor           =     0.1341
Overall figure of merit              =     0.8630
ML based su of positional parameters =     0.0872
ML based su of thermal parameters    =     2.9455
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    88114.406       25930.770       664722.31      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.23687871    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    646267.31    

-------------------------------------------------------------------------------
             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  =   -0.1298
Partial structure    1: scale =     0.3748, B  =   48.8529
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                     =     0.1605
Free R factor                        =     0.2039
Average Fourier shell correlation    =     0.9609
AverageFree Fourier shell correlation=     0.9514
Average correlation coefficient      =     0.9373
Overall figure of merit              =     0.8674
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    87688.352       10564.470       646267.31       664722.31    


     CGMAT cycle number =      3

 Weight matrix   0.24042638    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    644016.94    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =   -0.0736
Partial structure    1: scale =     0.3757, B  =   47.0704
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                     =     0.1593
Free R factor                        =     0.2031
Average Fourier shell correlation    =     0.9615
AverageFree Fourier shell correlation=     0.9519
Average correlation coefficient      =     0.9385
Overall figure of merit              =     0.8684
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    87554.242       9286.3145       644016.94       646267.31    


     CGMAT cycle number =      4

 Weight matrix   0.24334702    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    643184.00    

-------------------------------------------------------------------------------
             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 =     0.0403, B  =   -0.0675
Partial structure    1: scale =     0.3760, B  =   46.9855
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                     =     0.1589
Free R factor                        =     0.2030
Average Fourier shell correlation    =     0.9618
AverageFree Fourier shell correlation=     0.9522
Average correlation coefficient      =     0.9391
Overall figure of merit              =     0.8690
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    87497.211       8866.8867       643184.00       644016.94    


     CGMAT cycle number =      5

 Weight matrix   0.24553040    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    642742.13    

-------------------------------------------------------------------------------
             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 =     0.0403, B  =   -0.1184
Partial structure    1: scale =     0.3761, B  =   46.9953
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                        =     0.2031
Average Fourier shell correlation    =     0.9620
AverageFree Fourier shell correlation=     0.9525
Average correlation coefficient      =     0.9394
Overall figure of merit              =     0.8695
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    87450.078       8766.7080       642742.13       643184.00    


     CGMAT cycle number =      6

 Weight matrix   0.24642287    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    642477.06    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =   -0.0847
Partial structure    1: scale =     0.3806, B  =   47.6808
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                        =     0.2030
Average Fourier shell correlation    =     0.9621
AverageFree Fourier shell correlation=     0.9526
Average correlation coefficient      =     0.9396
Overall figure of merit              =     0.8697
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    87408.297       8804.5215       642477.06       642742.13    


     CGMAT cycle number =      7

 Weight matrix   0.24658298    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    642382.25    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =   -0.0986
Partial structure    1: scale =     0.3809, B  =   47.6471
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                        =     0.2031
Average Fourier shell correlation    =     0.9622
AverageFree Fourier shell correlation=     0.9526
Average correlation coefficient      =     0.9397
Overall figure of merit              =     0.8697
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    87395.250       8804.2734       642382.25       642477.06    


     CGMAT cycle number =      8

 Weight matrix   0.24701467    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    642252.06    

-------------------------------------------------------------------------------
             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 =     0.0404, B  =   -0.0934
Partial structure    1: scale =     0.3812, B  =   47.6881
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1584
Free R factor                        =     0.2034
Average Fourier shell correlation    =     0.9622
AverageFree Fourier shell correlation=     0.9526
Average correlation coefficient      =     0.9398
Overall figure of merit              =     0.8697
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    87375.859       8814.7070       642252.06       642382.25    


     CGMAT cycle number =      9

 Weight matrix   0.24706696    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    642184.94    

-------------------------------------------------------------------------------
             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 =     0.0404, B  =   -0.0885
Partial structure    1: scale =     0.3814, B  =   47.6223
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1583
Free R factor                        =     0.2037
Average Fourier shell correlation    =     0.9623
AverageFree Fourier shell correlation=     0.9526
Average correlation coefficient      =     0.9398
Overall figure of merit              =     0.8697
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    87367.156       8810.6162       642184.94       642252.06    


     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.= 0.925 id.= 3.000 dev= -2.08 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   0.24698207    
 Actual weight    7.2495699      is applied to the X-ray term
Norm of X_ray positional gradient                34.3
Norm of Geom. positional gradient                34.3
Norm of X_ray B-factor gradient                  112.
Norm of Geom. B-factor gradient                  116.
Product of X_ray and Geom posit. gradients     -0.114E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.413E+08
 Cosine of angle between them                      -0.989


Residuals: XRAY=     0.6333E+06 GEOM=      8812.     TOTAL=     0.6421E+06
 function value    642146.38    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2103     1.770     1.644
Bond angles  : others                          3242     1.431     1.582
Torsion angles, period  1. refined              184     7.022     5.000
Torsion angles, period  2. refined               90    37.183    22.778
Torsion angles, period  3. refined              268    14.354    15.000
Torsion angles, period  4. refined                9    10.844    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                   306     0.269     0.200
VDW repulsions.others                          1384     0.206     0.200
VDW; torsion: refined_atoms                     710     0.171     0.200
VDW; torsion.others                             785     0.083     0.200
HBOND: refined_atoms                            240     0.205     0.200
HBOND.others                                      2     0.070     0.200
VDW repulsions: symmetry: refined_atoms          10     0.233     0.200
VDW repulsions: symmetry: others                 25     0.195     0.200
HBOND: symmetry: refined_atoms                   22     0.204     0.200
HBOND: symmetry: others                           1     0.085     0.200
M. chain bond B values: refined atoms           745     1.572     1.221
M. chain bond B values: others                  745     1.571     1.221
M. chain angle B values: refined atoms          926     2.520     1.813
M. chain angle B values: others                 927     2.519     1.812
S. chain bond B values: refined atoms           811     2.708     1.584
S. chain bond B values: others                  810     2.704     1.584
S. chain angle B values: refined atoms         1177     4.279     2.221
S. chain angle B values: others                1178     4.278     2.220
Long range B values: refined atoms             1862     7.106    17.279
Long range B values: others                    1767     6.782    15.961
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =   -0.0891
Partial structure    1: scale =     0.3814, B  =   47.4540
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2193 100.00   480.1   483.8  0.15  0.16     118   464.8   479.9  0.18  0.19
 0.104    3720 100.00   384.7   368.5  0.16  0.15     204   387.9   362.5  0.20  0.19
 0.173    4698  99.96   247.7   241.8  0.16  0.14     244   241.9   244.5  0.24  0.20
 0.242    5516 100.00   187.7   188.4  0.16  0.13     288   192.3   192.7  0.20  0.16
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle   10. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1509   0.941    684   0.854   2193   0.913  0.972  0.9750  0.9753  0.9449  0.9434
  0.1042   3026   0.902    694   0.800   3720   0.883  0.998  0.9622  0.9684  0.9288  0.9465
  0.1733   4013   0.865    685   0.762   4698   0.850  0.976  0.9390  0.9564  0.8660  0.9369
  0.2425   4810   0.874    709   0.763   5519   0.860  0.955  0.9481  0.9580  0.8979  0.9366
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16130
Percentage observed                  =    99.9823
Percentage of free reflections       =     5.0283
Overall R factor                     =     0.1583
Free R factor                        =     0.2040
Average Fourier shell correlation    =     0.9623
AverageFree Fourier shell correlation=     0.9526
Overall weighted R factor            =     0.1468
Free weighted R factor               =     0.1880
Overall weighted R2 factor           =     0.1777
Free weighted R2 factor              =     0.2243
Average correlation coefficient      =     0.9399
Overall correlation coefficient      =     0.9560
Free correlation coefficient         =     0.9349
Cruickshanks DPI for coordinate error=     0.1399
DPI based on free R factor           =     0.1331
Overall figure of merit              =     0.8696
ML based su of positional parameters =     0.0830
ML based su of thermal parameters    =     2.7935
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    87361.688       8811.7148       642146.38       642184.94    

    ****                              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.= 0.926 id.= 3.000 dev= -2.07 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 LABOUT FreeR_flag=FreeR_flag FP=FP SIGFP=SIGFP FC=FC PHIC=PHIC FC_ALL=FC_ALL PHIC_ALL=PHIC_ALL FWT=FWT PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM FC_ALL_LS=FC_ALL_LS PHIC_ALL_LS=PHIC_ALL_LS

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R04_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     1.770     1.644
Bond angles  : others                          3242     1.431     1.582
Torsion angles, period  1. refined              184     7.020     5.000
Torsion angles, period  2. refined               90    37.177    22.778
Torsion angles, period  3. refined              268    14.336    15.000
Torsion angles, period  4. refined                9    10.868    15.000
Chiral centres: refined atoms                   196     0.084     0.200
Planar groups: refined atoms                   1736     0.009     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   308     0.268     0.200
VDW repulsions.others                          1381     0.206     0.200
VDW; torsion: refined_atoms                     710     0.171     0.200
VDW; torsion.others                             785     0.083     0.200
HBOND: refined_atoms                            239     0.206     0.200
HBOND.others                                      2     0.074     0.200
VDW repulsions: symmetry: refined_atoms          10     0.233     0.200
VDW repulsions: symmetry: others                 26     0.192     0.200
HBOND: symmetry: refined_atoms                   23     0.200     0.200
HBOND: symmetry: others                           1     0.086     0.200
M. chain bond B values: refined atoms           745     1.573     1.222
M. chain bond B values: others                  745     1.572     1.222
M. chain angle B values: refined atoms          926     2.522     1.814
M. chain angle B values: others                 927     2.521     1.813
S. chain bond B values: refined atoms           811     2.708     1.585
S. chain bond B values: others                  810     2.704     1.584
S. chain angle B values: refined atoms         1177     4.278     2.222
S. chain angle B values: others                1178     4.276     2.221
Long range B values: refined atoms             1863     7.102    17.270
Long range B values: others                    1768     6.774    15.952
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =   -0.0889
Partial structure    1: scale =     0.3814, B  =   47.4032
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2193 100.00   480.0   483.7  0.15  0.16     118   464.8   479.7  0.18  0.19
 0.104    3720 100.00   384.7   368.4  0.16  0.15     204   387.9   362.2  0.20  0.19
 0.173    4698  99.96   247.6   241.7  0.16  0.14     244   241.8   244.5  0.24  0.20
 0.242    5516 100.00   187.7   188.4  0.16  0.13     288   192.3   192.5  0.20  0.16
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1509   0.940    684   0.853   2193   0.913  0.972  0.9748  0.9752  0.9443  0.9434
  0.1042   3026   0.902    694   0.799   3720   0.883  0.998  0.9621  0.9683  0.9286  0.9466
  0.1733   4013   0.865    685   0.762   4698   0.850  0.976  0.9390  0.9563  0.8659  0.9368
  0.2425   4810   0.874    709   0.763   5519   0.860  0.955  0.9480  0.9580  0.8977  0.9367
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16130
Percentage observed                  =    99.9823
Percentage of free reflections       =     5.0283
Overall R factor                     =     0.1583
Free R factor                        =     0.2045
Average Fourier shell correlation    =     0.9622
AverageFree Fourier shell correlation=     0.9525
Overall weighted R factor            =     0.1468
Free weighted R factor               =     0.1886
Overall weighted R2 factor           =     0.1776
Free weighted R2 factor              =     0.2258
Average correlation coefficient      =     0.9399
Overall correlation coefficient      =     0.9560
Free correlation coefficient         =     0.9346
Cruickshanks DPI for coordinate error=     0.1399
DPI based on free R factor           =     0.1333
Overall figure of merit              =     0.8694
ML based su of positional parameters =     0.0830
ML based su of thermal parameters    =     2.7935
-----------------------------------------------------------------------------
  Time in seconds: CPU =        11.94
             Elapsed =         128.00

    ****           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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1630   0.2057   0.863       88114.    4811.9   0.0139  1.092   1.849  1.074   0.085
       1   0.1605   0.2039   0.867       87688.    4799.5   0.0116  0.846   1.751  1.009   0.085
       2   0.1593   0.2031   0.868       87554.    4795.0   0.0119  0.871   1.757  1.013   0.085
       3   0.1589   0.2030   0.869       87497.    4792.3   0.0119  0.877   1.761  1.016   0.084
       4   0.1586   0.2031   0.870       87450.    4791.1   0.0120  0.881   1.764  1.018   0.085
       5   0.1585   0.2030   0.870       87408.    4789.6   0.0120  0.882   1.766  1.020   0.085
       6   0.1585   0.2031   0.870       87395.    4789.2   0.0120  0.882   1.767  1.021   0.085
       7   0.1584   0.2034   0.870       87376.    4788.6   0.0120  0.881   1.768  1.022   0.084
       8   0.1583   0.2037   0.870       87367.    4788.3   0.0120  0.881   1.769  1.023   0.084
       9   0.1583   0.2040   0.870       87362.    4788.6   0.0120  0.882   1.770  1.023   0.084
      10   0.1583   0.2045   0.869       87361.    4789.2   0.0120  0.881   1.770  1.023   0.084
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1630   0.1583
             R free    0.2057   0.2045
     Rms BondLength    0.0139   0.0120
      Rms BondAngle    1.8493   1.7702
     Rms ChirVolume    0.0845   0.0844
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      44.0s System:    0.1s Elapsed:     0:44