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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 26/ 5/2020 Run time: 15:03:17 


 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 18
  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_R18_2-00A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R18_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_R18_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:    18
  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_R18_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=   2.034 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=   2.236 ideal_dist=   2.090
            ch:AAA  res:  88  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   1.848 ideal_dist=   1.720
            ch:AAA  res:  93  CYS              at:SG  .->ch:AAA  res: 157  TYR              at:CE1 .
  INFO:     link is found (not be used) dist=   2.221 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=   2.343 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=   2.435 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=   2.033 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                           18
Number of "free" reflections        871
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.= 1.567 id.= 1.337 dev= -0.230 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.= 0.912 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   0.21822010    
 Actual weight    7.2495699      is applied to the X-ray term
Norm of X_ray positional gradient                39.0
Norm of Geom. positional gradient                87.2
Norm of X_ray B-factor gradient                  130.
Norm of Geom. B-factor gradient                 0.221E+05
Product of X_ray and Geom posit. gradients     -0.642E+07
 Cosine of angle between them                      -0.195
Product of X_ray and Geom B-fact gradients     -0.347E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.6387E+06 GEOM=     0.2635E+05 TOTAL=     0.6650E+06
 function value    665032.06    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.801     1.644
Bond angles  : others                          3242     2.349     1.582
Torsion angles, period  1. refined              184     7.263     5.000
Torsion angles, period  2. refined               90    36.618    22.778
Torsion angles, period  3. refined              268    14.884    15.000
Torsion angles, period  4. refined                9    11.639    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                   330     0.252     0.200
VDW repulsions.others                          1340     0.230     0.200
VDW; torsion: refined_atoms                     711     0.170     0.200
VDW; torsion.others                             706     0.079     0.200
HBOND: refined_atoms                            235     0.209     0.200
HBOND.others                                      3     0.079     0.200
VDW repulsions: symmetry: refined_atoms          14     0.201     0.200
VDW repulsions: symmetry: others                 29     0.168     0.200
HBOND: symmetry: refined_atoms                   17     0.274     0.200
HBOND: symmetry: others                           1     0.140     0.200
M. chain bond B values: refined atoms           745     1.519     1.189
M. chain bond B values: others                  745     1.518     1.190
M. chain angle B values: refined atoms          926     2.486     1.765
M. chain angle B values: others                 927     2.485     1.765
S. chain bond B values: refined atoms           811     2.400     1.517
S. chain bond B values: others                  810     2.396     1.517
S. chain angle B values: refined atoms         1177     3.840     2.132
S. chain angle B values: others                1178     3.839     2.131
Long range B values: refined atoms             1883     6.858    16.871
Long range B values: others                    1785     6.500    15.534
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =    0.3279
Partial structure    1: scale =     0.3758, B  =   48.9330
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2184 100.00   477.2   481.3  0.15  0.16     127   523.7   536.3  0.17  0.19
 0.104    3720 100.00   384.8   367.9  0.16  0.15     204   393.0   377.4  0.22  0.20
 0.173    4688  99.96   248.0   242.5  0.16  0.13     254   240.9   240.5  0.24  0.20
 0.242    5518 100.00   188.1   188.5  0.19  0.15     286   189.8   191.6  0.22  0.17
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1508   0.923    676   0.821   2184   0.891  0.957  0.9712  0.9732  0.9289  0.9465
  0.1042   3030   0.876    690   0.766   3720   0.855  0.994  0.9486  0.9595  0.9041  0.9426
  0.1733   3998   0.869    690   0.770   4688   0.855  0.980  0.9387  0.9584  0.8660  0.9403
  0.2425   4819   0.860    702   0.749   5521   0.846  0.947  0.9434  0.9492  0.8927  0.9159
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16113
Percentage observed                  =    99.9823
Percentage of free reflections       =     5.1284
Overall R factor                     =     0.1639
Free R factor                        =     0.2097
Average Fourier shell correlation    =     0.9575
AverageFree Fourier shell correlation=     0.9473
Overall weighted R factor            =     0.1503
Free weighted R factor               =     0.1928
Overall weighted R2 factor           =     0.1803
Free weighted R2 factor              =     0.2299
Average correlation coefficient      =     0.9333
Overall correlation coefficient      =     0.9540
Free correlation coefficient         =     0.9308
Cruickshanks DPI for coordinate error=     0.1450
DPI based on free R factor           =     0.1369
Overall figure of merit              =     0.8567
ML based su of positional parameters =     0.0884
ML based su of thermal parameters    =     2.9574
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    88098.648       26354.723       665032.06      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.24153991    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    645168.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.011     0.013
Bond distances: others                         1393     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =   -0.1215
Partial structure    1: scale =     0.3751, B  =   48.8427
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                     =     0.1615
Free R factor                        =     0.2072
Average Fourier shell correlation    =     0.9609
AverageFree Fourier shell correlation=     0.9505
Average correlation coefficient      =     0.9373
Overall figure of merit              =     0.8660
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    87568.563       10333.807       645168.25       665032.06    


     CGMAT cycle number =      3

 Weight matrix   0.24669337    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    642567.25    

-------------------------------------------------------------------------------
             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  =   -0.0690
Partial structure    1: scale =     0.3758, B  =   46.6804
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                     =     0.1599
Free R factor                        =     0.2059
Average Fourier shell correlation    =     0.9618
AverageFree Fourier shell correlation=     0.9514
Average correlation coefficient      =     0.9390
Overall figure of merit              =     0.8676
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    87374.852       9137.1650       642567.25       645168.25    


     CGMAT cycle number =      4

 Weight matrix   0.24868053    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    641634.94    

-------------------------------------------------------------------------------
             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  =   -0.0610
Partial structure    1: scale =     0.3761, B  =   46.6889
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                     =     0.1593
Free R factor                        =     0.2055
Average Fourier shell correlation    =     0.9621
AverageFree Fourier shell correlation=     0.9517
Average correlation coefficient      =     0.9397
Overall figure of merit              =     0.8681
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    87300.367       8744.8311       641634.94       642567.25    


     CGMAT cycle number =      5

 Weight matrix   0.24991925    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    641217.25    

-------------------------------------------------------------------------------
             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  =   -0.0410
Partial structure    1: scale =     0.3765, B  =   46.8522
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                     =     0.1590
Free R factor                        =     0.2055
Average Fourier shell correlation    =     0.9623
AverageFree Fourier shell correlation=     0.9519
Average correlation coefficient      =     0.9401
Overall figure of merit              =     0.8685
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    87251.695       8679.9814       641217.25       641634.94    


     CGMAT cycle number =      6

 Weight matrix   0.25005075    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    641086.06    

-------------------------------------------------------------------------------
             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 =     0.0404, B  =   -0.0475
Partial structure    1: scale =     0.3766, B  =   46.8519
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                     =     0.1589
Free R factor                        =     0.2058
Average Fourier shell correlation    =     0.9624
AverageFree Fourier shell correlation=     0.9519
Average correlation coefficient      =     0.9403
Overall figure of merit              =     0.8685
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    87231.875       8692.5273       641086.06       641217.25    


     CGMAT cycle number =      7

 Weight matrix   0.24995197    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    641037.19    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =   -0.0502
Partial structure    1: scale =     0.3766, B  =   46.9338
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                     =     0.1588
Free R factor                        =     0.2061
Average Fourier shell correlation    =     0.9624
AverageFree Fourier shell correlation=     0.9519
Average correlation coefficient      =     0.9405
Overall figure of merit              =     0.8684
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    87224.156       8699.5791       641037.19       641086.06    


     CGMAT cycle number =      8

 Weight matrix   0.24965787    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    640988.00    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =   -0.0463
Partial structure    1: scale =     0.3764, B  =   46.8939
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1587
Free R factor                        =     0.2066
Average Fourier shell correlation    =     0.9624
AverageFree Fourier shell correlation=     0.9518
Average correlation coefficient      =     0.9407
Overall figure of merit              =     0.8683
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    87217.023       8702.0371       640988.00       641037.19    


     CGMAT cycle number =      9

 Weight matrix   0.24913435    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    640988.44    

-------------------------------------------------------------------------------
             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  =   -0.0431
Partial structure    1: scale =     0.3764, B  =   46.7800
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1587
Free R factor                        =     0.2068
Average Fourier shell correlation    =     0.9624
AverageFree Fourier shell correlation=     0.9517
Average correlation coefficient      =     0.9407
Overall figure of merit              =     0.8681
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    87219.773       8690.2920       641006.06       640988.00    

 fvalues    87219.773       8690.2920       640992.63       640996.13    
 fvalues    87219.773       8690.2920       640992.63       640996.13    


     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.= 0.936 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   0.24883209    
 Actual weight    7.2495699      is applied to the X-ray term
Norm of X_ray positional gradient                34.2
Norm of Geom. positional gradient                34.2
Norm of X_ray B-factor gradient                  115.
Norm of Geom. B-factor gradient                  118.
Product of X_ray and Geom posit. gradients     -0.113E+08
 Cosine of angle between them                      -0.998
Product of X_ray and Geom B-fact gradients     -0.435E+08
 Cosine of angle between them                      -0.997


Residuals: XRAY=     0.6323E+06 GEOM=      8688.     TOTAL=     0.6410E+06
 function value    640998.81    

-------------------------------------------------------------------------------
             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     1.752     1.644
Bond angles  : others                          3242     1.445     1.582
Torsion angles, period  1. refined              184     6.982     5.000
Torsion angles, period  2. refined               90    36.720    22.778
Torsion angles, period  3. refined              268    14.175    15.000
Torsion angles, period  4. refined                9    11.379    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                   309     0.262     0.200
VDW repulsions.others                          1350     0.204     0.200
VDW; torsion: refined_atoms                     715     0.171     0.200
VDW; torsion.others                             787     0.082     0.200
HBOND: refined_atoms                            241     0.205     0.200
HBOND.others                                      1     0.088     0.200
VDW repulsions: symmetry: refined_atoms          11     0.225     0.200
VDW repulsions: symmetry: others                 30     0.169     0.200
HBOND: symmetry: refined_atoms                   20     0.253     0.200
HBOND: symmetry: others                           1     0.109     0.200
M. chain bond B values: refined atoms           745     1.563     1.212
M. chain bond B values: others                  745     1.562     1.213
M. chain angle B values: refined atoms          926     2.518     1.800
M. chain angle B values: others                 927     2.517     1.799
S. chain bond B values: refined atoms           811     2.621     1.565
S. chain bond B values: others                  810     2.618     1.565
S. chain angle B values: refined atoms         1177     4.135     2.196
S. chain angle B values: others                1178     4.133     2.196
Long range B values: refined atoms             1872     7.126    17.364
Long range B values: others                    1769     6.790    15.876
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =   -0.0431
Partial structure    1: scale =     0.3764, B  =   46.7301
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   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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2184 100.00   476.9   482.1  0.15  0.16     127   523.4   537.5  0.17  0.19
 0.104    3720 100.00   384.6   367.2  0.16  0.15     204   392.8   377.0  0.21  0.20
 0.173    4688  99.96   247.8   242.3  0.16  0.13     254   240.8   240.1  0.24  0.20
 0.242    5518 100.00   188.0   188.9  0.16  0.13     286   189.7   191.9  0.21  0.16
$$

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

 $TABLE: Cycle   10. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1508   0.934    676   0.836   2184   0.904  0.959  0.9718  0.9748  0.9242  0.9448
  0.1042   3030   0.883    690   0.773   3720   0.862  0.994  0.9521  0.9616  0.9080  0.9422
  0.1733   3998   0.875    690   0.776   4688   0.861  0.980  0.9417  0.9602  0.8705  0.9409
  0.2425   4819   0.878    702   0.768   5521   0.864  0.951  0.9511  0.9597  0.9065  0.9380
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16113
Percentage observed                  =    99.9823
Percentage of free reflections       =     5.1284
Overall R factor                     =     0.1587
Free R factor                        =     0.2071
Average Fourier shell correlation    =     0.9623
AverageFree Fourier shell correlation=     0.9516
Overall weighted R factor            =     0.1485
Free weighted R factor               =     0.1926
Overall weighted R2 factor           =     0.1811
Free weighted R2 factor              =     0.2313
Average correlation coefficient      =     0.9408
Overall correlation coefficient      =     0.9555
Free correlation coefficient         =     0.9322
Cruickshanks DPI for coordinate error=     0.1404
DPI based on free R factor           =     0.1352
Overall figure of merit              =     0.8679
ML based su of positional parameters =     0.0827
ML based su of thermal parameters    =     2.7495
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    87220.461       8687.6777       641001.38       640996.13    

 fvalues    87220.461       8687.6777       640999.63       640998.50    
 fvalues    87220.461       8687.6777       640999.63       640998.50    

    ****                              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.= 0.936 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_R18_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     1.752     1.644
Bond angles  : others                          3242     1.445     1.582
Torsion angles, period  1. refined              184     6.981     5.000
Torsion angles, period  2. refined               90    36.718    22.778
Torsion angles, period  3. refined              268    14.171    15.000
Torsion angles, period  4. refined                9    11.380    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                   309     0.262     0.200
VDW repulsions.others                          1349     0.204     0.200
VDW; torsion: refined_atoms                     717     0.171     0.200
VDW; torsion.others                             787     0.082     0.200
HBOND: refined_atoms                            241     0.205     0.200
HBOND.others                                      1     0.088     0.200
VDW repulsions: symmetry: refined_atoms          11     0.225     0.200
VDW repulsions: symmetry: others                 30     0.169     0.200
HBOND: symmetry: refined_atoms                   20     0.253     0.200
HBOND: symmetry: others                           1     0.109     0.200
M. chain bond B values: refined atoms           745     1.563     1.212
M. chain bond B values: others                  745     1.562     1.213
M. chain angle B values: refined atoms          926     2.519     1.800
M. chain angle B values: others                 927     2.517     1.799
S. chain bond B values: refined atoms           811     2.620     1.565
S. chain bond B values: others                  810     2.618     1.565
S. chain angle B values: refined atoms         1177     4.134     2.196
S. chain angle B values: others                1178     4.133     2.196
Long range B values: refined atoms             1873     7.125    17.364
Long range B values: others                    1770     6.789    15.877
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =   -0.0428
Partial structure    1: scale =     0.3764, B  =   46.7249
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2184 100.00   476.9   482.1  0.15  0.16     127   523.4   537.5  0.17  0.19
 0.104    3720 100.00   384.6   367.3  0.16  0.15     204   392.8   377.0  0.21  0.20
 0.173    4688  99.96   247.8   242.3  0.16  0.13     254   240.8   240.1  0.24  0.20
 0.242    5518 100.00   188.0   188.9  0.16  0.13     286   189.7   191.9  0.21  0.16
$$

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

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1508   0.934    676   0.836   2184   0.904  0.959  0.9719  0.9748  0.9242  0.9448
  0.1042   3030   0.883    690   0.773   3720   0.862  0.994  0.9521  0.9616  0.9080  0.9422
  0.1733   3998   0.875    690   0.776   4688   0.861  0.980  0.9416  0.9602  0.8705  0.9409
  0.2425   4819   0.878    702   0.768   5521   0.864  0.951  0.9511  0.9597  0.9065  0.9380
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16113
Percentage observed                  =    99.9823
Percentage of free reflections       =     5.1284
Overall R factor                     =     0.1587
Free R factor                        =     0.2071
Average Fourier shell correlation    =     0.9623
AverageFree Fourier shell correlation=     0.9516
Overall weighted R factor            =     0.1485
Free weighted R factor               =     0.1927
Overall weighted R2 factor           =     0.1812
Free weighted R2 factor              =     0.2313
Average correlation coefficient      =     0.9408
Overall correlation coefficient      =     0.9555
Free correlation coefficient         =     0.9322
Cruickshanks DPI for coordinate error=     0.1404
DPI based on free R factor           =     0.1352
Overall figure of merit              =     0.8679
ML based su of positional parameters =     0.0827
ML based su of thermal parameters    =     2.7495
-----------------------------------------------------------------------------
  Time in seconds: CPU =        14.51
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1639   0.2097   0.857       88099.    4944.3   0.0133  1.034   1.801  1.046   0.084
       1   0.1615   0.2072   0.866       87569.    4929.6   0.0112  0.820   1.716  0.993   0.083
       2   0.1599   0.2059   0.868       87375.    4922.8   0.0118  0.862   1.734  1.003   0.084
       3   0.1593   0.2055   0.868       87300.    4920.4   0.0119  0.871   1.742  1.008   0.084
       4   0.1590   0.2055   0.869       87252.    4918.5   0.0119  0.874   1.746  1.011   0.084
       5   0.1589   0.2058   0.868       87232.    4918.6   0.0119  0.875   1.750  1.013   0.084
       6   0.1588   0.2061   0.868       87224.    4919.1   0.0119  0.874   1.751  1.014   0.084
       7   0.1587   0.2066   0.868       87217.    4919.3   0.0119  0.873   1.752  1.015   0.084
       8   0.1587   0.2068   0.868       87219.    4920.2   0.0118  0.872   1.752  1.015   0.084
       9   0.1587   0.2071   0.868       87221.    4920.9   0.0118  0.871   1.752  1.015   0.084
      10   0.1587   0.2071   0.868       87220.    4920.8   0.0118  0.871   1.752  1.015   0.084
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1639   0.1587
             R free    0.2097   0.2071
     Rms BondLength    0.0133   0.0118
      Rms BondAngle    1.8014   1.7520
     Rms ChirVolume    0.0837   0.0838
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      46.5s System:    0.2s Elapsed:     0:47