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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 26/ 5/2020 Run time: 14:31:33 


 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 5
  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_R05_2-00A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R05_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_R05_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:     5
  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_R05_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=   2.045 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=   2.233 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=   1.849 ideal_dist=   1.720
            ch:AAA  res:  93  CYS              at:SG  .->ch:AAA  res: 157  TYR              at:CE1 .
  INFO:     link is found (not be used) dist=   2.224 ideal_dist=   2.090
            ch:AAA  res: 140  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.352 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=   2.466 ideal_dist=   2.235
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:SG  .
  INFO:     link is found (not be used) dist=   1.979 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                            5
Number of "free" reflections        829
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.= 1.452 id.= 1.337 dev= -0.115 sig.= 0.011
A    125 LEU C   . - A    126 ARG N   . mod.= 1.544 id.= 1.337 dev= -0.207 sig.= 0.011

    ****                              VDW outliers                              ****

VDW deviations from the ideal >10.000Sigma or dist <  1.000 will be monitored

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.911 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    31   31   65
 Minimum acceptable grid spacing:    73   73  154
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    31   31   65
 Minimum acceptable grid spacing:    73   73  154
 Weight matrix   0.22714631    
 Actual weight    7.2495699      is applied to the X-ray term
Norm of X_ray positional gradient                42.8
Norm of Geom. positional gradient                87.7
Norm of X_ray B-factor gradient                  142.
Norm of Geom. B-factor gradient                 0.206E+05
Product of X_ray and Geom posit. gradients     -0.711E+07
 Cosine of angle between them                      -0.195
Product of X_ray and Geom B-fact gradients     -0.361E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.6399E+06 GEOM=     0.2562E+05 TOTAL=     0.6655E+06
 function value    665497.00    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.014     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.811     1.644
Bond angles  : others                          3242     2.353     1.582
Torsion angles, period  1. refined              184     7.324     5.000
Torsion angles, period  2. refined               90    36.361    22.778
Torsion angles, period  3. refined              268    14.881    15.000
Torsion angles, period  4. refined                9    12.644    15.000
Chiral centres: refined atoms                   196     0.085     0.200
Planar groups: refined atoms                   1736     0.012     0.020
Planar groups: others                           331     0.015     0.020
VDW repulsions: refined_atoms                   320     0.257     0.200
VDW repulsions.others                          1365     0.229     0.200
VDW; torsion: refined_atoms                     716     0.170     0.200
VDW; torsion.others                             708     0.080     0.200
HBOND: refined_atoms                            231     0.212     0.200
HBOND.others                                      3     0.041     0.200
VDW repulsions: symmetry: refined_atoms           8     0.257     0.200
VDW repulsions: symmetry: others                 29     0.156     0.200
HBOND: symmetry: refined_atoms                   16     0.263     0.200
HBOND: symmetry: others                           1     0.071     0.200
M. chain bond B values: refined atoms           745     1.504     1.178
M. chain bond B values: others                  745     1.503     1.179
M. chain angle B values: refined atoms          926     2.443     1.749
M. chain angle B values: others                 927     2.441     1.748
S. chain bond B values: refined atoms           811     2.420     1.512
S. chain bond B values: others                  810     2.415     1.511
S. chain angle B values: refined atoms         1177     3.891     2.123
S. chain angle B values: others                1178     3.889     2.123
Long range B values: refined atoms             1875     6.843    16.663
Long range B values: others                    1775     6.504    15.338
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =    0.3594
Partial structure    1: scale =     0.3763, B  =   49.1102
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    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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2194 100.00   482.9   487.7  0.16  0.17     117   412.0   424.0  0.19  0.19
 0.104    3744 100.00   384.4   368.1  0.15  0.14     180   394.6   384.7  0.20  0.19
 0.173    4676  99.96   247.6   242.1  0.16  0.13     266   244.1   240.4  0.22  0.19
 0.242    5541 100.00   188.2   189.0  0.19  0.15     263   182.8   180.9  0.23  0.20
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1514   0.934    680   0.846   2194   0.907  0.958  0.9656  0.9753  0.9338  0.9425
  0.1042   3047   0.893    697   0.788   3744   0.874  1.000  0.9580  0.9668  0.9122  0.9484
  0.1733   3973   0.867    703   0.763   4676   0.852  0.979  0.9408  0.9580  0.8643  0.9402
  0.2425   4831   0.863    711   0.746   5542   0.848  0.947  0.9337  0.9481  0.8580  0.9128
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16156
Percentage observed                  =    99.9823
Percentage of free reflections       =     4.8752
Overall R factor                     =     0.1634
Free R factor                        =     0.2089
Average Fourier shell correlation    =     0.9590
AverageFree Fourier shell correlation=     0.9458
Overall weighted R factor            =     0.1495
Free weighted R factor               =     0.1895
Overall weighted R2 factor           =     0.1800
Free weighted R2 factor              =     0.2217
Average correlation coefficient      =     0.9330
Overall correlation coefficient      =     0.9544
Free correlation coefficient         =     0.9251
Cruickshanks DPI for coordinate error=     0.1441
DPI based on free R factor           =     0.1361
Overall figure of merit              =     0.8630
ML based su of positional parameters =     0.0866
ML based su of thermal parameters    =     2.9318
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    88264.820       25615.025       665497.00      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.25519812    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    646202.63    

-------------------------------------------------------------------------------
             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  =   -0.1025
Partial structure    1: scale =     0.3765, B  =   49.0186
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1609
Free R factor                        =     0.2061
Average Fourier shell correlation    =     0.9624
AverageFree Fourier shell correlation=     0.9495
Average correlation coefficient      =     0.9374
Overall figure of merit              =     0.8721
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    87686.141       10515.815       646202.63       665497.00    


     CGMAT cycle number =      3

 Weight matrix   0.26040170    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    643521.94    

-------------------------------------------------------------------------------
             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  =   -0.0714
Partial structure    1: scale =     0.3764, B  =   47.0202
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1593
Free R factor                        =     0.2053
Average Fourier shell correlation    =     0.9632
AverageFree Fourier shell correlation=     0.9504
Average correlation coefficient      =     0.9393
Overall figure of merit              =     0.8738
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    87453.063       9524.8730       643521.94       646202.63    


     CGMAT cycle number =      4

 Weight matrix   0.26173183    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    642598.44    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =   -0.0482
Partial structure    1: scale =     0.3766, B  =   47.1716
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1587
Free R factor                        =     0.2051
Average Fourier shell correlation    =     0.9634
AverageFree Fourier shell correlation=     0.9506
Average correlation coefficient      =     0.9398
Overall figure of merit              =     0.8743
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    87370.195       9202.1260       642598.44       643521.94    


     CGMAT cycle number =      5

 Weight matrix   0.26158667    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    642303.31    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =   -0.0422
Partial structure    1: scale =     0.3766, B  =   47.2414
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1585
Free R factor                        =     0.2055
Average Fourier shell correlation    =     0.9635
AverageFree Fourier shell correlation=     0.9507
Average correlation coefficient      =     0.9401
Overall figure of merit              =     0.8743
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    87337.359       9144.9961       642303.31       642598.44    


     CGMAT cycle number =      6

 Weight matrix   0.26215896    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    642135.44    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =   -0.0473
Partial structure    1: scale =     0.3768, B  =   47.2637
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1584
Free R factor                        =     0.2056
Average Fourier shell correlation    =     0.9636
AverageFree Fourier shell correlation=     0.9508
Average correlation coefficient      =     0.9403
Overall figure of merit              =     0.8744
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    87313.523       9149.9424       642135.44       642303.31    


     CGMAT cycle number =      7

 Weight matrix   0.26191357    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    642043.25    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =   -0.0471
Partial structure    1: scale =     0.3765, B  =   47.2195
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1583
Free R factor                        =     0.2058
Average Fourier shell correlation    =     0.9636
AverageFree Fourier shell correlation=     0.9508
Average correlation coefficient      =     0.9404
Overall figure of merit              =     0.8744
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    87299.453       9159.7285       642043.25       642135.44    


     CGMAT cycle number =      8

 Weight matrix   0.26148960    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    641972.06    

-------------------------------------------------------------------------------
             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  =   -0.0494
Partial structure    1: scale =     0.3763, B  =   47.0984
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1582
Free R factor                        =     0.2060
Average Fourier shell correlation    =     0.9636
AverageFree Fourier shell correlation=     0.9507
Average correlation coefficient      =     0.9405
Overall figure of merit              =     0.8743
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    87289.594       9160.0605       641972.06       642043.25    


     CGMAT cycle number =      9

 Weight matrix   0.26087663    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    641948.88    

-------------------------------------------------------------------------------
             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  =   -0.0413
Partial structure    1: scale =     0.3757, B  =   46.9083
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1582
Free R factor                        =     0.2064
Average Fourier shell correlation    =     0.9636
AverageFree Fourier shell correlation=     0.9507
Average correlation coefficient      =     0.9406
Overall figure of merit              =     0.8741
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    87288.141       9147.3779       641948.88       641972.06    


     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.= 0.924 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   0.26090655    
 Actual weight    7.2495699      is applied to the X-ray term
Norm of X_ray positional gradient                36.2
Norm of Geom. positional gradient                36.2
Norm of X_ray B-factor gradient                  120.
Norm of Geom. B-factor gradient                  123.
Product of X_ray and Geom posit. gradients     -0.126E+08
 Cosine of angle between them                      -0.998
Product of X_ray and Geom B-fact gradients     -0.473E+08
 Cosine of angle between them                      -0.997


Residuals: XRAY=     0.6328E+06 GEOM=      9144.     TOTAL=     0.6419E+06
 function value    641924.88    

-------------------------------------------------------------------------------
             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     1.800     1.644
Bond angles  : others                          3242     1.462     1.582
Torsion angles, period  1. refined              184     7.001     5.000
Torsion angles, period  2. refined               90    36.594    22.778
Torsion angles, period  3. refined              268    14.306    15.000
Torsion angles, period  4. refined                9    12.810    15.000
Chiral centres: refined atoms                   196     0.085     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   316     0.263     0.200
VDW repulsions.others                          1361     0.206     0.200
VDW; torsion: refined_atoms                     721     0.173     0.200
VDW; torsion.others                             783     0.084     0.200
HBOND: refined_atoms                            234     0.207     0.200
HBOND.others                                      1     0.054     0.200
VDW repulsions: symmetry: refined_atoms           9     0.240     0.200
VDW repulsions: symmetry: others                 28     0.170     0.200
HBOND: symmetry: refined_atoms                   22     0.210     0.200
HBOND: symmetry: others                           1     0.095     0.200
M. chain bond B values: refined atoms           745     1.589     1.211
M. chain bond B values: others                  745     1.588     1.211
M. chain angle B values: refined atoms          926     2.548     1.797
M. chain angle B values: others                 927     2.546     1.797
S. chain bond B values: refined atoms           812     2.745     1.580
S. chain bond B values: others                  811     2.742     1.580
S. chain angle B values: refined atoms         1177     4.346     2.213
S. chain angle B values: others                1178     4.344     2.213
Long range B values: refined atoms             1872     7.134    17.270
Long range B values: others                    1771     6.798    15.851
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =   -0.0462
Partial structure    1: scale =     0.3754, B  =   46.9567
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2194 100.00   482.5   489.0  0.15  0.16     117   411.7   424.7  0.19  0.19
 0.104    3744 100.00   384.1   366.6  0.16  0.15     180   394.3   384.3  0.20  0.19
 0.173    4676  99.96   247.4   241.7  0.16  0.14     266   243.8   241.5  0.22  0.19
 0.242    5541 100.00   188.1   189.1  0.16  0.13     263   182.7   180.4  0.22  0.18
$$

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

 $TABLE: Cycle   10. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1514   0.945    680   0.860   2194   0.919  0.958  0.9686  0.9780  0.9352  0.9461
  0.1042   3047   0.898    697   0.796   3744   0.879  1.000  0.9589  0.9669  0.9123  0.9454
  0.1733   3973   0.873    703   0.771   4676   0.858  0.979  0.9431  0.9592  0.8656  0.9382
  0.2425   4831   0.882    711   0.765   5542   0.867  0.952  0.9445  0.9593  0.8816  0.9373
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16156
Percentage observed                  =    99.9823
Percentage of free reflections       =     4.8752
Overall R factor                     =     0.1581
Free R factor                        =     0.2065
Average Fourier shell correlation    =     0.9635
AverageFree Fourier shell correlation=     0.9506
Overall weighted R factor            =     0.1471
Free weighted R factor               =     0.1882
Overall weighted R2 factor           =     0.1790
Free weighted R2 factor              =     0.2199
Average correlation coefficient      =     0.9406
Overall correlation coefficient      =     0.9564
Free correlation coefficient         =     0.9277
Cruickshanks DPI for coordinate error=     0.1395
DPI based on free R factor           =     0.1345
Overall figure of merit              =     0.8741
ML based su of positional parameters =     0.0807
ML based su of thermal parameters    =     2.7047
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    87285.352       9143.6523       641924.88       641948.88    

    ****                              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.= 0.924 id.= 3.000 dev= -2.08 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_R05_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     1.801     1.644
Bond angles  : others                          3242     1.462     1.582
Torsion angles, period  1. refined              184     7.000     5.000
Torsion angles, period  2. refined               90    36.615    22.778
Torsion angles, period  3. refined              268    14.275    15.000
Torsion angles, period  4. refined                9    12.823    15.000
Chiral centres: refined atoms                   196     0.085     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   314     0.264     0.200
VDW repulsions.others                          1360     0.206     0.200
VDW; torsion: refined_atoms                     719     0.173     0.200
VDW; torsion.others                             792     0.084     0.200
HBOND: refined_atoms                            235     0.207     0.200
HBOND.others                                      1     0.059     0.200
VDW repulsions: symmetry: refined_atoms           9     0.240     0.200
VDW repulsions: symmetry: others                 28     0.170     0.200
HBOND: symmetry: refined_atoms                   23     0.207     0.200
HBOND: symmetry: others                           1     0.097     0.200
M. chain bond B values: refined atoms           745     1.591     1.212
M. chain bond B values: others                  745     1.589     1.212
M. chain angle B values: refined atoms          926     2.552     1.798
M. chain angle B values: others                 927     2.550     1.797
S. chain bond B values: refined atoms           812     2.750     1.580
S. chain bond B values: others                  811     2.747     1.580
S. chain angle B values: refined atoms         1177     4.352     2.214
S. chain angle B values: others                1178     4.350     2.213
Long range B values: refined atoms             1870     7.141    17.271
Long range B values: others                    1770     6.799    15.852
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0404, B  =   -0.0459
Partial structure    1: scale =     0.3756, B  =   47.0568
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2194 100.00   482.6   489.1  0.15  0.16     117   411.7   425.3  0.19  0.19
 0.104    3744 100.00   384.1   366.5  0.16  0.15     180   394.3   384.3  0.20  0.19
 0.173    4676  99.96   247.4   241.6  0.16  0.14     266   243.9   241.5  0.22  0.19
 0.242    5541 100.00   188.1   189.0  0.16  0.13     263   182.7   180.4  0.22  0.18
$$

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

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1514   0.945    680   0.861   2194   0.919  0.958  0.9685  0.9780  0.9347  0.9462
  0.1042   3047   0.897    697   0.796   3744   0.879  1.000  0.9588  0.9668  0.9121  0.9453
  0.1733   3973   0.873    703   0.770   4676   0.857  0.979  0.9428  0.9590  0.8651  0.9380
  0.2425   4831   0.882    711   0.765   5542   0.867  0.952  0.9446  0.9594  0.8821  0.9375
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16156
Percentage observed                  =    99.9823
Percentage of free reflections       =     4.8752
Overall R factor                     =     0.1581
Free R factor                        =     0.2067
Average Fourier shell correlation    =     0.9635
AverageFree Fourier shell correlation=     0.9505
Overall weighted R factor            =     0.1471
Free weighted R factor               =     0.1882
Overall weighted R2 factor           =     0.1788
Free weighted R2 factor              =     0.2200
Average correlation coefficient      =     0.9406
Overall correlation coefficient      =     0.9564
Free correlation coefficient         =     0.9275
Cruickshanks DPI for coordinate error=     0.1394
DPI based on free R factor           =     0.1346
Overall figure of merit              =     0.8739
ML based su of positional parameters =     0.0807
ML based su of thermal parameters    =     2.7047
-----------------------------------------------------------------------------
  Time in seconds: CPU =        12.78
             Elapsed =           0.00

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


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS: vs cycle :N:1,2,3:
:FOM vs cycle :N:1,4:
:-LL vs cycle :N:1,5:
:-LLfree vs cycle :N:1,6:
:Geometry vs cycle:N:1,7,8,9,10,11:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1634   0.2089   0.863       88265.    4657.0   0.0136  1.059   1.811  1.051   0.085
       1   0.1609   0.2061   0.872       87686.    4637.8   0.0118  0.867   1.751  1.013   0.084
       2   0.1593   0.2053   0.874       87453.    4631.5   0.0124  0.921   1.778  1.028   0.086
       3   0.1587   0.2051   0.874       87370.    4629.9   0.0125  0.928   1.790  1.035   0.086
       4   0.1585   0.2055   0.874       87337.    4630.4   0.0125  0.930   1.795  1.038   0.085
       5   0.1584   0.2056   0.874       87314.    4630.0   0.0125  0.928   1.797  1.039   0.085
       6   0.1583   0.2058   0.874       87299.    4630.3   0.0125  0.929   1.800  1.040   0.085
       7   0.1582   0.2060   0.874       87290.    4630.8   0.0125  0.928   1.801  1.040   0.085
       8   0.1582   0.2064   0.874       87288.    4631.6   0.0125  0.927   1.800  1.040   0.085
       9   0.1581   0.2065   0.874       87285.    4632.0   0.0125  0.926   1.800  1.040   0.085
      10   0.1581   0.2067   0.874       87290.    4632.9   0.0125  0.925   1.801  1.041   0.085
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1634   0.1581
             R free    0.2089   0.2067
     Rms BondLength    0.0136   0.0125
      Rms BondAngle    1.8107   1.8011
     Rms ChirVolume    0.0849   0.0849
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      44.8s System:    0.1s Elapsed:     0:45