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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: 14:41:17 


 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 9
  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_R09_2-00A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R09_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_R09_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:     9
  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_R09_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=   2.020 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=   2.253 ideal_dist=   2.090
            ch:AAA  res:  88  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   1.842 ideal_dist=   1.720
            ch:AAA  res:  93  CYS              at:SG  .->ch:AAA  res: 157  TYR              at:CE1 .
  INFO:     link is found (not be used) dist=   2.236 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=   2.346 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=   2.452 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=   2.044 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                            9
Number of "free" reflections        869
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.= 1.463 id.= 1.337 dev= -0.126 sig.= 0.011
A    125 LEU C   . - A    126 ARG N   . mod.= 1.572 id.= 1.337 dev= -0.235 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.= 0.906 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   0.25302267    
 Actual weight    7.2495699      is applied to the X-ray term
Norm of X_ray positional gradient                42.2
Norm of Geom. positional gradient                89.7
Norm of X_ray B-factor gradient                  142.
Norm of Geom. B-factor gradient                 0.210E+05
Product of X_ray and Geom posit. gradients     -0.810E+07
 Cosine of angle between them                      -0.221
Product of X_ray and Geom B-fact gradients     -0.415E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.6356E+06 GEOM=     0.2630E+05 TOTAL=     0.6619E+06
 function value    661912.50    

-------------------------------------------------------------------------------
             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     1.872     1.644
Bond angles  : others                          3242     2.359     1.582
Torsion angles, period  1. refined              184     7.250     5.000
Torsion angles, period  2. refined               90    36.932    22.778
Torsion angles, period  3. refined              268    14.780    15.000
Torsion angles, period  4. refined                9    10.697    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.013     0.020
Planar groups: others                           331     0.016     0.020
VDW repulsions: refined_atoms                   315     0.254     0.200
VDW repulsions.others                          1351     0.228     0.200
VDW; torsion: refined_atoms                     703     0.171     0.200
VDW; torsion.others                             696     0.080     0.200
HBOND: refined_atoms                            236     0.216     0.200
HBOND.others                                      3     0.051     0.200
VDW repulsions: symmetry: refined_atoms           9     0.224     0.200
VDW repulsions: symmetry: others                 23     0.175     0.200
HBOND: symmetry: refined_atoms                   16     0.251     0.200
HBOND: symmetry: others                           1     0.067     0.200
M. chain bond B values: refined atoms           745     1.547     1.172
M. chain bond B values: others                  745     1.547     1.172
M. chain angle B values: refined atoms          926     2.505     1.739
M. chain angle B values: others                 927     2.504     1.739
S. chain bond B values: refined atoms           812     2.529     1.505
S. chain bond B values: others                  811     2.525     1.505
S. chain angle B values: refined atoms         1177     3.996     2.111
S. chain angle B values: others                1178     3.994     2.111
Long range B values: refined atoms             1866     6.805    16.499
Long range B values: others                    1770     6.453    15.149
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =    0.3685
Partial structure    1: scale =     0.3721, B  =   49.3925
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle    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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2196 100.00   483.4   487.5  0.16  0.17     115   432.9   451.8  0.22  0.24
 0.104    3722 100.00   387.0   370.1  0.15  0.14     202   369.5   357.3  0.20  0.19
 0.173    4683  99.96   248.4   243.1  0.15  0.13     259   245.5   242.7  0.20  0.17
 0.242    5512 100.00   188.6   189.7  0.19  0.15     292   188.9   189.9  0.23  0.19
$$

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

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1509   0.913    687   0.816   2196   0.882  0.956  0.9552  0.9694  0.9084  0.9416
  0.1042   3026   0.906    696   0.806   3722   0.887  1.007  0.9578  0.9692  0.9182  0.9482
  0.1733   3987   0.890    696   0.798   4683   0.877  0.987  0.9533  0.9658  0.9004  0.9463
  0.2425   4814   0.864    701   0.748   5515   0.849  0.947  0.9356  0.9490  0.8490  0.9141
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16116
Percentage observed                  =    99.9823
Percentage of free reflections       =     5.1107
Overall R factor                     =     0.1620
Free R factor                        =     0.2110
Average Fourier shell correlation    =     0.9613
AverageFree Fourier shell correlation=     0.9486
Overall weighted R factor            =     0.1488
Free weighted R factor               =     0.1991
Overall weighted R2 factor           =     0.1800
Free weighted R2 factor              =     0.2383
Average correlation coefficient      =     0.9351
Overall correlation coefficient      =     0.9550
Free correlation coefficient         =     0.9226
Cruickshanks DPI for coordinate error=     0.1433
DPI based on free R factor           =     0.1377
Overall figure of merit              =     0.8704
ML based su of positional parameters =     0.0821
ML based su of thermal parameters    =     2.7750
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    87675.391       26303.633       661912.50      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.27102643    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    642973.00    

-------------------------------------------------------------------------------
             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 =     0.0402, B  =   -0.1228
Partial structure    1: scale =     0.3728, B  =   49.4893
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                     =     0.1600
Free R factor                        =     0.2091
Average Fourier shell correlation    =     0.9638
AverageFree Fourier shell correlation=     0.9512
Average correlation coefficient      =     0.9388
Overall figure of merit              =     0.8766
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    87202.969       10788.984       642973.00       661912.50    


     CGMAT cycle number =      3

 Weight matrix   0.27624491    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    640606.13    

-------------------------------------------------------------------------------
             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 =     0.0402, B  =   -0.0595
Partial structure    1: scale =     0.3730, B  =   47.7661
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                     =     0.1586
Free R factor                        =     0.2068
Average Fourier shell correlation    =     0.9646
AverageFree Fourier shell correlation=     0.9520
Average correlation coefficient      =     0.9403
Overall figure of merit              =     0.8780
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    87042.031       9588.8418       640606.13       642973.00    


     CGMAT cycle number =      4

 Weight matrix   0.27881733    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    639714.88    

-------------------------------------------------------------------------------
             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 =     0.0402, B  =   -0.0542
Partial structure    1: scale =     0.3735, B  =   47.8191
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                     =     0.1580
Free R factor                        =     0.2060
Average Fourier shell correlation    =     0.9649
AverageFree Fourier shell correlation=     0.9523
Average correlation coefficient      =     0.9409
Overall figure of merit              =     0.8786
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    86971.398       9209.6387       639714.88       640606.13    


     CGMAT cycle number =      5

 Weight matrix   0.28025717    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    639376.44    

-------------------------------------------------------------------------------
             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 =     0.0402, B  =   -0.0522
Partial structure    1: scale =     0.3739, B  =   47.8669
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                     =     0.1576
Free R factor                        =     0.2053
Average Fourier shell correlation    =     0.9651
AverageFree Fourier shell correlation=     0.9525
Average correlation coefficient      =     0.9412
Overall figure of merit              =     0.8789
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    86930.992       9164.1084       639376.44       639714.88    


     CGMAT cycle number =      6

 Weight matrix   0.28130198    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    639189.06    

-------------------------------------------------------------------------------
             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 =     0.0402, B  =   -0.0490
Partial structure    1: scale =     0.3744, B  =   48.0699
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                     =     0.1574
Free R factor                        =     0.2052
Average Fourier shell correlation    =     0.9652
AverageFree Fourier shell correlation=     0.9527
Average correlation coefficient      =     0.9414
Overall figure of merit              =     0.8792
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    86901.031       9193.9541       639189.06       639376.44    


     CGMAT cycle number =      7

 Weight matrix   0.28155765    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    639088.13    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =   -0.0567
Partial structure    1: scale =     0.3745, B  =   48.1289
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                     =     0.1573
Free R factor                        =     0.2053
Average Fourier shell correlation    =     0.9653
AverageFree Fourier shell correlation=     0.9527
Average correlation coefficient      =     0.9416
Overall figure of merit              =     0.8792
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    86884.391       9213.6641       639088.13       639189.06    


     CGMAT cycle number =      8

 Weight matrix   0.28118747    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    639073.19    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =   -0.0575
Partial structure    1: scale =     0.3746, B  =   48.1058
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                     =     0.1572
Free R factor                        =     0.2055
Average Fourier shell correlation    =     0.9653
AverageFree Fourier shell correlation=     0.9526
Average correlation coefficient      =     0.9417
Overall figure of merit              =     0.8791
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    86879.734       9232.5273       639073.19       639088.13    


     CGMAT cycle number =      9

 Weight matrix   0.28112751    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    638995.25    

-------------------------------------------------------------------------------
             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 =     0.0403, B  =   -0.0507
Partial structure    1: scale =     0.3751, B  =   48.1352
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                     =     0.1572
Free R factor                        =     0.2056
Average Fourier shell correlation    =     0.9653
AverageFree Fourier shell correlation=     0.9527
Average correlation coefficient      =     0.9418
Overall figure of merit              =     0.8791
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    86869.320       9230.0488       638995.25       639073.19    


     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   0.28107890    
 Actual weight    7.2495699      is applied to the X-ray term
Norm of X_ray positional gradient                37.0
Norm of Geom. positional gradient                37.0
Norm of X_ray B-factor gradient                  122.
Norm of Geom. B-factor gradient                  125.
Product of X_ray and Geom posit. gradients     -0.132E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.493E+08
 Cosine of angle between them                      -0.996


Residuals: XRAY=     0.6297E+06 GEOM=      9233.     TOTAL=     0.6390E+06
 function value    638970.56    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.830     1.644
Bond angles  : others                          3242     1.452     1.582
Torsion angles, period  1. refined              184     6.953     5.000
Torsion angles, period  2. refined               90    36.865    22.778
Torsion angles, period  3. refined              268    14.402    15.000
Torsion angles, period  4. refined                9    10.580    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   300     0.266     0.200
VDW repulsions.others                          1346     0.206     0.200
VDW; torsion: refined_atoms                     708     0.172     0.200
VDW; torsion.others                             777     0.084     0.200
HBOND: refined_atoms                            237     0.209     0.200
HBOND.others                                      2     0.066     0.200
VDW repulsions: symmetry: refined_atoms           7     0.242     0.200
VDW repulsions: symmetry: others                 23     0.183     0.200
HBOND: symmetry: refined_atoms                   18     0.230     0.200
HBOND: symmetry: others                           1     0.042     0.200
M. chain bond B values: refined atoms           745     1.604     1.201
M. chain bond B values: others                  745     1.603     1.201
M. chain angle B values: refined atoms          926     2.553     1.783
M. chain angle B values: others                 927     2.552     1.783
S. chain bond B values: refined atoms           812     2.760     1.563
S. chain bond B values: others                  811     2.757     1.563
S. chain angle B values: refined atoms         1177     4.311     2.189
S. chain angle B values: others                1178     4.309     2.189
Long range B values: refined atoms             1851     6.977    17.061
Long range B values: others                    1753     6.660    15.576
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =   -0.0555
Partial structure    1: scale =     0.3752, B  =   48.1515
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2196 100.00   483.1   487.9  0.16  0.17     115   432.7   451.9  0.22  0.24
 0.104    3722 100.00   386.8   369.4  0.15  0.14     202   369.3   355.5  0.19  0.19
 0.173    4683  99.96   248.2   243.0  0.15  0.13     259   245.3   242.5  0.19  0.16
 0.242    5512 100.00   188.5   189.8  0.17  0.13     292   188.8   190.7  0.22  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1509   0.929    687   0.836   2196   0.900  0.958  0.9602  0.9728  0.9070  0.9404
  0.1042   3026   0.912    696   0.813   3722   0.894  1.007  0.9603  0.9706  0.9206  0.9475
  0.1733   3987   0.898    696   0.805   4683   0.884  0.987  0.9570  0.9676  0.9081  0.9467
  0.2425   4814   0.871    701   0.756   5515   0.857  0.947  0.9406  0.9568  0.8595  0.9344
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16116
Percentage observed                  =    99.9823
Percentage of free reflections       =     5.1107
Overall R factor                     =     0.1572
Free R factor                        =     0.2057
Average Fourier shell correlation    =     0.9653
AverageFree Fourier shell correlation=     0.9527
Overall weighted R factor            =     0.1469
Free weighted R factor               =     0.1951
Overall weighted R2 factor           =     0.1803
Free weighted R2 factor              =     0.2368
Average correlation coefficient      =     0.9418
Overall correlation coefficient      =     0.9563
Free correlation coefficient         =     0.9247
Cruickshanks DPI for coordinate error=     0.1390
DPI based on free R factor           =     0.1342
Overall figure of merit              =     0.8791
ML based su of positional parameters =     0.0778
ML based su of thermal parameters    =     2.6347
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    86865.469       9233.2695       638970.56       638995.25    

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.925 id.= 3.000 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 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_R09_1-90A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.830     1.644
Bond angles  : others                          3242     1.452     1.582
Torsion angles, period  1. refined              184     6.950     5.000
Torsion angles, period  2. refined               90    36.866    22.778
Torsion angles, period  3. refined              268    14.394    15.000
Torsion angles, period  4. refined                9    10.570    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   302     0.265     0.200
VDW repulsions.others                          1351     0.205     0.200
VDW; torsion: refined_atoms                     708     0.172     0.200
VDW; torsion.others                             779     0.084     0.200
HBOND: refined_atoms                            236     0.210     0.200
HBOND.others                                      2     0.068     0.200
VDW repulsions: symmetry: refined_atoms           7     0.242     0.200
VDW repulsions: symmetry: others                 24     0.179     0.200
HBOND: symmetry: refined_atoms                   19     0.224     0.200
HBOND: symmetry: others                           1     0.042     0.200
M. chain bond B values: refined atoms           745     1.605     1.201
M. chain bond B values: others                  745     1.604     1.201
M. chain angle B values: refined atoms          926     2.555     1.783
M. chain angle B values: others                 927     2.553     1.783
S. chain bond B values: refined atoms           812     2.763     1.564
S. chain bond B values: others                  811     2.760     1.563
S. chain angle B values: refined atoms         1177     4.315     2.190
S. chain angle B values: others                1178     4.313     2.189
Long range B values: refined atoms             1852     7.020    17.071
Long range B values: others                    1755     6.706    15.612
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =   -0.0523
Partial structure    1: scale =     0.3754, B  =   48.0416
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2196 100.00   483.0   487.9  0.16  0.17     115   432.6   451.8  0.22  0.24
 0.104    3722 100.00   386.8   369.3  0.15  0.14     202   369.2   355.3  0.19  0.19
 0.173    4683  99.96   248.2   243.0  0.15  0.13     259   245.3   242.4  0.19  0.16
 0.242    5512 100.00   188.4   189.8  0.17  0.13     292   188.8   190.6  0.22  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1509   0.929    687   0.837   2196   0.900  0.958  0.9602  0.9729  0.9069  0.9404
  0.1042   3026   0.912    696   0.813   3722   0.894  1.007  0.9603  0.9706  0.9206  0.9474
  0.1733   3987   0.898    696   0.805   4683   0.884  0.987  0.9570  0.9676  0.9081  0.9467
  0.2425   4814   0.871    701   0.756   5515   0.857  0.947  0.9406  0.9568  0.8596  0.9346
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16116
Percentage observed                  =    99.9823
Percentage of free reflections       =     5.1107
Overall R factor                     =     0.1571
Free R factor                        =     0.2057
Average Fourier shell correlation    =     0.9653
AverageFree Fourier shell correlation=     0.9527
Overall weighted R factor            =     0.1468
Free weighted R factor               =     0.1951
Overall weighted R2 factor           =     0.1802
Free weighted R2 factor              =     0.2369
Average correlation coefficient      =     0.9419
Overall correlation coefficient      =     0.9563
Free correlation coefficient         =     0.9247
Cruickshanks DPI for coordinate error=     0.1390
DPI based on free R factor           =     0.1342
Overall figure of merit              =     0.8791
ML based su of positional parameters =     0.0778
ML based su of thermal parameters    =     2.6347
-----------------------------------------------------------------------------
  Time in seconds: CPU =        12.10
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1620   0.2110   0.870       87675.    4859.9   0.0145  1.115   1.872  1.076   0.087
       1   0.1600   0.2091   0.877       87203.    4851.2   0.0123  0.888   1.801  1.030   0.088
       2   0.1586   0.2068   0.878       87042.    4844.1   0.0127  0.922   1.812  1.038   0.088
       3   0.1580   0.2060   0.879       86971.    4841.4   0.0128  0.932   1.819  1.043   0.088
       4   0.1576   0.2053   0.879       86931.    4839.6   0.0129  0.937   1.823  1.046   0.088
       5   0.1574   0.2052   0.879       86901.    4838.1   0.0129  0.940   1.826  1.048   0.088
       6   0.1573   0.2053   0.879       86884.    4838.0   0.0130  0.942   1.828  1.050   0.088
       7   0.1572   0.2055   0.879       86880.    4838.4   0.0130  0.943   1.829  1.051   0.088
       8   0.1572   0.2056   0.879       86869.    4838.1   0.0130  0.943   1.830  1.051   0.088
       9   0.1572   0.2057   0.879       86865.    4838.2   0.0130  0.943   1.830  1.052   0.087
      10   0.1571   0.2057   0.879       86860.    4838.0   0.0130  0.943   1.830  1.052   0.087
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1620   0.1571
             R free    0.2110   0.2057
     Rms BondLength    0.0145   0.0130
      Rms BondAngle    1.8723   1.8302
     Rms ChirVolume    0.0874   0.0874
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      44.2s System:    0.1s Elapsed:     0:45