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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: 16:15:41 


 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 1.70     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- bins 4
  Data line--- ncyc 10
  Data line--- monitor MEDIum
  Data line--- free 2
  Data line--- END

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

 LABIN FP=FP SIGFP=SIGFP FREE=FreeR_flag

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


Input coordinate file.  Logical name - XYZIN actual file name  - CDO_complete_R02_1-80A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R02_1-70A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R02_1-70A.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       0.0865
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.7000
  Estimated number of reflections :      29131
  Free R exclusion - flag equals:     2
  Auto weighting. An attempt
  Refinement cycles       :    10
  Scaling type                           :
          Wilson scaling type with Guassians

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

  Scaling and SigmaA resln:    41.9635  1.7000

  Damping factors:     1.0000  1.0000  1.0000


    ****                    Geometry restraints and weights                     ****


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

 Planar groups (all and main chain)
          WEIGHT= 1.00 1.00

 Chiral centers
          Weight= 1.00

 NON-BONDED CONTACTS
          Overall weight                          =  1.00
          Sigma for simple VDW                    =  0.20
          Sigma for VDW trhough torsion angle     =  0.20
          Sigma for HBOND                         =  0.20
          Sigma for metal-ion                     =  0.20
          Sigma for DUMMY and other atom          =  0.30
          Distance for donor-accepetor = vdw1+vdw2+(-0.30)
          Distance for acceptor - H    = vdw1+     ( 0.10)
          VDW distance through torsion = vdw1+vdw2+(-0.30)
          Distance for DUMMY-others    = vdw1+vdw2+(-0.70)

 TORSION ANGLES
          Weight= 1.00

 THERMAL FACTORS
          Weight= 1.00
     Main chain bond (1-2 neighbour)          1.5A**2
     Main chain angle (1-3 neighbour)         2.0A**2
     Side chain bond                          3.0A**2
     Side chain angle                         4.5A**2

 RESTRAINTS AGAINST EXCESSIVE SHIFTS
     Positional parameters                   0.00A
     Thermal parameters                      0.00A
     Occupancy parameters                    0.00

 RADIUS OF CONFIDENCE
     Positional parameters 0.00A
     Thermal parameters    0.00A**2
     Occupancy parameters  0.00

Monitoring style is "MEDIUM". Complete information will be printed out in the
first and last cycle. In all other cycles minimum information will be printed out
Sigma cutoffs for printing out outliers
If deviation of restraint parameter > alpha*sigma then information will be printed out
Distance outliers      10.000
Angle outliers         10.000
Torsion outliers       10.000
Chiral volume outliers 10.000
Plane outliers         10.000
Non-bonding outliers   10.000
B value  outliers      10.000
Rigid bond outliers    10.000
Sphericity outliers    10.000
---------------------------------------------------------------

 Input file :CDO_complete_R02_1-80A.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=   2.059 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=   2.200 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=   1.847 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=   2.200 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=   2.403 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=   2.433 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=   2.102 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  PRO               190  AAA  is missing in the structure
  Number of chains                  :       4
  Total number of monomers          :     502
  Number of atoms                   :    3945
  Number of missing atoms           :       1
  Number of rebuilt atoms           :    1480
  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:      2949         0      2949
               Angles:      5344         0      5344
              Chirals:       196         0       196
               Planes:       453         0       453
             Torsions:      1556         0      1556
            Intervals:         0         0         0
--------------------------------------------------------------------------------


  Number of harmonic restraints       =            0
  Number of atoms in special position =            0
 -----------------------------------------------------


    ****                           Info from mtz file                           ****

FreeR flag                            2
Number of "free" reflections       1177
Number of   all  reflections      23491
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          23491

   Current auto weighting coefficient =    6.7496872    

 mode : HKRF


######  TLS Group Definitions ######



     CGMAT cycle number =      1

    ****                              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.= 0.914 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        :   120  120  256
 Maximuum H,K,L                 :    34   34   73
 Minimum acceptable grid spacing:    79   79  167
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    34   34   73
 Minimum acceptable grid spacing:    79   79  167
 Weight matrix   0.31099582    
 Actual weight    6.7496872      is applied to the X-ray term
Norm of X_ray positional gradient                40.3
Norm of Geom. positional gradient                80.6
Norm of X_ray B-factor gradient                  131.
Norm of Geom. B-factor gradient                  122.
Product of X_ray and Geom posit. gradients     -0.135E+08
 Cosine of angle between them                      -0.429
Product of X_ray and Geom B-fact gradients     -0.435E+08
 Cosine of angle between them                      -0.842


Residuals: XRAY=     0.7820E+06 GEOM=     0.1380E+05 TOTAL=     0.7958E+06
 function value    795789.69    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.035     0.017
Bond angles  : refined atoms                   2106     1.850     1.644
Bond angles  : others                          3238     2.364     1.580
Torsion angles, period  1. refined              185     6.956     5.000
Torsion angles, period  2. refined               90    36.275    22.778
Torsion angles, period  3. refined              268    14.220    15.000
Torsion angles, period  4. refined                9    11.808    15.000
Chiral centres: refined atoms                   196     0.089     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.014     0.020
VDW repulsions: refined_atoms                   304     0.248     0.200
VDW repulsions.others                          1339     0.222     0.200
VDW; torsion: refined_atoms                     728     0.173     0.200
VDW; torsion.others                             722     0.082     0.200
HBOND: refined_atoms                            211     0.198     0.200
HBOND.others                                      2     0.041     0.200
VDW repulsions: symmetry: refined_atoms           9     0.208     0.200
VDW repulsions: symmetry: others                 25     0.187     0.200
HBOND: symmetry: refined_atoms                   25     0.178     0.200
M. chain bond B values: refined atoms           746     1.638     1.293
M. chain bond B values: others                  746     1.635     1.293
M. chain angle B values: refined atoms          929     2.551     1.926
M. chain angle B values: others                 930     2.550     1.925
S. chain bond B values: refined atoms           811     3.025     1.687
S. chain bond B values: others                  810     3.022     1.687
S. chain angle B values: refined atoms         1177     4.739     2.360
S. chain angle B values: others                1178     4.737     2.360
Long range B values: refined atoms             1842     7.247    17.910
Long range B values: others                    1756     7.001    16.625
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =    1.0584
Partial structure    1: scale =     0.3823, B  =   43.5289
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3007 100.00   455.1   464.0  0.16  0.17     164   439.6   452.3  0.19  0.20
 0.130    5115 100.00   299.9   286.9  0.16  0.15     285   289.5   280.1  0.22  0.20
 0.216    6548  99.97   202.8   186.3  0.17  0.15     324   199.0   186.3  0.23  0.20
 0.303    7639 100.00   104.1   116.7  0.26  0.19     404   108.7   123.1  0.28  0.21
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2162   0.927    845   0.839   3007   0.902  0.951  0.9694  0.9744  0.9160  0.9431
  0.1301   4254   0.884    861   0.779   5115   0.866  0.999  0.9493  0.9630  0.8890  0.9443
  0.2165   5674   0.876    874   0.771   6548   0.862  1.046  0.9405  0.9582  0.8749  0.9380
  0.3028   6783   0.773    859   0.700   7642   0.765  0.819  0.9185  0.9227  0.8662  0.8953
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22312
Percentage observed                  =    99.9872
Percentage of free reflections       =     5.0109
Overall R factor                     =     0.1787
Free R factor                        =     0.2234
Average Fourier shell correlation    =     0.9493
AverageFree Fourier shell correlation=     0.9391
Overall weighted R factor            =     0.1574
Free weighted R factor               =     0.1980
Overall weighted R2 factor           =     0.1867
Free weighted R2 factor              =     0.2322
Average correlation coefficient      =     0.9255
Overall correlation coefficient      =     0.9584
Free correlation coefficient         =     0.9318
Cruickshanks DPI for coordinate error=     0.1083
DPI based on free R factor           =     0.1108
Overall figure of merit              =     0.8353
ML based su of positional parameters =     0.0714
ML based su of thermal parameters    =     2.2171
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    115855.49       13801.347       795789.69      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.35888538    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    786384.31    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =   -0.0660
Partial structure    1: scale =     0.3841, B  =   43.8351
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1783
Free R factor                        =     0.2226
Average Fourier shell correlation    =     0.9547
AverageFree Fourier shell correlation=     0.9449
Average correlation coefficient      =     0.9270
Overall figure of merit              =     0.8562
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    115227.56       8634.2910       786384.31       795789.69    


     CGMAT cycle number =      3

 Weight matrix   0.36729181    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    785269.88    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.014     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =   -0.0093
Partial structure    1: scale =     0.3875, B  =   44.1952
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1774
Free R factor                        =     0.2218
Average Fourier shell correlation    =     0.9558
AverageFree Fourier shell correlation=     0.9458
Average correlation coefficient      =     0.9287
Overall figure of merit              =     0.8592
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    114987.13       9142.7559       785269.88       786384.31    


     CGMAT cycle number =      4

 Weight matrix   0.33453214    
 Actual weight    6.1360793      is applied to the X-ray term


 function value    714410.13    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.014     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =   -0.0073
Partial structure    1: scale =     0.3878, B  =   44.0352
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1772
Free R factor                        =     0.2216
Average Fourier shell correlation    =     0.9560
AverageFree Fourier shell correlation=     0.9458
Average correlation coefficient      =     0.9293
Overall figure of merit              =     0.8595
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    114905.76       9339.2949       714410.13       785269.88    


     CGMAT cycle number =      5

 Weight matrix   0.30341321    
 Actual weight    5.5782537      is applied to the X-ray term


 function value    650225.75    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =   -0.0075
Partial structure    1: scale =     0.3880, B  =   43.9615
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1775
Free R factor                        =     0.2216
Average Fourier shell correlation    =     0.9559
AverageFree Fourier shell correlation=     0.9458
Average correlation coefficient      =     0.9291
Overall figure of merit              =     0.8594
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    114930.23       9115.7471       650225.75       714410.13    


     CGMAT cycle number =      6

 Weight matrix   0.30244705    
 Actual weight    5.5782537      is applied to the X-ray term


 function value    650242.81    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =   -0.0123
Partial structure    1: scale =     0.3881, B  =   43.7909
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1781
Free R factor                        =     0.2217
Average Fourier shell correlation    =     0.9557
AverageFree Fourier shell correlation=     0.9456
Average correlation coefficient      =     0.9286
Overall figure of merit              =     0.8593
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    114992.06       8778.5801       650259.88       650225.75    

 fvalues    114992.06       8778.5801       650243.13       650233.44    
 fvalues    114992.06       8778.5801       650243.13       650233.44    


     CGMAT cycle number =      7

 Weight matrix   0.30228329    
 Actual weight    5.5782537      is applied to the X-ray term


 function value    650244.00    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =   -0.0107
Partial structure    1: scale =     0.3882, B  =   43.7573
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1781
Free R factor                        =     0.2217
Average Fourier shell correlation    =     0.9556
AverageFree Fourier shell correlation=     0.9456
Average correlation coefficient      =     0.9286
Overall figure of merit              =     0.8593
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    114999.30       8752.4883       650250.13       650233.44    

 fvalues    114999.30       8752.4883       650243.69       650247.75    
 fvalues    114999.30       8752.4883       650243.69       650247.75    


     CGMAT cycle number =      8

 Weight matrix   0.30231142    
 Actual weight    5.5782537      is applied to the X-ray term


 function value    650243.56    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =   -0.0148
Partial structure    1: scale =     0.3882, B  =   43.7558
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1782
Free R factor                        =     0.2217
Average Fourier shell correlation    =     0.9556
AverageFree Fourier shell correlation=     0.9456
Average correlation coefficient      =     0.9286
Overall figure of merit              =     0.8593
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    115002.48       8730.5820       650243.56       650247.75    


     CGMAT cycle number =      9

 Weight matrix   0.30224383    
 Actual weight    5.5782537      is applied to the X-ray term


 function value    650237.38    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =   -0.0156
Partial structure    1: scale =     0.3883, B  =   43.7733
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1782
Free R factor                        =     0.2217
Average Fourier shell correlation    =     0.9556
AverageFree Fourier shell correlation=     0.9455
Average correlation coefficient      =     0.9286
Overall figure of merit              =     0.8592
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    115004.65       8712.2676       650237.38       650243.56    


     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.= 0.929 id.= 3.000 dev= -2.07 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        :   120  120  256
 Maximuum H,K,L                 :    34   34   73
 Minimum acceptable grid spacing:    79   79  167
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    34   34   73
 Minimum acceptable grid spacing:    79   79  167
 Weight matrix   0.30212250    
 Actual weight    5.5782537      is applied to the X-ray term
Norm of X_ray positional gradient                36.8
Norm of Geom. positional gradient                37.0
Norm of X_ray B-factor gradient                  114.
Norm of Geom. B-factor gradient                  116.
Product of X_ray and Geom posit. gradients     -0.132E+08
 Cosine of angle between them                      -0.998
Product of X_ray and Geom B-fact gradients     -0.425E+08
 Cosine of angle between them                      -0.999


Residuals: XRAY=     0.6415E+06 GEOM=      8696.     TOTAL=     0.6502E+06
 function value    650245.88    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.769     1.644
Bond angles  : others                          3238     1.500     1.580
Torsion angles, period  1. refined              185     6.868     5.000
Torsion angles, period  2. refined               90    35.931    22.778
Torsion angles, period  3. refined              268    13.704    15.000
Torsion angles, period  4. refined                9    11.688    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   299     0.249     0.200
VDW repulsions.others                          1340     0.198     0.200
VDW; torsion: refined_atoms                     728     0.173     0.200
VDW; torsion.others                             748     0.086     0.200
HBOND: refined_atoms                            209     0.192     0.200
HBOND.others                                      1     0.072     0.200
VDW repulsions: symmetry: refined_atoms           8     0.201     0.200
VDW repulsions: symmetry: others                 25     0.173     0.200
HBOND: symmetry: refined_atoms                   22     0.182     0.200
M. chain bond B values: refined atoms           746     1.618     1.395
M. chain bond B values: others                  746     1.615     1.396
M. chain angle B values: refined atoms          929     2.562     2.082
M. chain angle B values: others                 930     2.561     2.082
S. chain bond B values: refined atoms           811     2.964     1.791
S. chain bond B values: others                  810     2.959     1.791
S. chain angle B values: refined atoms         1177     4.654     2.518
S. chain angle B values: others                1178     4.652     2.517
Long range B values: refined atoms             1833     7.172    19.248
Long range B values: others                    1747     6.881    17.872
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =   -0.0162
Partial structure    1: scale =     0.3883, B  =   43.7753
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.45 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3007 100.00   455.0   464.0  0.16  0.17     164   439.5   453.3  0.19  0.19
 0.130    5115 100.00   299.8   286.2  0.16  0.15     285   289.4   278.7  0.22  0.19
 0.216    6548  99.97   202.7   186.2  0.17  0.15     324   199.0   185.6  0.23  0.19
 0.303    7639 100.00   104.1   115.9  0.25  0.19     404   108.6   123.0  0.28  0.21
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2162   0.940    845   0.861   3007   0.918  0.953  0.9723  0.9764  0.9204  0.9405
  0.1301   4254   0.888    861   0.781   5115   0.870  0.999  0.9507  0.9636  0.8915  0.9435
  0.2165   5674   0.883    874   0.781   6548   0.870  1.046  0.9439  0.9600  0.8796  0.9370
  0.3028   6783   0.829    859   0.751   7642   0.820  0.841  0.9323  0.9383  0.8672  0.9065
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22312
Percentage observed                  =    99.9872
Percentage of free reflections       =     5.0109
Overall R factor                     =     0.1782
Free R factor                        =     0.2216
Average Fourier shell correlation    =     0.9556
AverageFree Fourier shell correlation=     0.9455
Overall weighted R factor            =     0.1587
Free weighted R factor               =     0.1954
Overall weighted R2 factor           =     0.1890
Free weighted R2 factor              =     0.2278
Average correlation coefficient      =     0.9285
Overall correlation coefficient      =     0.9580
Free correlation coefficient         =     0.9339
Cruickshanks DPI for coordinate error=     0.1080
DPI based on free R factor           =     0.1099
Overall figure of merit              =     0.8592
ML based su of positional parameters =     0.0658
ML based su of thermal parameters    =     2.0105
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    115010.85       8696.2422       650263.25       650237.38    

 fvalues    115010.85       8696.2422       650252.50       650255.94    
 fvalues    115010.85       8696.2422       650252.50       650255.94    

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.929 id.= 3.000 dev= -2.07 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

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

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R02_1-70A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.768     1.644
Bond angles  : others                          3238     1.500     1.580
Torsion angles, period  1. refined              185     6.868     5.000
Torsion angles, period  2. refined               90    35.926    22.778
Torsion angles, period  3. refined              268    13.695    15.000
Torsion angles, period  4. refined                9    11.683    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   299     0.249     0.200
VDW repulsions.others                          1342     0.197     0.200
VDW; torsion: refined_atoms                     728     0.173     0.200
VDW; torsion.others                             748     0.086     0.200
HBOND: refined_atoms                            209     0.192     0.200
HBOND.others                                      1     0.072     0.200
VDW repulsions: symmetry: refined_atoms           8     0.201     0.200
VDW repulsions: symmetry: others                 25     0.173     0.200
HBOND: symmetry: refined_atoms                   22     0.182     0.200
M. chain bond B values: refined atoms           746     1.618     1.395
M. chain bond B values: others                  746     1.614     1.396
M. chain angle B values: refined atoms          929     2.561     2.082
M. chain angle B values: others                 930     2.560     2.082
S. chain bond B values: refined atoms           811     2.963     1.791
S. chain bond B values: others                  810     2.957     1.791
S. chain angle B values: refined atoms         1177     4.652     2.518
S. chain angle B values: others                1178     4.650     2.517
Long range B values: refined atoms             1833     7.171    19.247
Long range B values: others                    1747     6.879    17.872
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =   -0.0152
Partial structure    1: scale =     0.3883, B  =   43.8230
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.45 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3007 100.00   455.0   464.0  0.16  0.17     164   439.6   453.3  0.19  0.19
 0.130    5115 100.00   299.8   286.2  0.16  0.15     285   289.4   278.7  0.22  0.19
 0.216    6548  99.97   202.8   186.2  0.17  0.15     324   199.0   185.6  0.23  0.19
 0.303    7639 100.00   104.1   115.9  0.25  0.19     404   108.7   122.9  0.28  0.21
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2162   0.940    845   0.861   3007   0.918  0.953  0.9723  0.9764  0.9204  0.9405
  0.1301   4254   0.888    861   0.781   5115   0.870  0.999  0.9507  0.9635  0.8916  0.9435
  0.2165   5674   0.883    874   0.781   6548   0.870  1.046  0.9439  0.9600  0.8796  0.9370
  0.3028   6783   0.828    859   0.751   7642   0.820  0.841  0.9323  0.9383  0.8672  0.9066
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22312
Percentage observed                  =    99.9872
Percentage of free reflections       =     5.0109
Overall R factor                     =     0.1783
Free R factor                        =     0.2216
Average Fourier shell correlation    =     0.9556
AverageFree Fourier shell correlation=     0.9455
Overall weighted R factor            =     0.1587
Free weighted R factor               =     0.1953
Overall weighted R2 factor           =     0.1891
Free weighted R2 factor              =     0.2277
Average correlation coefficient      =     0.9285
Overall correlation coefficient      =     0.9580
Free correlation coefficient         =     0.9339
Cruickshanks DPI for coordinate error=     0.1080
DPI based on free R factor           =     0.1099
Overall figure of merit              =     0.8592
ML based su of positional parameters =     0.0658
ML based su of thermal parameters    =     2.0105
-----------------------------------------------------------------------------
  Time in seconds: CPU =        19.14
             Elapsed =         128.00

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


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS: vs cycle :N:1,2,3:
:FOM vs cycle :N:1,4:
:-LL vs cycle :N:1,5:
:-LLfree vs cycle :N:1,6:
:Geometry vs cycle:N:1,7,8,9,10,11:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1787   0.2234   0.835      115855.    6286.9   0.0134  0.982   1.850  1.067   0.089
       1   0.1783   0.2226   0.856      115228.    6261.4   0.0129  0.948   1.804  1.042   0.088
       2   0.1774   0.2218   0.859      114987.    6253.6   0.0136  1.006   1.827  1.059   0.090
       3   0.1772   0.2216   0.860      114906.    6251.9   0.0137  1.019   1.840  1.068   0.091
       4   0.1775   0.2216   0.859      114930.    6252.2   0.0132  0.978   1.816  1.055   0.090
       5   0.1781   0.2217   0.859      114994.    6253.8   0.0125  0.933   1.780  1.034   0.087
       6   0.1781   0.2217   0.859      114999.    6254.1   0.0125  0.931   1.777  1.033   0.087
       7   0.1782   0.2217   0.859      115002.    6254.1   0.0125  0.930   1.774  1.031   0.087
       8   0.1782   0.2217   0.859      115005.    6254.2   0.0125  0.928   1.772  1.030   0.087
       9   0.1782   0.2216   0.859      115009.    6254.2   0.0125  0.927   1.769  1.029   0.087
      10   0.1783   0.2216   0.859      115013.    6254.4   0.0124  0.927   1.768  1.028   0.087
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1787   0.1783
             R free    0.2234   0.2216
     Rms BondLength    0.0134   0.0124
      Rms BondAngle    1.8499   1.7683
     Rms ChirVolume    0.0886   0.0870
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      51.2s System:    0.2s Elapsed:     0:52