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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: 16:55:29 


 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 13
  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_R13_1-80A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R13_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_R13_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:    13
  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_R13_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=   2.051 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=   2.213 ideal_dist=   2.090
            ch:AAA  res:  88  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   1.849 ideal_dist=   1.720
            ch:AAA  res:  93  CYS              at:SG  .->ch:AAA  res: 157  TYR              at:CE1 .
  INFO:     link is found (not be used) dist=   2.189 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=   2.393 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=   2.405 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=   2.089 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                           13
Number of "free" reflections       1152
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.= 0.910 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   0.32461700    
 Actual weight    6.7496872      is applied to the X-ray term
Norm of X_ray positional gradient                43.4
Norm of Geom. positional gradient                78.8
Norm of X_ray B-factor gradient                  145.
Norm of Geom. B-factor gradient                  113.
Product of X_ray and Geom posit. gradients     -0.129E+08
 Cosine of angle between them                      -0.390
Product of X_ray and Geom B-fact gradients     -0.443E+08
 Cosine of angle between them                      -0.835


Residuals: XRAY=     0.7820E+06 GEOM=     0.1322E+05 TOTAL=     0.7952E+06
 function value    795193.75    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.035     0.017
Bond angles  : refined atoms                   2106     1.784     1.644
Bond angles  : others                          3238     2.348     1.580
Torsion angles, period  1. refined              185     7.090     5.000
Torsion angles, period  2. refined               90    37.038    22.778
Torsion angles, period  3. refined              268    14.303    15.000
Torsion angles, period  4. refined                9    10.809    15.000
Chiral centres: refined atoms                   196     0.084     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.013     0.020
VDW repulsions: refined_atoms                   311     0.240     0.200
VDW repulsions.others                          1340     0.222     0.200
VDW; torsion: refined_atoms                     720     0.172     0.200
VDW; torsion.others                             716     0.081     0.200
HBOND: refined_atoms                            229     0.197     0.200
HBOND.others                                      1     0.086     0.200
VDW repulsions: symmetry: refined_atoms           9     0.205     0.200
VDW repulsions: symmetry: others                 28     0.178     0.200
HBOND: symmetry: refined_atoms                   23     0.192     0.200
M. chain bond B values: refined atoms           746     1.636     1.295
M. chain bond B values: others                  746     1.635     1.295
M. chain angle B values: refined atoms          929     2.583     1.929
M. chain angle B values: others                 930     2.581     1.928
S. chain bond B values: refined atoms           811     2.841     1.679
S. chain bond B values: others                  810     2.837     1.678
S. chain angle B values: refined atoms         1177     4.497     2.355
S. chain angle B values: others                1178     4.495     2.355
Long range B values: refined atoms             1863     7.444    18.267
Long range B values: others                    1764     7.011    16.788
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =    1.0687
Partial structure    1: scale =     0.3873, B  =   45.0874
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3027 100.00   453.4   462.2  0.16  0.17     144   466.1   471.7  0.16  0.17
 0.130    5104 100.00   299.3   286.6  0.16  0.15     296   297.1   279.4  0.19  0.18
 0.216    6539  99.97   202.7   186.4  0.17  0.15     333   197.4   179.5  0.22  0.19
 0.303    7664 100.00   104.0   116.7  0.27  0.20     379   108.7   122.2  0.28  0.21
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2173   0.933    854   0.858   3027   0.912  0.953  0.9727  0.9756  0.9216  0.9424
  0.1301   4242   0.896    862   0.794   5104   0.879  1.004  0.9595  0.9653  0.9323  0.9439
  0.2165   5656   0.885    883   0.780   6539   0.871  1.047  0.9486  0.9608  0.9067  0.9378
  0.3028   6797   0.778    870   0.705   7667   0.770  0.821  0.9196  0.9199  0.8840  0.8882
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22337
Percentage observed                  =    99.9872
Percentage of free reflections       =     4.9044
Overall R factor                     =     0.1800
Free R factor                        =     0.2061
Average Fourier shell correlation    =     0.9498
AverageFree Fourier shell correlation=     0.9449
Overall weighted R factor            =     0.1575
Free weighted R factor               =     0.1801
Overall weighted R2 factor           =     0.1856
Free weighted R2 factor              =     0.2042
Average correlation coefficient      =     0.9228
Overall correlation coefficient      =     0.9578
Free correlation coefficient         =     0.9456
Cruickshanks DPI for coordinate error=     0.1089
DPI based on free R factor           =     0.1022
Overall figure of merit              =     0.8437
ML based su of positional parameters =     0.0699
ML based su of thermal parameters    =     2.1921
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    115853.31       13220.104       795193.75      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.37452039    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    786086.44    

-------------------------------------------------------------------------------
             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  =   -0.0655
Partial structure    1: scale =     0.3874, B  =   45.0215
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                     =     0.1785
Free R factor                        =     0.2040
Average Fourier shell correlation    =     0.9549
AverageFree Fourier shell correlation=     0.9498
Average correlation coefficient      =     0.9253
Overall figure of merit              =     0.8606
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    115184.35       8628.1348       786086.44       795193.75    


     CGMAT cycle number =      3

 Weight matrix   0.38149267    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    785143.13    

-------------------------------------------------------------------------------
             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  =   -0.0266
Partial structure    1: scale =     0.3877, B  =   45.1977
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.44 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1774
Free R factor                        =     0.2030
Average Fourier shell correlation    =     0.9560
AverageFree Fourier shell correlation=     0.9506
Average correlation coefficient      =     0.9272
Overall figure of merit              =     0.8630
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    114946.82       9288.0742       785143.13       786086.44    


     CGMAT cycle number =      4

 Weight matrix   0.34899566    
 Actual weight    6.1360793      is applied to the X-ray term


 function value    714315.88    

-------------------------------------------------------------------------------
             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 =     0.0427, B  =   -0.0028
Partial structure    1: scale =     0.3879, B  =   45.3172
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.44 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1771
Free R factor                        =     0.2026
Average Fourier shell correlation    =     0.9563
AverageFree Fourier shell correlation=     0.9509
Average correlation coefficient      =     0.9279
Overall figure of merit              =     0.8636
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    114857.35       9542.0488       714315.88       785143.13    


     CGMAT cycle number =      5

 Weight matrix   0.31853923    
 Actual weight    5.5782537      is applied to the X-ray term


 function value    650103.94    

-------------------------------------------------------------------------------
             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 =     0.0427, B  =   -0.0297
Partial structure    1: scale =     0.3879, B  =   45.1368
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.44 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1773
Free R factor                        =     0.2023
Average Fourier shell correlation    =     0.9564
AverageFree Fourier shell correlation=     0.9510
Average correlation coefficient      =     0.9279
Overall figure of merit              =     0.8642
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    114871.91       9319.2793       650103.94       714315.88    


     CGMAT cycle number =      6

 Weight matrix   0.31807387    
 Actual weight    5.5782537      is applied to the X-ray term


 function value    650086.06    

-------------------------------------------------------------------------------
             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  =   -0.0413
Partial structure    1: scale =     0.3880, B  =   45.0181
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.44 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1777
Free R factor                        =     0.2025
Average Fourier shell correlation    =     0.9563
AverageFree Fourier shell correlation=     0.9510
Average correlation coefficient      =     0.9275
Overall figure of merit              =     0.8644
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    114924.50       9008.0762       650086.06       650103.94    


     CGMAT cycle number =      7

 Weight matrix   0.31717193    
 Actual weight    5.5782537      is applied to the X-ray term


 function value    650111.81    

-------------------------------------------------------------------------------
             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  =   -0.0321
Partial structure    1: scale =     0.3879, B  =   44.9609
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.44 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1779
Free R factor                        =     0.2026
Average Fourier shell correlation    =     0.9563
AverageFree Fourier shell correlation=     0.9509
Average correlation coefficient      =     0.9275
Overall figure of merit              =     0.8642
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    114940.98       8930.5156       650107.44       650086.06    

 fvalues    114940.98       8930.5156       650126.13       650100.44    
 fvalues    114940.98       8930.5156       650126.13       650100.44    


     CGMAT cycle number =      8

 Weight matrix   0.31652108    
 Actual weight    5.5782537      is applied to the X-ray term


 function value    650131.56    

-------------------------------------------------------------------------------
             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  =   -0.0241
Partial structure    1: scale =     0.3879, B  =   44.9310
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.44 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1779
Free R factor                        =     0.2026
Average Fourier shell correlation    =     0.9563
AverageFree Fourier shell correlation=     0.9509
Average correlation coefficient      =     0.9275
Overall figure of merit              =     0.8641
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    114946.13       8916.7871       650102.00       650100.44    
 fvalues    114946.13       8916.7871       650102.00       650115.50    


     CGMAT cycle number =      9

 Weight matrix   0.31641448    
 Actual weight    5.5782537      is applied to the X-ray term


 function value    650127.19    

-------------------------------------------------------------------------------
             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  =   -0.0224
Partial structure    1: scale =     0.3878, B  =   44.8977
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.44 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1779
Free R factor                        =     0.2025
Average Fourier shell correlation    =     0.9563
AverageFree Fourier shell correlation=     0.9509
Average correlation coefficient      =     0.9275
Overall figure of merit              =     0.8641
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    114951.45       8901.0293       650083.94       650115.50    
 fvalues    114951.45       8901.0293       650083.94       650129.31    


     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.= 0.923 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        :   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   0.31692648    
 Actual weight    5.5782537      is applied to the X-ray term
Norm of X_ray positional gradient                37.9
Norm of Geom. positional gradient                37.9
Norm of X_ray B-factor gradient                  117.
Norm of Geom. B-factor gradient                  119.
Product of X_ray and Geom posit. gradients     -0.139E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.451E+08
 Cosine of angle between them                      -0.997


Residuals: XRAY=     0.6412E+06 GEOM=      8885.     TOTAL=     0.6501E+06
 function value    650087.81    

-------------------------------------------------------------------------------
             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     1.786     1.644
Bond angles  : others                          3238     1.493     1.580
Torsion angles, period  1. refined              185     6.992     5.000
Torsion angles, period  2. refined               90    36.562    22.778
Torsion angles, period  3. refined              268    14.087    15.000
Torsion angles, period  4. refined                9    10.750    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                   307     0.243     0.200
VDW repulsions.others                          1349     0.197     0.200
VDW; torsion: refined_atoms                     725     0.172     0.200
VDW; torsion.others                             791     0.083     0.200
HBOND: refined_atoms                            219     0.197     0.200
HBOND.others                                      1     0.125     0.200
VDW repulsions: symmetry: refined_atoms          10     0.180     0.200
VDW repulsions: symmetry: others                 27     0.174     0.200
HBOND: symmetry: refined_atoms                   23     0.193     0.200
M. chain bond B values: refined atoms           746     1.702     1.395
M. chain bond B values: others                  746     1.700     1.395
M. chain angle B values: refined atoms          929     2.675     2.080
M. chain angle B values: others                 930     2.673     2.080
S. chain bond B values: refined atoms           811     3.010     1.802
S. chain bond B values: others                  810     3.004     1.801
S. chain angle B values: refined atoms         1177     4.721     2.532
S. chain angle B values: others                1178     4.719     2.531
Long range B values: refined atoms             1850     7.592    19.580
Long range B values: others                    1755     7.130    18.056
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =   -0.0293
Partial structure    1: scale =     0.3878, B  =   44.9484
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.44 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3027 100.00   453.2   462.9  0.16  0.17     144   465.9   470.5  0.17  0.17
 0.130    5104 100.00   299.1   285.7  0.16  0.15     296   297.0   278.1  0.19  0.18
 0.216    6539  99.97   202.6   186.5  0.17  0.15     333   197.3   179.6  0.21  0.18
 0.303    7664 100.00   104.0   116.1  0.25  0.19     379   108.6   121.8  0.27  0.21
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2173   0.940    854   0.867   3027   0.919  0.953  0.9745  0.9768  0.9222  0.9414
  0.1301   4242   0.899    862   0.799   5104   0.882  1.004  0.9612  0.9662  0.9354  0.9443
  0.2165   5656   0.895    883   0.791   6539   0.881  1.047  0.9524  0.9634  0.9108  0.9384
  0.3028   6797   0.825    870   0.748   7667   0.816  0.838  0.9324  0.9355  0.8882  0.9017
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22337
Percentage observed                  =    99.9872
Percentage of free reflections       =     4.9044
Overall R factor                     =     0.1780
Free R factor                        =     0.2025
Average Fourier shell correlation    =     0.9563
AverageFree Fourier shell correlation=     0.9509
Overall weighted R factor            =     0.1575
Free weighted R factor               =     0.1787
Overall weighted R2 factor           =     0.1871
Free weighted R2 factor              =     0.2032
Average correlation coefficient      =     0.9275
Overall correlation coefficient      =     0.9582
Free correlation coefficient         =     0.9472
Cruickshanks DPI for coordinate error=     0.1077
DPI based on free R factor           =     0.1004
Overall figure of merit              =     0.8642
ML based su of positional parameters =     0.0642
ML based su of thermal parameters    =     1.9820
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    114946.88       8885.0303       650087.81       650129.31    

    ****                              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.= 0.923 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_R13_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     1.784     1.644
Bond angles  : others                          3238     1.493     1.580
Torsion angles, period  1. refined              185     6.989     5.000
Torsion angles, period  2. refined               90    36.511    22.778
Torsion angles, period  3. refined              268    14.044    15.000
Torsion angles, period  4. refined                9    10.738    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                   307     0.243     0.200
VDW repulsions.others                          1349     0.197     0.200
VDW; torsion: refined_atoms                     726     0.172     0.200
VDW; torsion.others                             795     0.083     0.200
HBOND: refined_atoms                            219     0.197     0.200
HBOND.others                                      1     0.125     0.200
VDW repulsions: symmetry: refined_atoms          10     0.180     0.200
VDW repulsions: symmetry: others                 27     0.175     0.200
HBOND: symmetry: refined_atoms                   24     0.189     0.200
M. chain bond B values: refined atoms           746     1.701     1.395
M. chain bond B values: others                  746     1.699     1.395
M. chain angle B values: refined atoms          929     2.672     2.080
M. chain angle B values: others                 930     2.671     2.080
S. chain bond B values: refined atoms           811     3.008     1.801
S. chain bond B values: others                  810     3.001     1.801
S. chain angle B values: refined atoms         1177     4.716     2.531
S. chain angle B values: others                1178     4.714     2.531
Long range B values: refined atoms             1851     7.586    19.591
Long range B values: others                    1756     7.125    18.067
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =   -0.0274
Partial structure    1: scale =     0.3874, B  =   45.2558
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3027 100.00   453.2   463.1  0.16  0.17     144   465.9   470.5  0.17  0.17
 0.130    5104 100.00   299.1   285.8  0.16  0.15     296   297.0   278.2  0.19  0.18
 0.216    6539  99.97   202.6   186.5  0.17  0.15     333   197.3   179.6  0.21  0.18
 0.303    7664 100.00   104.0   116.0  0.25  0.19     379   108.6   121.8  0.27  0.21
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2173   0.940    854   0.867   3027   0.919  0.952  0.9746  0.9766  0.9226  0.9407
  0.1301   4242   0.899    862   0.799   5104   0.882  1.004  0.9612  0.9661  0.9354  0.9442
  0.2165   5656   0.895    883   0.791   6539   0.881  1.047  0.9524  0.9634  0.9108  0.9384
  0.3028   6797   0.825    870   0.748   7667   0.816  0.838  0.9325  0.9355  0.8882  0.9018
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22337
Percentage observed                  =    99.9872
Percentage of free reflections       =     4.9044
Overall R factor                     =     0.1783
Free R factor                        =     0.2023
Average Fourier shell correlation    =     0.9563
AverageFree Fourier shell correlation=     0.9509
Overall weighted R factor            =     0.1580
Free weighted R factor               =     0.1785
Overall weighted R2 factor           =     0.1881
Free weighted R2 factor              =     0.2037
Average correlation coefficient      =     0.9275
Overall correlation coefficient      =     0.9580
Free correlation coefficient         =     0.9473
Cruickshanks DPI for coordinate error=     0.1078
DPI based on free R factor           =     0.1003
Overall figure of merit              =     0.8641
ML based su of positional parameters =     0.0642
ML based su of thermal parameters    =     1.9820
-----------------------------------------------------------------------------
  Time in seconds: CPU =        19.83
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1800   0.2061   0.844      115853.    6107.4   0.0123  0.909   1.784  1.025   0.084
       1   0.1785   0.2040   0.861      115184.    6085.9   0.0129  0.953   1.791  1.031   0.087
       2   0.1774   0.2030   0.863      114947.    6079.8   0.0136  1.014   1.834  1.059   0.090
       3   0.1771   0.2026   0.864      114857.    6076.3   0.0138  1.025   1.853  1.071   0.091
       4   0.1773   0.2023   0.864      114872.    6075.2   0.0132  0.983   1.834  1.060   0.090
       5   0.1777   0.2025   0.864      114925.    6077.0   0.0125  0.939   1.802  1.042   0.088
       6   0.1779   0.2026   0.864      114943.    6078.0   0.0125  0.933   1.791  1.036   0.087
       7   0.1779   0.2026   0.864      114949.    6078.4   0.0125  0.933   1.790  1.036   0.087
       8   0.1779   0.2025   0.864      114951.    6078.6   0.0124  0.931   1.788  1.035   0.087
       9   0.1780   0.2025   0.864      114947.    6078.5   0.0124  0.930   1.786  1.034   0.087
      10   0.1783   0.2023   0.864      114968.    6078.4   0.0124  0.929   1.784  1.033   0.087
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1800   0.1783
             R free    0.2061   0.2023
     Rms BondLength    0.0123   0.0124
      Rms BondAngle    1.7838   1.7842
     Rms ChirVolume    0.0844   0.0869
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      51.9s System:    0.1s Elapsed:     0:52