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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: 20:28:22 


 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 1.42     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 1
  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_R01_1-50A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R01_1-42A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R01_1-42A.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       0.1240
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.4200
  Estimated number of reflections :      51186
  Free R exclusion - flag equals:     1
  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  1.4200

  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_R01_1-50A.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=   2.070 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=   2.196 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=   1.834 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=   2.207 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=   2.409 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=   2.387 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=   2.078 ideal_dist=   1.870
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:OD  .
  --------------------------------
  --- title of input coord file ---

  PDB_code:xxxx
  PDB_name:----
  PDB_date:26-MAY-20
  --------------------------------
  ATTENTION: atom:OXT  THR               171  AAA  is missing in the structure
  ATTENTION: atom:OXT  PRO               190  AAA  is missing in the structure
  Number of chains                  :       4
  Total number of monomers          :     502
  Number of atoms                   :    3948
  Number of missing atoms           :       0
  Number of rebuilt atoms           :    1482
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0

_ccp4_form_factor.scat_method    'Sum of Gaussians'
_ccp4_form_factor.scat_data_source  X-ray


 loop_
     _atom_type_symbol
     _atom_type_scat_Cromer_Mann_a1
     _atom_type_scat_Cromer_Mann_b1
     _atom_type_scat_Cromer_Mann_a2
     _atom_type_scat_Cromer_Mann_b2
     _atom_type_scat_Cromer_Mann_a3
     _atom_type_scat_Cromer_Mann_b3
     _atom_type_scat_Cromer_Mann_a4
     _atom_type_scat_Cromer_Mann_b4
     _atom_type_scat_Cromer_Mann_c


  N     12.2220   0.0057   3.1346   9.8933   2.0141  28.9975   1.1672   0.5826 -11.5379
  H      0.4930  10.5109   0.3229  26.1257   0.1402   3.1424   0.0408  57.7997   0.0030
  C      2.3103  20.8439   1.0201  10.2075   1.5888   0.5687   0.8651  51.6512   0.2156
  O      3.0487  13.2771   2.2870   5.7011   1.5464   0.3239   0.8671  32.9089   0.2508
  S      6.9054   1.4679   5.2035  22.2151   1.4379   0.2536   1.5863  56.1720   1.0490
  FE    11.7738   4.7611   7.3600   0.3072   3.5235  15.3535   2.3054  76.8805   1.2805


 Number of distances         :           0
 Number of angles            :           0
 Number of torsions          :           0
 Number of planes            :           0
 Number of chirals           :           0
 Number of intervals         :           0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
                        Standard  External       All
                Bonds:      2950         0      2950
               Angles:      5345         0      5345
              Chirals:       196         0       196
               Planes:       451         0       451
             Torsions:      1553         0      1553
            Intervals:         0         0         0
--------------------------------------------------------------------------------


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


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

FreeR flag                            1
Number of "free" reflections       1973
Number of   all  reflections      39817
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          39817

   Current auto weighting coefficient =    6.0498405    

 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.= 0.900 id.= 3.000 dev= -2.10 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        :   144  144  288
 Maximuum H,K,L                 :    41   41   87
 Minimum acceptable grid spacing:    91   91  192
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  288
 Maximuum H,K,L                 :    41   41   87
 Minimum acceptable grid spacing:    91   91  192
 Weight matrix   0.24402149    
 Actual weight    6.0498405      is applied to the X-ray term
Norm of X_ray positional gradient                36.6
Norm of Geom. positional gradient                82.9
Norm of X_ray B-factor gradient                  92.3
Norm of Geom. B-factor gradient                 0.246E+05
Product of X_ray and Geom posit. gradients     -0.150E+08
 Cosine of angle between them                      -0.509
Product of X_ray and Geom B-fact gradients     -0.293E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.1066E+07 GEOM=     0.2809E+05 TOTAL=     0.1094E+07
 function value    1094364.9    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.845     1.644
Bond angles  : others                          3242     2.360     1.582
Torsion angles, period  1. refined              184     6.801     5.000
Torsion angles, period  2. refined               90    35.578    22.778
Torsion angles, period  3. refined              268    12.670    15.000
Torsion angles, period  4. refined                9    11.860    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.016     0.020
VDW repulsions: refined_atoms                   295     0.273     0.200
VDW repulsions.others                          1342     0.230     0.200
VDW; torsion: refined_atoms                     722     0.173     0.200
VDW; torsion.others                             715     0.081     0.200
HBOND: refined_atoms                            219     0.197     0.200
HBOND.others                                      2     0.069     0.200
VDW repulsions: symmetry: refined_atoms           8     0.201     0.200
VDW repulsions: symmetry: others                 25     0.183     0.200
HBOND: symmetry: refined_atoms                   22     0.179     0.200
M. chain bond B values: refined atoms           745     1.829     1.620
M. chain bond B values: others                  745     1.823     1.620
M. chain angle B values: refined atoms          926     2.807     2.418
M. chain angle B values: others                 927     2.806     2.418
S. chain bond B values: refined atoms           811     3.274     2.038
S. chain bond B values: others                  810     3.269     2.037
S. chain angle B values: refined atoms         1177     4.997     2.884
S. chain angle B values: others                1178     4.995     2.883
Long range B values: refined atoms             1840     7.172    22.259
Long range B values: others                    1750     6.940    20.764
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =    0.8027
Partial structure    1: scale =     0.3953, B  =   46.0574
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5058 100.00   379.1   388.9  0.17  0.18     271   381.2   395.1  0.20  0.20
 0.186    8679  99.98   205.1   181.2  0.19  0.17     464   213.0   190.4  0.23  0.20
 0.310   11067 100.00    91.7    88.4  0.23  0.20     580    92.2    89.7  0.26  0.22
 0.434   12853  98.63    38.7    47.9  0.47  0.46     642    38.0    47.8  0.48  0.47
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3832   0.905   1226   0.781   5058   0.875  0.949  0.9590  0.9666  0.8951  0.9364
  0.1863   7431   0.862   1248   0.757   8679   0.847  1.093  0.9479  0.9560  0.8978  0.9370
  0.3102   9814   0.796   1253   0.720  11067   0.787  0.948  0.9263  0.9328  0.8960  0.9127
  0.4340  11605   0.338   1248   0.303  12853   0.335  0.338  0.5766  0.6093  0.6258  0.6497
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37657
Percentage observed                  =    99.4927
Percentage of free reflections       =     4.9402
Overall R factor                     =     0.2181
Free R factor                        =     0.2463
Average Fourier shell correlation    =     0.8323
AverageFree Fourier shell correlation=     0.8212
Overall weighted R factor            =     0.1824
Free weighted R factor               =     0.2071
Overall weighted R2 factor           =     0.2124
Free weighted R2 factor              =     0.2336
Average correlation coefficient      =     0.8317
Overall correlation coefficient      =     0.9602
Free correlation coefficient         =     0.9426
Cruickshanks DPI for coordinate error=     0.0776
DPI based on free R factor           =     0.0787
Overall figure of merit              =     0.6583
ML based su of positional parameters =     0.0763
ML based su of thermal parameters    =     2.2264
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    176248.31       28090.742       1094364.9      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.30441248    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1069612.6    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =   -0.0707
Partial structure    1: scale =     0.3943, B  =   45.2026
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2189
Free R factor                        =     0.2468
Average Fourier shell correlation    =     0.8504
AverageFree Fourier shell correlation=     0.8407
Average correlation coefficient      =     0.8298
Overall figure of merit              =     0.6913
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    175132.42       10089.331       1069612.6       1094364.9    


     CGMAT cycle number =      3

 Weight matrix   0.31205934    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1067353.3    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =   -0.0067
Partial structure    1: scale =     0.3941, B  =   41.6441
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2180
Free R factor                        =     0.2460
Average Fourier shell correlation    =     0.8545
AverageFree Fourier shell correlation=     0.8447
Average correlation coefficient      =     0.8311
Overall figure of merit              =     0.6957
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    174924.09       9090.3535       1067353.3       1069612.6    


     CGMAT cycle number =      4

 Weight matrix   0.31344017    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1066700.9    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =    0.0018
Partial structure    1: scale =     0.3943, B  =   38.5351
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2178
Free R factor                        =     0.2457
Average Fourier shell correlation    =     0.8554
AverageFree Fourier shell correlation=     0.8455
Average correlation coefficient      =     0.8317
Overall figure of merit              =     0.6966
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    174880.30       8703.0059       1066700.9       1067353.3    


     CGMAT cycle number =      5

 Weight matrix   0.31391567    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1066542.4    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =    0.0104
Partial structure    1: scale =     0.3945, B  =   38.5382
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2177
Free R factor                        =     0.2456
Average Fourier shell correlation    =     0.8555
AverageFree Fourier shell correlation=     0.8456
Average correlation coefficient      =     0.8320
Overall figure of merit              =     0.6968
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    174864.42       8640.4463       1066542.4       1066700.9    


     CGMAT cycle number =      6

 Weight matrix   0.31417739    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1066501.8    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =    0.0097
Partial structure    1: scale =     0.3947, B  =   38.6033
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2177
Free R factor                        =     0.2456
Average Fourier shell correlation    =     0.8555
AverageFree Fourier shell correlation=     0.8457
Average correlation coefficient      =     0.8321
Overall figure of merit              =     0.6969
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    174856.98       8644.8340       1066501.8       1066542.4    


     CGMAT cycle number =      7

 Weight matrix   0.31480673    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1066463.1    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =    0.0024
Partial structure    1: scale =     0.3948, B  =   38.6148
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2176
Free R factor                        =     0.2457
Average Fourier shell correlation    =     0.8556
AverageFree Fourier shell correlation=     0.8457
Average correlation coefficient      =     0.8321
Overall figure of merit              =     0.6970
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    174850.17       8647.4805       1066463.1       1066501.8    


     CGMAT cycle number =      8

 Weight matrix   0.31417301    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1066520.5    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =    0.0111
Partial structure    1: scale =     0.3947, B  =   38.6422
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2176
Free R factor                        =     0.2458
Average Fourier shell correlation    =     0.8555
AverageFree Fourier shell correlation=     0.8455
Average correlation coefficient      =     0.8320
Overall figure of merit              =     0.6968
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    174863.31       8653.3613       1066549.8       1066463.1    

 fvalues    174863.31       8653.3613       1066526.4       1066548.5    
 fvalues    174863.31       8653.3613       1066526.4       1066548.5    


     CGMAT cycle number =      9

 Weight matrix   0.31389818    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1066562.3    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =    0.0126
Partial structure    1: scale =     0.3947, B  =   38.6575
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2176
Free R factor                        =     0.2458
Average Fourier shell correlation    =     0.8554
AverageFree Fourier shell correlation=     0.8455
Average correlation coefficient      =     0.8320
Overall figure of merit              =     0.6968
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    174866.34       8646.5947       1066540.0       1066548.5    
 fvalues    174866.34       8646.5947       1066540.0       1066560.1    


     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.= 0.919 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        :   144  144  288
 Maximuum H,K,L                 :    41   41   87
 Minimum acceptable grid spacing:    91   91  192
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  288
 Maximuum H,K,L                 :    41   41   87
 Minimum acceptable grid spacing:    91   91  192
 Weight matrix   0.31406453    
 Actual weight    6.0498405      is applied to the X-ray term
Norm of X_ray positional gradient                42.9
Norm of Geom. positional gradient                42.9
Norm of X_ray B-factor gradient                  101.
Norm of Geom. B-factor gradient                  99.9
Product of X_ray and Geom posit. gradients     -0.178E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.324E+08
 Cosine of angle between them                      -0.999


Residuals: XRAY=     0.1058E+07 GEOM=      8644.     TOTAL=     0.1067E+07
 function value    1066537.8    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.833     1.644
Bond angles  : others                          3242     1.494     1.582
Torsion angles, period  1. refined              184     6.798     5.000
Torsion angles, period  2. refined               90    35.513    22.778
Torsion angles, period  3. refined              268    12.644    15.000
Torsion angles, period  4. refined                9    11.828    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   293     0.274     0.200
VDW repulsions.others                          1353     0.204     0.200
VDW; torsion: refined_atoms                     719     0.173     0.200
VDW; torsion.others                             783     0.084     0.200
HBOND: refined_atoms                            218     0.196     0.200
HBOND.others                                      1     0.088     0.200
VDW repulsions: symmetry: refined_atoms           9     0.187     0.200
VDW repulsions: symmetry: others                 27     0.162     0.200
HBOND: symmetry: refined_atoms                   21     0.180     0.200
M. chain bond B values: refined atoms           745     1.860     1.697
M. chain bond B values: others                  745     1.854     1.697
M. chain angle B values: refined atoms          926     2.843     2.534
M. chain angle B values: others                 927     2.842     2.534
S. chain bond B values: refined atoms           811     3.321     2.120
S. chain bond B values: others                  810     3.315     2.120
S. chain angle B values: refined atoms         1177     5.075     3.006
S. chain angle B values: others                1178     5.073     3.005
Long range B values: refined atoms             1834     7.273    23.166
Long range B values: others                    1744     6.996    21.629
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =    0.0119
Partial structure    1: scale =     0.3949, B  =   38.6891
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5058 100.00   379.6   389.4  0.17  0.18     271   381.6   395.4  0.20  0.20
 0.186    8679  99.98   205.4   181.5  0.19  0.17     464   213.2   190.7  0.23  0.20
 0.310   11067 100.00    91.8    88.6  0.23  0.20     580    92.3    89.9  0.26  0.22
 0.434   12853  98.63    38.7    47.9  0.47  0.46     642    38.1    47.9  0.47  0.47
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3832   0.926   1226   0.817   5058   0.899  0.953  0.9645  0.9729  0.8957  0.9368
  0.1863   7431   0.882   1248   0.779   8679   0.868  1.095  0.9530  0.9612  0.8988  0.9370
  0.3102   9814   0.819   1253   0.744  11067   0.811  0.954  0.9324  0.9394  0.8961  0.9136
  0.4340  11605   0.407   1248   0.370  12853   0.404  0.383  0.6391  0.6656  0.6226  0.6497
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37657
Percentage observed                  =    99.4927
Percentage of free reflections       =     4.9402
Overall R factor                     =     0.2176
Free R factor                        =     0.2459
Average Fourier shell correlation    =     0.8555
AverageFree Fourier shell correlation=     0.8455
Overall weighted R factor            =     0.1820
Free weighted R factor               =     0.2067
Overall weighted R2 factor           =     0.2120
Free weighted R2 factor              =     0.2323
Average correlation coefficient      =     0.8320
Overall correlation coefficient      =     0.9604
Free correlation coefficient         =     0.9430
Cruickshanks DPI for coordinate error=     0.0775
DPI based on free R factor           =     0.0785
Overall figure of merit              =     0.6968
ML based su of positional parameters =     0.0672
ML based su of thermal parameters    =     1.9445
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    174863.09       8643.9316       1066537.8       1066560.1    

    ****                              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.= 0.919 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
          28          24          36  0.70425701      2.37302221E-02  0.70425248    
          36           8          36  0.70425701      2.37302221E-02  0.70425248    

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R01_1-42A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.833     1.644
Bond angles  : others                          3242     1.494     1.582
Torsion angles, period  1. refined              184     6.799     5.000
Torsion angles, period  2. refined               90    35.509    22.778
Torsion angles, period  3. refined              268    12.642    15.000
Torsion angles, period  4. refined                9    11.819    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   294     0.273     0.200
VDW repulsions.others                          1352     0.204     0.200
VDW; torsion: refined_atoms                     719     0.173     0.200
VDW; torsion.others                             784     0.084     0.200
HBOND: refined_atoms                            219     0.196     0.200
HBOND.others                                      1     0.088     0.200
VDW repulsions: symmetry: refined_atoms           9     0.187     0.200
VDW repulsions: symmetry: others                 26     0.164     0.200
HBOND: symmetry: refined_atoms                   21     0.180     0.200
M. chain bond B values: refined atoms           745     1.860     1.697
M. chain bond B values: others                  745     1.855     1.698
M. chain angle B values: refined atoms          926     2.843     2.534
M. chain angle B values: others                 927     2.842     2.534
S. chain bond B values: refined atoms           811     3.320     2.120
S. chain bond B values: others                  810     3.315     2.120
S. chain angle B values: refined atoms         1177     5.075     3.006
S. chain angle B values: others                1178     5.072     3.005
Long range B values: refined atoms             1836     7.292    23.233
Long range B values: others                    1746     7.016    21.701
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =    0.0127
Partial structure    1: scale =     0.3950, B  =   38.6880
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5058 100.00   379.6   389.4  0.17  0.18     271   381.6   395.4  0.20  0.20
 0.186    8679  99.98   205.4   181.5  0.19  0.17     464   213.2   190.7  0.23  0.20
 0.310   11067 100.00    91.8    88.6  0.23  0.20     580    92.3    89.9  0.26  0.22
 0.434   12853  98.63    38.7    47.9  0.47  0.46     642    38.1    47.9  0.47  0.47
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3832   0.926   1226   0.818   5058   0.900  0.953  0.9645  0.9729  0.8957  0.9368
  0.1863   7431   0.882   1248   0.779   8679   0.868  1.095  0.9530  0.9612  0.8988  0.9370
  0.3102   9814   0.819   1253   0.744  11067   0.811  0.954  0.9324  0.9394  0.8962  0.9136
  0.4340  11605   0.407   1248   0.370  12853   0.404  0.383  0.6390  0.6655  0.6226  0.6497
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37657
Percentage observed                  =    99.4927
Percentage of free reflections       =     4.9402
Overall R factor                     =     0.2176
Free R factor                        =     0.2459
Average Fourier shell correlation    =     0.8554
AverageFree Fourier shell correlation=     0.8455
Overall weighted R factor            =     0.1820
Free weighted R factor               =     0.2067
Overall weighted R2 factor           =     0.2120
Free weighted R2 factor              =     0.2323
Average correlation coefficient      =     0.8320
Overall correlation coefficient      =     0.9604
Free correlation coefficient         =     0.9430
Cruickshanks DPI for coordinate error=     0.0775
DPI based on free R factor           =     0.0785
Overall figure of merit              =     0.6968
ML based su of positional parameters =     0.0672
ML based su of thermal parameters    =     1.9445
-----------------------------------------------------------------------------
  Time in seconds: CPU =        27.12
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2181   0.2463   0.658      176248.    9367.4   0.0132  0.992   1.845  1.072   0.090
       1   0.2189   0.2468   0.691      175132.    9339.0   0.0119  0.899   1.771  1.028   0.087
       2   0.2180   0.2460   0.696      174924.    9332.3   0.0129  0.970   1.807  1.050   0.089
       3   0.2178   0.2457   0.697      174880.    9330.2   0.0129  0.976   1.820  1.058   0.089
       4   0.2177   0.2456   0.697      174864.    9329.6   0.0130  0.979   1.825  1.061   0.090
       5   0.2177   0.2456   0.697      174857.    9329.3   0.0130  0.980   1.829  1.063   0.090
       6   0.2176   0.2457   0.697      174850.    9329.1   0.0130  0.981   1.831  1.064   0.090
       7   0.2176   0.2458   0.697      174859.    9329.4   0.0130  0.981   1.833  1.065   0.090
       8   0.2176   0.2458   0.697      174867.    9329.9   0.0130  0.981   1.833  1.065   0.090
       9   0.2176   0.2459   0.697      174863.    9330.0   0.0130  0.981   1.833  1.065   0.090
      10   0.2176   0.2459   0.697      174865.    9330.0   0.0130  0.981   1.833  1.065   0.090
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2181   0.2176
             R free    0.2463   0.2459
     Rms BondLength    0.0132   0.0130
      Rms BondAngle    1.8454   1.8333
     Rms ChirVolume    0.0904   0.0902
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      59.4s System:    0.2s Elapsed:     1:00