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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: 21:35:26 


 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 1.60     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 0
  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_step0-01A_R00_1-61A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-60A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_step0-01A_R00_1-60A.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       0.0977
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.6000
  Estimated number of reflections :      36894
  Free R exclusion - flag equals:     0
  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  1.6000

  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_step0-01A_R00_1-61A.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=   2.055 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=   2.194 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=   1.829 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=   2.219 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=   2.417 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=   2.394 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=   2.140 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:22-OCT-19
  --------------------------------
  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                            0
Number of "free" reflections       1433
Number of   all  reflections      28041
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          28041

   Current auto weighting coefficient =    6.4996524    

 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.= 0.896 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        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Weight matrix   0.29194301    
 Actual weight    6.4996524      is applied to the X-ray term
Norm of X_ray positional gradient                36.6
Norm of Geom. positional gradient                82.3
Norm of X_ray B-factor gradient                  106.
Norm of Geom. B-factor gradient                  113.
Product of X_ray and Geom posit. gradients     -0.143E+08
 Cosine of angle between them                      -0.491
Product of X_ray and Geom B-fact gradients     -0.339E+08
 Cosine of angle between them                      -0.879


Residuals: XRAY=     0.8722E+06 GEOM=     0.1347E+05 TOTAL=     0.8856E+06
 function value    885649.69    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.035     0.017
Bond angles  : refined atoms                   2106     1.853     1.644
Bond angles  : others                          3238     2.367     1.580
Torsion angles, period  1. refined              185     6.804     5.000
Torsion angles, period  2. refined               90    34.974    22.778
Torsion angles, period  3. refined              268    13.200    15.000
Torsion angles, period  4. refined                9    12.372    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.017     0.020
VDW repulsions: refined_atoms                   301     0.246     0.200
VDW repulsions.others                          1343     0.219     0.200
VDW; torsion: refined_atoms                     731     0.174     0.200
VDW; torsion.others                             719     0.082     0.200
HBOND: refined_atoms                            215     0.201     0.200
HBOND.others                                      2     0.047     0.200
VDW repulsions: symmetry: refined_atoms           8     0.203     0.200
VDW repulsions: symmetry: others                 22     0.206     0.200
HBOND: symmetry: refined_atoms                   22     0.205     0.200
M. chain bond B values: refined atoms           746     1.741     1.497
M. chain bond B values: others                  746     1.736     1.497
M. chain angle B values: refined atoms          929     2.707     2.235
M. chain angle B values: others                 930     2.706     2.235
S. chain bond B values: refined atoms           811     3.135     1.896
S. chain bond B values: others                  810     3.130     1.896
S. chain angle B values: refined atoms         1177     4.763     2.678
S. chain angle B values: others                1178     4.761     2.677
Long range B values: refined atoms             1851     7.314    20.733
Long range B values: others                    1762     7.069    19.342
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =    0.0881
Partial structure    1: scale =     0.3867, B  =   41.6390
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3613 100.00   432.2   441.7  0.17  0.17     169   436.1   442.6  0.20  0.21
 0.147    6097  99.97   258.5   243.6  0.17  0.15     347   262.0   240.8  0.23  0.21
 0.244    7806 100.00   167.1   151.1  0.19  0.16     412   171.9   156.9  0.22  0.19
 0.342    9086 100.00    71.5    85.4  0.32  0.25     504    69.5    84.6  0.37  0.30
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2636   0.910    977   0.803   3613   0.881  0.948  0.9626  0.9690  0.9071  0.9371
  0.1468   5122   0.865    975   0.767   6097   0.849  1.018  0.9390  0.9549  0.8723  0.9377
  0.2444   6820   0.865    986   0.758   7806   0.852  1.053  0.9502  0.9567  0.9051  0.9391
  0.3419   8114   0.677    976   0.596   9090   0.669  0.715  0.8553  0.8743  0.8124  0.8693
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26606
Percentage observed                  =    99.9893
Percentage of free reflections       =     5.1074
Overall R factor                     =     0.1921
Free R factor                        =     0.2356
Average Fourier shell correlation    =     0.9298
AverageFree Fourier shell correlation=     0.9155
Overall weighted R factor            =     0.1677
Free weighted R factor               =     0.2076
Overall weighted R2 factor           =     0.1991
Free weighted R2 factor              =     0.2436
Average correlation coefficient      =     0.9147
Overall correlation coefficient      =     0.9583
Free correlation coefficient         =     0.9347
Cruickshanks DPI for coordinate error=     0.0966
DPI based on free R factor           =     0.1008
Overall figure of merit              =     0.7926
ML based su of positional parameters =     0.0723
ML based su of thermal parameters    =     2.1632
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    134188.13       13473.498       885649.69      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.37006652    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    873401.88    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0665
Partial structure    1: scale =     0.3865, B  =   41.7062
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1924
Free R factor                        =     0.2349
Average Fourier shell correlation    =     0.9418
AverageFree Fourier shell correlation=     0.9291
Average correlation coefficient      =     0.9135
Overall figure of merit              =     0.8304
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    133071.11       8485.9355       873401.88       885649.69    


     CGMAT cycle number =      3

 Weight matrix   0.38082844    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    872520.44    

-------------------------------------------------------------------------------
             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 =     0.0441, B  =   -0.0161
Partial structure    1: scale =     0.3865, B  =   41.6901
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1919
Free R factor                        =     0.2349
Average Fourier shell correlation    =     0.9437
AverageFree Fourier shell correlation=     0.9309
Average correlation coefficient      =     0.9146
Overall figure of merit              =     0.8365
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    132882.27       8831.9004       872520.44       873401.88    


     CGMAT cycle number =      4

 Weight matrix   0.38142169    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    872406.81    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0027
Partial structure    1: scale =     0.3865, B  =   41.6441
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1919
Free R factor                        =     0.2348
Average Fourier shell correlation    =     0.9439
AverageFree Fourier shell correlation=     0.9310
Average correlation coefficient      =     0.9151
Overall figure of merit              =     0.8372
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    132848.66       8936.7334       872406.81       872520.44    


     CGMAT cycle number =      5

 Weight matrix   0.38119781    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    872411.81    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =    0.0004
Partial structure    1: scale =     0.3866, B  =   41.5609
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1919
Free R factor                        =     0.2349
Average Fourier shell correlation    =     0.9440
AverageFree Fourier shell correlation=     0.9310
Average correlation coefficient      =     0.9153
Overall figure of merit              =     0.8371
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03

 fvalues    132841.31       8976.2480       872398.63       872406.81    


     CGMAT cycle number =      6

 Weight matrix   0.38084301    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    872412.44    

-------------------------------------------------------------------------------
             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 =     0.0441, B  =   -0.0006
Partial structure    1: scale =     0.3865, B  =   41.4511
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1919
Free R factor                        =     0.2349
Average Fourier shell correlation    =     0.9440
AverageFree Fourier shell correlation=     0.9309
Average correlation coefficient      =     0.9153
Overall figure of merit              =     0.8371
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    132842.33       8985.3369       872441.63       872398.63    

 fvalues    132842.33       8985.3369       872427.44       872414.25    
 fvalues    132842.33       8985.3369       872427.44       872414.25    


     CGMAT cycle number =      7

 Weight matrix   0.38068882    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    872420.13    

-------------------------------------------------------------------------------
             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 =     0.0441, B  =   -0.0008
Partial structure    1: scale =     0.3865, B  =   41.4455
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1920
Free R factor                        =     0.2349
Average Fourier shell correlation    =     0.9440
AverageFree Fourier shell correlation=     0.9309
Average correlation coefficient      =     0.9153
Overall figure of merit              =     0.8370
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    132843.50       8984.9727       872444.88       872414.25    

 fvalues    132843.50       8984.9727       872430.06       872421.56    
 fvalues    132843.50       8984.9727       872430.06       872421.56    


     CGMAT cycle number =      8

 Weight matrix   0.38054574    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    872423.81    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0002
Partial structure    1: scale =     0.3865, B  =   41.4426
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1920
Free R factor                        =     0.2349
Average Fourier shell correlation    =     0.9439
AverageFree Fourier shell correlation=     0.9309
Average correlation coefficient      =     0.9153
Overall figure of merit              =     0.8370
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    132844.09       8983.6611       872429.88       872421.56    

 fvalues    132844.09       8983.6611       872426.88       872424.13    
 fvalues    132844.09       8983.6611       872426.88       872424.13    


     CGMAT cycle number =      9

 Weight matrix   0.38052773    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    872426.75    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0004
Partial structure    1: scale =     0.3865, B  =   41.4394
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1920
Free R factor                        =     0.2349
Average Fourier shell correlation    =     0.9439
AverageFree Fourier shell correlation=     0.9309
Average correlation coefficient      =     0.9153
Overall figure of merit              =     0.8370
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    132844.59       8983.7217       872426.88       872424.13    
 fvalues    132844.59       8983.7217       872426.88       872427.44    


     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.= 0.908 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        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Weight matrix   0.38051429    
 Actual weight    6.4996524      is applied to the X-ray term
Norm of X_ray positional gradient                43.3
Norm of Geom. positional gradient                43.3
Norm of X_ray B-factor gradient                  118.
Norm of Geom. B-factor gradient                  118.
Product of X_ray and Geom posit. gradients     -0.181E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.447E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.8634E+06 GEOM=      8984.     TOTAL=     0.8724E+06
 function value    872427.69    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2106     1.857     1.644
Bond angles  : others                          3238     1.524     1.580
Torsion angles, period  1. refined              185     6.794     5.000
Torsion angles, period  2. refined               90    34.898    22.778
Torsion angles, period  3. refined              268    13.221    15.000
Torsion angles, period  4. refined                9    12.337    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   301     0.247     0.200
VDW repulsions.others                          1350     0.196     0.200
VDW; torsion: refined_atoms                     730     0.174     0.200
VDW; torsion.others                             750     0.086     0.200
HBOND: refined_atoms                            215     0.200     0.200
HBOND.others                                      1     0.035     0.200
VDW repulsions: symmetry: refined_atoms           8     0.205     0.200
VDW repulsions: symmetry: others                 22     0.197     0.200
HBOND: symmetry: refined_atoms                   22     0.224     0.200
M. chain bond B values: refined atoms           746     1.749     1.507
M. chain bond B values: others                  746     1.744     1.507
M. chain angle B values: refined atoms          929     2.726     2.251
M. chain angle B values: others                 930     2.725     2.251
S. chain bond B values: refined atoms           811     3.145     1.908
S. chain bond B values: others                  810     3.141     1.908
S. chain angle B values: refined atoms         1177     4.780     2.695
S. chain angle B values: others                1178     4.778     2.694
Long range B values: refined atoms             1848     7.282    20.822
Long range B values: others                    1759     7.034    19.427
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0005
Partial structure    1: scale =     0.3865, B  =   41.4432
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3613 100.00   432.6   442.1  0.17  0.17     169   436.5   443.5  0.20  0.21
 0.147    6097  99.97   258.7   243.6  0.17  0.15     347   262.2   241.1  0.23  0.20
 0.244    7806 100.00   167.2   151.3  0.19  0.16     412   172.0   157.0  0.22  0.19
 0.342    9086 100.00    71.5    85.4  0.32  0.25     504    69.5    84.7  0.37  0.30
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2636   0.924    977   0.824   3613   0.897  0.950  0.9661  0.9723  0.9076  0.9375
  0.1468   5122   0.869    975   0.770   6097   0.853  1.018  0.9400  0.9557  0.8731  0.9375
  0.2444   6820   0.876    986   0.771   7806   0.863  1.053  0.9536  0.9602  0.9062  0.9393
  0.3419   8114   0.789    976   0.708   9090   0.780  0.760  0.8942  0.9109  0.8120  0.8711
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26606
Percentage observed                  =    99.9893
Percentage of free reflections       =     5.1074
Overall R factor                     =     0.1920
Free R factor                        =     0.2349
Average Fourier shell correlation    =     0.9439
AverageFree Fourier shell correlation=     0.9309
Overall weighted R factor            =     0.1676
Free weighted R factor               =     0.2070
Overall weighted R2 factor           =     0.1986
Free weighted R2 factor              =     0.2429
Average correlation coefficient      =     0.9153
Overall correlation coefficient      =     0.9584
Free correlation coefficient         =     0.9351
Cruickshanks DPI for coordinate error=     0.0965
DPI based on free R factor           =     0.1005
Overall figure of merit              =     0.8370
ML based su of positional parameters =     0.0633
ML based su of thermal parameters    =     1.8423
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    132844.92       8983.8018       872433.44       872427.44    

 fvalues    132844.92       8983.8018       872433.50       872429.63    
 fvalues    132844.92       8983.8018       872433.50       872429.63    

    ****                              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.= 0.908 id.= 3.000 dev= -2.09 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_step0-01A_R00_1-60A.mtz 




-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2106     1.857     1.644
Bond angles  : others                          3238     1.524     1.580
Torsion angles, period  1. refined              185     6.794     5.000
Torsion angles, period  2. refined               90    34.898    22.778
Torsion angles, period  3. refined              268    13.221    15.000
Torsion angles, period  4. refined                9    12.337    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   301     0.247     0.200
VDW repulsions.others                          1351     0.196     0.200
VDW; torsion: refined_atoms                     730     0.174     0.200
VDW; torsion.others                             751     0.086     0.200
HBOND: refined_atoms                            215     0.200     0.200
HBOND.others                                      1     0.034     0.200
VDW repulsions: symmetry: refined_atoms           8     0.205     0.200
VDW repulsions: symmetry: others                 22     0.197     0.200
HBOND: symmetry: refined_atoms                   22     0.224     0.200
M. chain bond B values: refined atoms           746     1.749     1.507
M. chain bond B values: others                  746     1.744     1.507
M. chain angle B values: refined atoms          929     2.726     2.251
M. chain angle B values: others                 930     2.725     2.251
S. chain bond B values: refined atoms           811     3.145     1.908
S. chain bond B values: others                  810     3.141     1.908
S. chain angle B values: refined atoms         1177     4.780     2.695
S. chain angle B values: others                1178     4.778     2.694
Long range B values: refined atoms             1848     7.282    20.822
Long range B values: others                    1759     7.034    19.427
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0018
Partial structure    1: scale =     0.3865, B  =   41.4465
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3613 100.00   432.6   442.1  0.17  0.17     169   436.5   443.5  0.20  0.21
 0.147    6097  99.97   258.8   243.7  0.17  0.15     347   262.3   241.1  0.23  0.20
 0.244    7806 100.00   167.2   151.3  0.19  0.16     412   172.0   157.0  0.22  0.19
 0.342    9086 100.00    71.5    85.4  0.32  0.25     504    69.5    84.7  0.37  0.30
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2636   0.924    977   0.824   3613   0.897  0.950  0.9661  0.9723  0.9076  0.9375
  0.1468   5122   0.869    975   0.770   6097   0.853  1.018  0.9400  0.9557  0.8731  0.9375
  0.2444   6820   0.876    986   0.771   7806   0.863  1.053  0.9536  0.9602  0.9062  0.9393
  0.3419   8114   0.789    976   0.708   9090   0.780  0.760  0.8942  0.9109  0.8120  0.8711
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26606
Percentage observed                  =    99.9893
Percentage of free reflections       =     5.1074
Overall R factor                     =     0.1920
Free R factor                        =     0.2349
Average Fourier shell correlation    =     0.9439
AverageFree Fourier shell correlation=     0.9309
Overall weighted R factor            =     0.1676
Free weighted R factor               =     0.2070
Overall weighted R2 factor           =     0.1986
Free weighted R2 factor              =     0.2429
Average correlation coefficient      =     0.9153
Overall correlation coefficient      =     0.9584
Free correlation coefficient         =     0.9351
Cruickshanks DPI for coordinate error=     0.0965
DPI based on free R factor           =     0.1005
Overall figure of merit              =     0.8370
ML based su of positional parameters =     0.0633
ML based su of thermal parameters    =     1.8423
-----------------------------------------------------------------------------
  Time in seconds: CPU =        24.76
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1921   0.2356   0.793      134188.    7390.3   0.0132  0.987   1.853  1.078   0.090
       1   0.1924   0.2349   0.830      133071.    7348.8   0.0121  0.905   1.789  1.039   0.087
       2   0.1919   0.2349   0.837      132882.    7342.5   0.0130  0.974   1.826  1.062   0.089
       3   0.1919   0.2348   0.837      132849.    7341.9   0.0131  0.983   1.843  1.073   0.090
       4   0.1919   0.2349   0.837      132843.    7342.4   0.0132  0.986   1.852  1.078   0.090
       5   0.1919   0.2349   0.837      132842.    7342.9   0.0132  0.987   1.856  1.080   0.090
       6   0.1920   0.2349   0.837      132843.    7343.1   0.0132  0.987   1.856  1.080   0.090
       7   0.1920   0.2349   0.837      132844.    7343.2   0.0132  0.987   1.856  1.080   0.090
       8   0.1920   0.2349   0.837      132844.    7343.3   0.0132  0.987   1.856  1.080   0.090
       9   0.1920   0.2349   0.837      132845.    7343.3   0.0132  0.987   1.857  1.080   0.090
      10   0.1920   0.2349   0.837      132846.    7343.3   0.0132  0.987   1.857  1.080   0.090
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1921   0.1920
             R free    0.2356   0.2349
     Rms BondLength    0.0132   0.0132
      Rms BondAngle    1.8529   1.8566
     Rms ChirVolume    0.0895   0.0897
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      56.9s System:    0.2s Elapsed:     0:57