###############################################################
 ###############################################################
 ###############################################################
 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 27/ 5/2020 Run time: 03:05:13 


 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 1.48     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_1-49A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-48A.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_1-48A.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       0.1141
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.4800
  Estimated number of reflections :      44185
  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  1.4800

  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_1-49A.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=   2.056 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=   1.831 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=   2.220 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=   2.407 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=   2.385 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=   2.111 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       1758
Number of   all  reflections      35246
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          35246

   Current auto weighting coefficient =    6.1996336    

 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        :   144  144  280
 Maximuum H,K,L                 :    39   39   83
 Minimum acceptable grid spacing:    88   88  186
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   83
 Minimum acceptable grid spacing:    88   88  186
 Weight matrix   0.26847509    
 Actual weight    6.1996336      is applied to the X-ray term
Norm of X_ray positional gradient                36.5
Norm of Geom. positional gradient                83.1
Norm of X_ray B-factor gradient                  93.1
Norm of Geom. B-factor gradient                  104.
Product of X_ray and Geom posit. gradients     -0.146E+08
 Cosine of angle between them                      -0.497
Product of X_ray and Geom B-fact gradients     -0.278E+08
 Cosine of angle between them                      -0.895


Residuals: XRAY=     0.1000E+07 GEOM=     0.1331E+05 TOTAL=     0.1013E+07
 function value    1013294.8    

-------------------------------------------------------------------------------
             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     1.856     1.644
Bond angles  : others                          3238     2.368     1.580
Torsion angles, period  1. refined              185     6.761     5.000
Torsion angles, period  2. refined               90    34.695    22.778
Torsion angles, period  3. refined              268    13.343    15.000
Torsion angles, period  4. refined                9    12.363    15.000
Chiral centres: refined atoms                   196     0.091     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.018     0.020
VDW repulsions: refined_atoms                   302     0.246     0.200
VDW repulsions.others                          1337     0.220     0.200
VDW; torsion: refined_atoms                     728     0.174     0.200
VDW; torsion.others                             719     0.082     0.200
HBOND: refined_atoms                            206     0.202     0.200
HBOND.others                                      1     0.070     0.200
VDW repulsions: symmetry: refined_atoms           8     0.201     0.200
VDW repulsions: symmetry: others                 23     0.202     0.200
HBOND: symmetry: refined_atoms                   22     0.164     0.200
M. chain bond B values: refined atoms           746     1.823     1.629
M. chain bond B values: others                  746     1.818     1.629
M. chain angle B values: refined atoms          929     2.808     2.435
M. chain angle B values: others                 930     2.807     2.434
S. chain bond B values: refined atoms           811     3.259     2.045
S. chain bond B values: others                  810     3.254     2.044
S. chain angle B values: refined atoms         1177     4.956     2.895
S. chain angle B values: others                1178     4.954     2.894
Long range B values: refined atoms             1840     7.741    22.310
Long range B values: others                    1755     7.458    20.917
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0459, B  =    0.0973
Partial structure    1: scale =     0.3922, B  =   38.1441
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.058    4513 100.00   400.3   409.9  0.17  0.18     212   395.3   400.0  0.21  0.21
 0.172    7677  99.98   221.9   201.0  0.18  0.16     430   233.1   210.0  0.22  0.20
 0.286    9763 100.00   115.8   107.5  0.21  0.19     550   114.3   107.6  0.25  0.22
 0.400   11526 100.00    46.8    58.4  0.42  0.38     566    47.0    59.3  0.44  0.41
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0576   3376   0.900   1137   0.791   4513   0.872  0.946  0.9584  0.9670  0.9027  0.9361
  0.1716   6527   0.866   1150   0.765   7677   0.851  1.066  0.9455  0.9550  0.8898  0.9334
  0.2856   8629   0.827   1134   0.745   9763   0.817  1.005  0.9339  0.9440  0.8957  0.9287
  0.3995  10374   0.518   1159   0.454  11533   0.512  0.523  0.7287  0.7365  0.7247  0.7565
 $$
Resolution limits                    =     41.964     1.480
Number of used reflections           =      33486
Percentage observed                  =    99.9915
Percentage of free reflections       =     4.9881
Overall R factor                     =     0.2097
Free R factor                        =     0.2465
Average Fourier shell correlation    =     0.8781
AverageFree Fourier shell correlation=     0.8736
Overall weighted R factor            =     0.1774
Free weighted R factor               =     0.2123
Overall weighted R2 factor           =     0.2064
Free weighted R2 factor              =     0.2477
Average correlation coefficient      =     0.8715
Overall correlation coefficient      =     0.9595
Free correlation coefficient         =     0.9394
Cruickshanks DPI for coordinate error=     0.0837
DPI based on free R factor           =     0.0869
Overall figure of merit              =     0.7271
ML based su of positional parameters =     0.0737
ML based su of thermal parameters    =     2.1381
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    161296.94       13312.868       1013294.8      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.33900416    
 Actual weight    6.1996336      is applied to the X-ray term


 function value    1001227.6    

-------------------------------------------------------------------------------
             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 =     0.0458, B  =   -0.0654
Partial structure    1: scale =     0.3916, B  =   38.1495
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2102
Free R factor                        =     0.2451
Average Fourier shell correlation    =     0.8935
AverageFree Fourier shell correlation=     0.8897
Average correlation coefficient      =     0.8697
Overall figure of merit              =     0.7522
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    160170.59       8228.6416       1001227.6       1013294.8    


     CGMAT cycle number =      3

 Weight matrix   0.35215306    
 Actual weight    6.1996336      is applied to the X-ray term


 function value    999930.56    

-------------------------------------------------------------------------------
             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 =     0.0458, B  =   -0.0001
Partial structure    1: scale =     0.3916, B  =   38.1510
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2095
Free R factor                        =     0.2454
Average Fourier shell correlation    =     0.8995
AverageFree Fourier shell correlation=     0.8952
Average correlation coefficient      =     0.8708
Overall figure of merit              =     0.7664
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    159897.52       8624.5820       999930.56       1001227.6    


     CGMAT cycle number =      4

 Weight matrix   0.34838268    
 Actual weight    6.1996336      is applied to the X-ray term


 function value    1000198.1    

-------------------------------------------------------------------------------
             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 =     0.0458, B  =    0.0068
Partial structure    1: scale =     0.3921, B  =   38.1903
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2095
Free R factor                        =     0.2455
Average Fourier shell correlation    =     0.8979
AverageFree Fourier shell correlation=     0.8935
Average correlation coefficient      =     0.8714
Overall figure of merit              =     0.7601
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02

 fvalues    159857.88       8705.1055       999765.38       999930.56    


     CGMAT cycle number =      5

 Weight matrix   0.34916130    
 Actual weight    6.1996336      is applied to the X-ray term


 function value    1000141.8    

-------------------------------------------------------------------------------
             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 =     0.0458, B  =    0.0019
Partial structure    1: scale =     0.3922, B  =   38.1983
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2095
Free R factor                        =     0.2457
Average Fourier shell correlation    =     0.8981
AverageFree Fourier shell correlation=     0.8937
Average correlation coefficient      =     0.8715
Overall figure of merit              =     0.7608
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03

 fvalues    159848.69       8733.3916       999736.69       999765.38    


     CGMAT cycle number =      6

 Weight matrix   0.34844550    
 Actual weight    6.1996336      is applied to the X-ray term


 function value    1000146.5    

-------------------------------------------------------------------------------
             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 =     0.0458, B  =    0.0106
Partial structure    1: scale =     0.3924, B  =   38.2587
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2095
Free R factor                        =     0.2457
Average Fourier shell correlation    =     0.8981
AverageFree Fourier shell correlation=     0.8936
Average correlation coefficient      =     0.8716
Overall figure of merit              =     0.7607
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    159849.55       8740.9531       1000161.2       999736.69    

 fvalues    159849.55       8740.9531       1000139.8       999749.56    
 fvalues    159849.55       8740.9531       1000139.8       999749.56    


     CGMAT cycle number =      7

 Weight matrix   0.34890679    
 Actual weight    6.1996336      is applied to the X-ray term


 function value    1000128.6    

-------------------------------------------------------------------------------
             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 =     0.0458, B  =    0.0038
Partial structure    1: scale =     0.3924, B  =   38.2596
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2095
Free R factor                        =     0.2457
Average Fourier shell correlation    =     0.8982
AverageFree Fourier shell correlation=     0.8936
Average correlation coefficient      =     0.8716
Overall figure of merit              =     0.7609
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05

 fvalues    159846.44       8739.0156       999728.38       999749.56    


     CGMAT cycle number =      8

 Weight matrix   0.34833714    
 Actual weight    6.1996336      is applied to the X-ray term


 function value    1000150.3    

-------------------------------------------------------------------------------
             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 =     0.0458, B  =    0.0105
Partial structure    1: scale =     0.3925, B  =   38.2651
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2095
Free R factor                        =     0.2457
Average Fourier shell correlation    =     0.8981
AverageFree Fourier shell correlation=     0.8936
Average correlation coefficient      =     0.8715
Overall figure of merit              =     0.7608
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    159849.52       8733.8994       1000128.3       999728.38    

 fvalues    159849.52       8733.8994       1000122.6       999742.31    
 fvalues    159849.52       8733.8994       1000122.6       999742.31    


     CGMAT cycle number =      9

 Weight matrix   0.34847158    
 Actual weight    6.1996336      is applied to the X-ray term


 function value    1000134.4    

-------------------------------------------------------------------------------
             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 =     0.0458, B  =    0.0093
Partial structure    1: scale =     0.3925, B  =   38.2741
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2095
Free R factor                        =     0.2457
Average Fourier shell correlation    =     0.8981
AverageFree Fourier shell correlation=     0.8936
Average correlation coefficient      =     0.8715
Overall figure of merit              =     0.7608
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    159851.06       8733.5186       1000127.6       999742.31    

 fvalues    159851.06       8733.5186       1000128.8       999751.50    
 fvalues    159851.06       8733.5186       1000128.8       999751.50    


     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.= 0.911 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        :   144  144  280
 Maximuum H,K,L                 :    39   39   83
 Minimum acceptable grid spacing:    88   88  186
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   83
 Minimum acceptable grid spacing:    88   88  186
 Weight matrix   0.34862918    
 Actual weight    6.1996336      is applied to the X-ray term
Norm of X_ray positional gradient                43.4
Norm of Geom. positional gradient                43.4
Norm of X_ray B-factor gradient                  108.
Norm of Geom. B-factor gradient                  107.
Product of X_ray and Geom posit. gradients     -0.182E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.371E+08
 Cosine of angle between them                      -0.999


Residuals: XRAY=     0.9914E+06 GEOM=      8733.     TOTAL=     0.1000E+07
 function value    1000126.9    

-------------------------------------------------------------------------------
             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     1.850     1.644
Bond angles  : others                          3238     1.515     1.580
Torsion angles, period  1. refined              185     6.752     5.000
Torsion angles, period  2. refined               90    34.628    22.778
Torsion angles, period  3. refined              268    13.318    15.000
Torsion angles, period  4. refined                9    12.444    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   305     0.244     0.200
VDW repulsions.others                          1369     0.194     0.200
VDW; torsion: refined_atoms                     729     0.174     0.200
VDW; torsion.others                             759     0.086     0.200
HBOND: refined_atoms                            210     0.199     0.200
HBOND.others                                      1     0.025     0.200
VDW repulsions: symmetry: refined_atoms           8     0.200     0.200
VDW repulsions: symmetry: others                 23     0.188     0.200
HBOND: symmetry: refined_atoms                   22     0.166     0.200
M. chain bond B values: refined atoms           746     1.820     1.640
M. chain bond B values: others                  746     1.814     1.640
M. chain angle B values: refined atoms          929     2.807     2.450
M. chain angle B values: others                 930     2.806     2.450
S. chain bond B values: refined atoms           811     3.264     2.057
S. chain bond B values: others                  810     3.259     2.056
S. chain angle B values: refined atoms         1177     4.963     2.913
S. chain angle B values: others                1178     4.960     2.912
Long range B values: refined atoms             1846     7.728    22.470
Long range B values: others                    1760     7.456    21.062
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0458, B  =    0.0071
Partial structure    1: scale =     0.3925, B  =   38.2762
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.058    4513 100.00   400.7   410.2  0.17  0.18     212   395.7   400.9  0.21  0.21
 0.172    7677  99.98   222.1   201.3  0.18  0.16     430   233.3   210.3  0.22  0.20
 0.286    9763 100.00   115.9   107.7  0.21  0.19     550   114.4   107.7  0.25  0.22
 0.400   11526 100.00    46.8    58.5  0.42  0.38     566    47.1    59.5  0.44  0.41
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0576   3376   0.916   1137   0.815   4513   0.890  0.948  0.9627  0.9709  0.9027  0.9358
  0.1716   6527   0.880   1150   0.781   7677   0.865  1.068  0.9488  0.9585  0.8913  0.9340
  0.2856   8629   0.845   1134   0.763   9763   0.835  1.008  0.9404  0.9503  0.8961  0.9288
  0.3995  10374   0.584   1159   0.525  11533   0.578  0.552  0.7803  0.7853  0.7244  0.7562
 $$
Resolution limits                    =     41.964     1.480
Number of used reflections           =      33486
Percentage observed                  =    99.9915
Percentage of free reflections       =     4.9881
Overall R factor                     =     0.2095
Free R factor                        =     0.2457
Average Fourier shell correlation    =     0.8981
AverageFree Fourier shell correlation=     0.8936
Overall weighted R factor            =     0.1772
Free weighted R factor               =     0.2118
Overall weighted R2 factor           =     0.2064
Free weighted R2 factor              =     0.2479
Average correlation coefficient      =     0.8715
Overall correlation coefficient      =     0.9596
Free correlation coefficient         =     0.9396
Cruickshanks DPI for coordinate error=     0.0836
DPI based on free R factor           =     0.0866
Overall figure of merit              =     0.7609
ML based su of positional parameters =     0.0646
ML based su of thermal parameters    =     1.8547
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02

 fvalues    159847.06       8733.3613       999726.63       999751.50    

    ****                              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.= 0.911 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_1-48A.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     1.850     1.644
Bond angles  : others                          3238     1.515     1.580
Torsion angles, period  1. refined              185     6.752     5.000
Torsion angles, period  2. refined               90    34.627    22.778
Torsion angles, period  3. refined              268    13.318    15.000
Torsion angles, period  4. refined                9    12.444    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   305     0.244     0.200
VDW repulsions.others                          1371     0.194     0.200
VDW; torsion: refined_atoms                     729     0.174     0.200
VDW; torsion.others                             759     0.086     0.200
HBOND: refined_atoms                            210     0.199     0.200
HBOND.others                                      1     0.025     0.200
VDW repulsions: symmetry: refined_atoms           8     0.200     0.200
VDW repulsions: symmetry: others                 23     0.188     0.200
HBOND: symmetry: refined_atoms                   22     0.166     0.200
M. chain bond B values: refined atoms           746     1.820     1.640
M. chain bond B values: others                  746     1.814     1.640
M. chain angle B values: refined atoms          929     2.807     2.450
M. chain angle B values: others                 930     2.806     2.450
S. chain bond B values: refined atoms           811     3.264     2.057
S. chain bond B values: others                  810     3.259     2.057
S. chain angle B values: refined atoms         1177     4.963     2.913
S. chain angle B values: others                1178     4.960     2.912
Long range B values: refined atoms             1846     7.729    22.470
Long range B values: others                    1760     7.456    21.062
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0458, B  =    0.0019
Partial structure    1: scale =     0.3925, B  =   38.2788
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.058    4513 100.00   400.6   410.2  0.17  0.18     212   395.7   400.9  0.21  0.21
 0.172    7677  99.98   222.1   201.4  0.18  0.16     430   233.3   210.3  0.22  0.20
 0.286    9763 100.00   115.9   107.8  0.21  0.19     550   114.4   107.8  0.25  0.22
 0.400   11526 100.00    46.8    58.5  0.42  0.38     566    47.1    59.5  0.45  0.41
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0576   3376   0.916   1137   0.815   4513   0.890  0.948  0.9627  0.9709  0.9027  0.9358
  0.1716   6527   0.880   1150   0.781   7677   0.865  1.068  0.9488  0.9585  0.8913  0.9341
  0.2856   8629   0.845   1134   0.763   9763   0.835  1.008  0.9405  0.9503  0.8961  0.9288
  0.3995  10374   0.584   1159   0.525  11533   0.578  0.552  0.7804  0.7854  0.7244  0.7562
 $$
Resolution limits                    =     41.964     1.480
Number of used reflections           =      33486
Percentage observed                  =    99.9915
Percentage of free reflections       =     4.9881
Overall R factor                     =     0.2095
Free R factor                        =     0.2457
Average Fourier shell correlation    =     0.8982
AverageFree Fourier shell correlation=     0.8937
Overall weighted R factor            =     0.1772
Free weighted R factor               =     0.2118
Overall weighted R2 factor           =     0.2064
Free weighted R2 factor              =     0.2479
Average correlation coefficient      =     0.8715
Overall correlation coefficient      =     0.9596
Free correlation coefficient         =     0.9397
Cruickshanks DPI for coordinate error=     0.0836
DPI based on free R factor           =     0.0866
Overall figure of merit              =     0.7610
ML based su of positional parameters =     0.0646
ML based su of thermal parameters    =     1.8547
-----------------------------------------------------------------------------
  Time in seconds: CPU =        30.38
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2097   0.2465   0.727      161297.    8657.3   0.0132  0.995   1.856  1.081   0.091
       1   0.2102   0.2451   0.752      160171.    8623.2   0.0119  0.897   1.783  1.037   0.087
       2   0.2095   0.2454   0.766      159898.    8613.9   0.0130  0.977   1.824  1.061   0.090
       3   0.2095   0.2455   0.760      159928.    8617.0   0.0131  0.985   1.839  1.070   0.090
       4   0.2095   0.2457   0.761      159914.    8617.0   0.0131  0.987   1.846  1.074   0.090
       5   0.2095   0.2457   0.761      159914.    8617.3   0.0131  0.988   1.849  1.076   0.090
       6   0.2095   0.2457   0.761      159911.    8617.3   0.0131  0.988   1.849  1.076   0.090
       7   0.2095   0.2457   0.761      159915.    8617.5   0.0131  0.988   1.850  1.076   0.090
       8   0.2095   0.2457   0.761      159913.    8617.4   0.0131  0.988   1.850  1.076   0.090
       9   0.2095   0.2457   0.761      159912.    8617.4   0.0131  0.988   1.850  1.076   0.090
      10   0.2095   0.2457   0.761      159909.    8617.4   0.0131  0.988   1.850  1.076   0.090
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2097   0.2095
             R free    0.2465   0.2457
     Rms BondLength    0.0132   0.0131
      Rms BondAngle    1.8565   1.8498
     Rms ChirVolume    0.0911   0.0904
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      61.6s System:    0.2s Elapsed:     1:02