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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: 13:51:51 


 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 1.89     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_1-90A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-89A.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_1-89A.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       0.0700
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.8900
  Estimated number of reflections :      21862
  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  1.8900

  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_1-90A.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=   2.010 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=   2.204 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=   1.868 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=   2.210 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=   2.381 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=   2.424 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=   2.124 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        878
Number of   all  reflections      17251
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          17251

   Current auto weighting coefficient =    7.2245507    

 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.= 0.934 id.= 3.000 dev= -2.07 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    31   31   65
 Minimum acceptable grid spacing:    73   73  154
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    31   31   65
 Minimum acceptable grid spacing:    73   73  154
 Weight matrix   0.21944311    
 Actual weight    7.2245507      is applied to the X-ray term
Norm of X_ray positional gradient                31.5
Norm of Geom. positional gradient                77.7
Norm of X_ray B-factor gradient                  106.
Norm of Geom. B-factor gradient                  107.
Product of X_ray and Geom posit. gradients     -0.917E+07
 Cosine of angle between them                      -0.387
Product of X_ray and Geom B-fact gradients     -0.341E+08
 Cosine of angle between them                      -0.930


Residuals: XRAY=     0.6439E+06 GEOM=     0.1272E+05 TOTAL=     0.6566E+06
 function value    656626.13    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.035     0.017
Bond angles  : refined atoms                   2106     1.720     1.644
Bond angles  : others                          3238     2.345     1.580
Torsion angles, period  1. refined              185     6.973     5.000
Torsion angles, period  2. refined               90    36.939    22.778
Torsion angles, period  3. refined              268    13.982    15.000
Torsion angles, period  4. refined                9    11.099    15.000
Chiral centres: refined atoms                   196     0.083     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.016     0.020
VDW repulsions: refined_atoms                   301     0.242     0.200
VDW repulsions.others                          1334     0.219     0.200
VDW; torsion: refined_atoms                     714     0.171     0.200
VDW; torsion.others                             707     0.080     0.200
HBOND: refined_atoms                            226     0.212     0.200
VDW repulsions: symmetry: refined_atoms           9     0.215     0.200
VDW repulsions: symmetry: others                 24     0.205     0.200
HBOND: symmetry: refined_atoms                   20     0.218     0.200
M. chain bond B values: refined atoms           746     1.538     1.221
M. chain bond B values: others                  746     1.537     1.221
M. chain angle B values: refined atoms          929     2.481     1.817
M. chain angle B values: others                 930     2.480     1.817
S. chain bond B values: refined atoms           811     2.511     1.554
S. chain bond B values: others                  810     2.508     1.554
S. chain angle B values: refined atoms         1177     3.936     2.185
S. chain angle B values: others                1178     3.934     2.185
Long range B values: refined atoms             1850     6.581    16.960
Long range B values: others                    1754     6.288    15.600
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =   -0.0977
Partial structure    1: scale =     0.3765, B  =   46.5773
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2251 100.00   480.7   485.7  0.16  0.17     100   475.0   478.2  0.20  0.22
 0.105    3784 100.00   381.3   364.5  0.16  0.15     193   389.2   365.8  0.21  0.19
 0.175    4751  99.96   245.9   240.6  0.16  0.13     279   258.7   249.0  0.22  0.19
 0.245    5580 100.00   184.4   185.1  0.17  0.13     303   186.7   186.7  0.23  0.20
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0355   1554   0.910    697   0.805   2251   0.877  0.959  0.9607  0.9685  0.9119  0.9415
  0.1053   3080   0.884    704   0.777   3784   0.864  0.996  0.9487  0.9631  0.8818  0.9452
  0.1752   4053   0.865    698   0.770   4751   0.851  0.981  0.9431  0.9566  0.8807  0.9386
  0.2450   4881   0.856    704   0.736   5585   0.841  0.948  0.9369  0.9535  0.8614  0.9369
 $$
Resolution limits                    =     41.964     1.890
Number of used reflections           =      16370
Percentage observed                  =    99.9826
Percentage of free reflections       =     5.0849
Overall R factor                     =     0.1605
Free R factor                        =     0.2169
Average Fourier shell correlation    =     0.9587
AverageFree Fourier shell correlation=     0.9441
Overall weighted R factor            =     0.1498
Free weighted R factor               =     0.2009
Overall weighted R2 factor           =     0.1821
Free weighted R2 factor              =     0.2421
Average correlation coefficient      =     0.9399
Overall correlation coefficient      =     0.9555
Free correlation coefficient         =     0.9138
Cruickshanks DPI for coordinate error=     0.1392
DPI based on free R factor           =     0.1397
Overall figure of merit              =     0.8543
ML based su of positional parameters =     0.0880
ML based su of thermal parameters    =     2.9183
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    89127.266       12721.664       656626.13      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.22847803    
 Actual weight    7.2245507      is applied to the X-ray term


 function value    650648.31    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =   -0.1062
Partial structure    1: scale =     0.3763, B  =   46.6017
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1605
Free R factor                        =     0.2161
Average Fourier shell correlation    =     0.9599
AverageFree Fourier shell correlation=     0.9455
Average correlation coefficient      =     0.9403
Overall figure of merit              =     0.8586
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    88925.938       8198.3789       650648.31       656626.13    


     CGMAT cycle number =      3

 Weight matrix   0.22883587    
 Actual weight    7.2245507      is applied to the X-ray term


 function value    650556.38    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =   -0.1115
Partial structure    1: scale =     0.3762, B  =   46.6817
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1603
Free R factor                        =     0.2159
Average Fourier shell correlation    =     0.9600
AverageFree Fourier shell correlation=     0.9456
Average correlation coefficient      =     0.9404
Overall figure of merit              =     0.8588
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    88907.594       8238.9297       650556.38       650648.31    


     CGMAT cycle number =      4

 Weight matrix   0.22892438    
 Actual weight    7.2245507      is applied to the X-ray term


 function value    650518.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =   -0.1110
Partial structure    1: scale =     0.3761, B  =   46.6614
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1602
Free R factor                        =     0.2158
Average Fourier shell correlation    =     0.9600
AverageFree Fourier shell correlation=     0.9456
Average correlation coefficient      =     0.9405
Overall figure of merit              =     0.8589
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    88901.148       8247.4063       650518.25       650556.38    


     CGMAT cycle number =      5

 Weight matrix   0.22881690    
 Actual weight    7.2245507      is applied to the X-ray term


 function value    650525.94    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =   -0.1144
Partial structure    1: scale =     0.3760, B  =   46.6210
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1602
Free R factor                        =     0.2157
Average Fourier shell correlation    =     0.9600
AverageFree Fourier shell correlation=     0.9456
Average correlation coefficient      =     0.9405
Overall figure of merit              =     0.8589
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03


 fvalues    88902.789       8244.4746       650531.31       650518.25    

 fvalues    88902.789       8244.4746       650522.13       650527.19    
 fvalues    88902.789       8244.4746       650522.13       650527.19    


     CGMAT cycle number =      6

 Weight matrix   0.22878706    
 Actual weight    7.2245507      is applied to the X-ray term


 function value    650529.38    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =   -0.1156
Partial structure    1: scale =     0.3761, B  =   46.6254
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1602
Free R factor                        =     0.2158
Average Fourier shell correlation    =     0.9600
AverageFree Fourier shell correlation=     0.9456
Average correlation coefficient      =     0.9405
Overall figure of merit              =     0.8589
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    88903.508       8241.1084       650533.88       650527.19    

 fvalues    88903.508       8241.1084       650550.56       650529.00    
 fvalues    88903.508       8241.1084       650550.56       650529.00    


     CGMAT cycle number =      7

 Weight matrix   0.22882879    
 Actual weight    7.2245507      is applied to the X-ray term


 function value    650520.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =   -0.1159
Partial structure    1: scale =     0.3761, B  =   46.5621
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1602
Free R factor                        =     0.2157
Average Fourier shell correlation    =     0.9600
AverageFree Fourier shell correlation=     0.9456
Average correlation coefficient      =     0.9405
Overall figure of merit              =     0.8589
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    88902.578       8239.0469       650520.25       650529.00    


     CGMAT cycle number =      8

 Weight matrix   0.22870266    
 Actual weight    7.2245507      is applied to the X-ray term


 function value    650519.13    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =   -0.1163
Partial structure    1: scale =     0.3762, B  =   46.5909
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1602
Free R factor                        =     0.2157
Average Fourier shell correlation    =     0.9600
AverageFree Fourier shell correlation=     0.9455
Average correlation coefficient      =     0.9405
Overall figure of merit              =     0.8588
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    88903.469       8231.5156       650519.13       650520.25    


     CGMAT cycle number =      9

 Weight matrix   0.22874261    
 Actual weight    7.2245507      is applied to the X-ray term


 function value    650505.50    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =   -0.1139
Partial structure    1: scale =     0.3762, B  =   46.5793
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1602
Free R factor                        =     0.2157
Average Fourier shell correlation    =     0.9600
AverageFree Fourier shell correlation=     0.9456
Average correlation coefficient      =     0.9405
Overall figure of merit              =     0.8589
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    88901.648       8231.0918       650505.50       650519.13    


     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.= 0.952 id.= 3.000 dev= -2.05 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        :   112  112  240
 Maximuum H,K,L                 :    31   31   65
 Minimum acceptable grid spacing:    73   73  154
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    31   31   65
 Minimum acceptable grid spacing:    73   73  154
 Weight matrix   0.22885847    
 Actual weight    7.2245507      is applied to the X-ray term
Norm of X_ray positional gradient                31.9
Norm of Geom. positional gradient                31.9
Norm of X_ray B-factor gradient                  107.
Norm of Geom. B-factor gradient                  112.
Product of X_ray and Geom posit. gradients     -0.983E+07
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.382E+08
 Cosine of angle between them                      -0.984


Residuals: XRAY=     0.6423E+06 GEOM=      8230.     TOTAL=     0.6505E+06
 function value    650483.75    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.720     1.644
Bond angles  : others                          3238     1.435     1.580
Torsion angles, period  1. refined              185     6.988     5.000
Torsion angles, period  2. refined               90    36.829    22.778
Torsion angles, period  3. refined              268    13.873    15.000
Torsion angles, period  4. refined                9    11.144    15.000
Chiral centres: refined atoms                   196     0.084     0.200
Planar groups: refined atoms                   1743     0.009     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   298     0.243     0.200
VDW repulsions.others                          1353     0.194     0.200
VDW; torsion: refined_atoms                     716     0.170     0.200
VDW; torsion.others                             752     0.084     0.200
HBOND: refined_atoms                            226     0.211     0.200
VDW repulsions: symmetry: refined_atoms           6     0.259     0.200
VDW repulsions: symmetry: others                 24     0.190     0.200
HBOND: symmetry: refined_atoms                   20     0.214     0.200
HBOND: symmetry: others                           1     0.001     0.200
M. chain bond B values: refined atoms           746     1.551     1.225
M. chain bond B values: others                  746     1.549     1.225
M. chain angle B values: refined atoms          929     2.498     1.823
M. chain angle B values: others                 930     2.497     1.823
S. chain bond B values: refined atoms           812     2.502     1.558
S. chain bond B values: others                  811     2.499     1.558
S. chain angle B values: refined atoms         1177     3.924     2.192
S. chain angle B values: others                1178     3.922     2.192
Long range B values: refined atoms             1850     6.582    16.981
Long range B values: others                    1753     6.288    15.606
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =   -0.1149
Partial structure    1: scale =     0.3762, B  =   46.6013
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2251 100.00   481.2   486.3  0.16  0.17     100   475.5   479.5  0.20  0.22
 0.105    3784 100.00   381.7   364.4  0.16  0.15     193   389.6   365.3  0.21  0.19
 0.175    4751  99.96   246.2   240.8  0.16  0.13     279   258.9   248.9  0.22  0.19
 0.245    5580 100.00   184.6   185.5  0.17  0.13     303   186.9   186.9  0.23  0.20
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0355   1554   0.921    697   0.816   2251   0.888  0.959  0.9632  0.9707  0.9122  0.9412
  0.1053   3080   0.886    704   0.780   3784   0.867  0.996  0.9500  0.9639  0.8834  0.9451
  0.1752   4053   0.868    698   0.772   4751   0.854  0.981  0.9440  0.9575  0.8818  0.9392
  0.2450   4881   0.861    704   0.742   5585   0.846  0.948  0.9385  0.9552  0.8626  0.9381
 $$
Resolution limits                    =     41.964     1.890
Number of used reflections           =      16370
Percentage observed                  =    99.9826
Percentage of free reflections       =     5.0849
Overall R factor                     =     0.1602
Free R factor                        =     0.2156
Average Fourier shell correlation    =     0.9600
AverageFree Fourier shell correlation=     0.9456
Overall weighted R factor            =     0.1498
Free weighted R factor               =     0.1998
Overall weighted R2 factor           =     0.1826
Free weighted R2 factor              =     0.2412
Average correlation coefficient      =     0.9405
Overall correlation coefficient      =     0.9555
Free correlation coefficient         =     0.9145
Cruickshanks DPI for coordinate error=     0.1390
DPI based on free R factor           =     0.1389
Overall figure of merit              =     0.8589
ML based su of positional parameters =     0.0860
ML based su of thermal parameters    =     2.8568
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    88898.766       8230.1055       650483.75       650505.50    

    ****                              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.= 0.952 id.= 3.000 dev= -2.05 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_1-89A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.720     1.644
Bond angles  : others                          3238     1.435     1.580
Torsion angles, period  1. refined              185     6.988     5.000
Torsion angles, period  2. refined               90    36.822    22.778
Torsion angles, period  3. refined              268    13.866    15.000
Torsion angles, period  4. refined                9    11.148    15.000
Chiral centres: refined atoms                   196     0.084     0.200
Planar groups: refined atoms                   1743     0.009     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   297     0.243     0.200
VDW repulsions.others                          1352     0.194     0.200
VDW; torsion: refined_atoms                     716     0.170     0.200
VDW; torsion.others                             756     0.084     0.200
HBOND: refined_atoms                            226     0.211     0.200
VDW repulsions: symmetry: refined_atoms           6     0.259     0.200
VDW repulsions: symmetry: others                 24     0.190     0.200
HBOND: symmetry: refined_atoms                   21     0.209     0.200
HBOND: symmetry: others                           1     0.001     0.200
M. chain bond B values: refined atoms           746     1.551     1.225
M. chain bond B values: others                  746     1.550     1.225
M. chain angle B values: refined atoms          929     2.498     1.823
M. chain angle B values: others                 930     2.497     1.823
S. chain bond B values: refined atoms           812     2.502     1.558
S. chain bond B values: others                  811     2.499     1.558
S. chain angle B values: refined atoms         1177     3.925     2.193
S. chain angle B values: others                1178     3.923     2.192
Long range B values: refined atoms             1849     6.575    16.969
Long range B values: others                    1752     6.280    15.592
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =   -0.1152
Partial structure    1: scale =     0.3762, B  =   46.7111
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2251 100.00   481.4   486.3  0.16  0.17     100   475.7   479.5  0.20  0.22
 0.105    3784 100.00   381.8   364.4  0.16  0.15     193   389.7   365.3  0.21  0.19
 0.175    4751  99.96   246.2   240.8  0.16  0.13     279   259.0   248.9  0.22  0.19
 0.245    5580 100.00   184.7   185.5  0.16  0.13     303   187.0   186.9  0.23  0.20
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0355   1554   0.921    697   0.816   2251   0.888  0.959  0.9632  0.9707  0.9121  0.9412
  0.1053   3080   0.886    704   0.780   3784   0.866  0.996  0.9499  0.9639  0.8833  0.9451
  0.1752   4053   0.868    698   0.772   4751   0.854  0.981  0.9440  0.9575  0.8819  0.9392
  0.2450   4881   0.861    704   0.742   5585   0.846  0.948  0.9385  0.9552  0.8625  0.9382
 $$
Resolution limits                    =     41.964     1.890
Number of used reflections           =      16370
Percentage observed                  =    99.9826
Percentage of free reflections       =     5.0849
Overall R factor                     =     0.1602
Free R factor                        =     0.2156
Average Fourier shell correlation    =     0.9600
AverageFree Fourier shell correlation=     0.9456
Overall weighted R factor            =     0.1498
Free weighted R factor               =     0.1998
Overall weighted R2 factor           =     0.1826
Free weighted R2 factor              =     0.2413
Average correlation coefficient      =     0.9405
Overall correlation coefficient      =     0.9555
Free correlation coefficient         =     0.9145
Cruickshanks DPI for coordinate error=     0.1390
DPI based on free R factor           =     0.1389
Overall figure of merit              =     0.8589
ML based su of positional parameters =     0.0860
ML based su of thermal parameters    =     2.8568
-----------------------------------------------------------------------------
  Time in seconds: CPU =        15.70
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1605   0.2169   0.854       89127.    4950.8   0.0113  0.835   1.720  0.998   0.083
       1   0.1605   0.2161   0.859       88926.    4947.2   0.0109  0.810   1.700  0.988   0.084
       2   0.1603   0.2159   0.859       88908.    4947.0   0.0112  0.831   1.713  0.996   0.084
       3   0.1602   0.2158   0.859       88901.    4946.8   0.0112  0.833   1.717  0.999   0.084
       4   0.1602   0.2157   0.859       88903.    4947.0   0.0112  0.834   1.719  1.000   0.084
       5   0.1602   0.2158   0.859       88904.    4947.1   0.0112  0.834   1.719  1.000   0.084
       6   0.1602   0.2157   0.859       88903.    4947.0   0.0112  0.834   1.719  1.000   0.084
       7   0.1602   0.2157   0.859       88903.    4947.2   0.0112  0.834   1.720  1.001   0.084
       8   0.1602   0.2157   0.859       88902.    4947.1   0.0112  0.834   1.720  1.001   0.084
       9   0.1602   0.2156   0.859       88899.    4947.0   0.0112  0.834   1.720  1.001   0.084
      10   0.1602   0.2156   0.859       88903.    4947.3   0.0112  0.834   1.720  1.001   0.084
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1605   0.1602
             R free    0.2169   0.2156
     Rms BondLength    0.0113   0.0112
      Rms BondAngle    1.7204   1.7201
     Rms ChirVolume    0.0834   0.0841
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      47.9s System:    0.2s Elapsed:     0:48