###############################################################
 ###############################################################
 ###############################################################
 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 26/ 5/2020 Run time: 13:44:20 


 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 1.90     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_1-91A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-90A.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_1-90A.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       0.0693
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.9000
  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  1.9000

  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_1-91A.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=   2.005 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=   2.205 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=   1.871 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=   2.211 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=   2.380 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=   2.421 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=   2.123 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        864
Number of   all  reflections      16986
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          16986

   Current auto weighting coefficient =    7.2495699    

 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.= 0.938 id.= 3.000 dev= -2.06 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   0.21935156    
 Actual weight    7.2495699      is applied to the X-ray term
Norm of X_ray positional gradient                32.2
Norm of Geom. positional gradient                77.6
Norm of X_ray B-factor gradient                  109.
Norm of Geom. B-factor gradient                  106.
Product of X_ray and Geom posit. gradients     -0.885E+07
 Cosine of angle between them                      -0.366
Product of X_ray and Geom B-fact gradients     -0.341E+08
 Cosine of angle between them                      -0.913


Residuals: XRAY=     0.6373E+06 GEOM=     0.1267E+05 TOTAL=     0.6499E+06
 function value    649928.13    

-------------------------------------------------------------------------------
             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     1.711     1.644
Bond angles  : others                          3238     2.346     1.580
Torsion angles, period  1. refined              185     7.011     5.000
Torsion angles, period  2. refined               90    36.770    22.778
Torsion angles, period  3. refined              268    14.123    15.000
Torsion angles, period  4. refined                9    11.467    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                   302     0.241     0.200
VDW repulsions.others                          1332     0.220     0.200
VDW; torsion: refined_atoms                     716     0.170     0.200
VDW; torsion.others                             710     0.079     0.200
HBOND: refined_atoms                            232     0.208     0.200
VDW repulsions: symmetry: refined_atoms           9     0.212     0.200
VDW repulsions: symmetry: others                 24     0.207     0.200
HBOND: symmetry: refined_atoms                   21     0.212     0.200
M. chain bond B values: refined atoms           746     1.536     1.215
M. chain bond B values: others                  746     1.535     1.215
M. chain angle B values: refined atoms          929     2.481     1.809
M. chain angle B values: others                 930     2.479     1.808
S. chain bond B values: refined atoms           811     2.471     1.544
S. chain bond B values: others                  810     2.468     1.543
S. chain angle B values: refined atoms         1177     3.892     2.171
S. chain angle B values: others                1178     3.890     2.171
Long range B values: refined atoms             1856     6.556    17.028
Long range B values: others                    1754     6.238    15.587
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =   -0.0658
Partial structure    1: scale =     0.3758, B  =   46.4317
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2213 100.00   480.9   485.4  0.16  0.17      98   477.2   481.9  0.20  0.23
 0.104    3735 100.00   386.0   369.0  0.16  0.15     189   387.1   362.0  0.22  0.20
 0.173    4666  99.96   247.1   242.1  0.16  0.13     276   264.7   255.4  0.22  0.19
 0.242    5503 100.00   188.5   189.0  0.16  0.13     301   190.3   190.4  0.23  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1524   0.908    689   0.803   2213   0.875  0.959  0.9602  0.9683  0.9118  0.9417
  0.1042   3040   0.882    695   0.775   3735   0.862  0.997  0.9472  0.9631  0.8777  0.9447
  0.1733   3977   0.864    689   0.767   4666   0.850  0.979  0.9457  0.9567  0.8901  0.9396
  0.2425   4801   0.864    705   0.745   5506   0.849  0.955  0.9386  0.9550  0.8625  0.9365
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16120
Percentage observed                  =    99.9823
Percentage of free reflections       =     5.0871
Overall R factor                     =     0.1601
Free R factor                        =     0.2167
Average Fourier shell correlation    =     0.9592
AverageFree Fourier shell correlation=     0.9452
Overall weighted R factor            =     0.1497
Free weighted R factor               =     0.2013
Overall weighted R2 factor           =     0.1820
Free weighted R2 factor              =     0.2429
Average correlation coefficient      =     0.9400
Overall correlation coefficient      =     0.9553
Free correlation coefficient         =     0.9132
Cruickshanks DPI for coordinate error=     0.1416
DPI based on free R factor           =     0.1414
Overall figure of merit              =     0.8559
ML based su of positional parameters =     0.0881
ML based su of thermal parameters    =     2.9251
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    87903.320       12666.854       649928.13      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.22636995    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    644050.00    

-------------------------------------------------------------------------------
             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 =     0.0402, B  =   -0.1318
Partial structure    1: scale =     0.3759, B  =   46.6143
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1600
Free R factor                        =     0.2162
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9463
Average correlation coefficient      =     0.9406
Overall figure of merit              =     0.8596
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    87712.234       8173.9824       644050.00       649928.13    


     CGMAT cycle number =      3

 Weight matrix   0.22646640    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    643975.25    

-------------------------------------------------------------------------------
             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 =     0.0402, B  =   -0.1278
Partial structure    1: scale =     0.3763, B  =   46.4220
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1597
Free R factor                        =     0.2161
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9463
Average correlation coefficient      =     0.9408
Overall figure of merit              =     0.8598
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    87695.109       8223.4531       643975.25       644050.00    


     CGMAT cycle number =      4

 Weight matrix   0.22629133    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    643961.38    

-------------------------------------------------------------------------------
             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 =     0.0402, B  =   -0.1278
Partial structure    1: scale =     0.3765, B  =   46.4561
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1596
Free R factor                        =     0.2161
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9463
Average correlation coefficient      =     0.9408
Overall figure of merit              =     0.8597
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    87691.523       8235.5869       643961.38       643975.25    


     CGMAT cycle number =      5

 Weight matrix   0.22634172    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    643921.56    

-------------------------------------------------------------------------------
             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 =     0.0402, B  =   -0.1327
Partial structure    1: scale =     0.3766, B  =   46.4914
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1597
Free R factor                        =     0.2159
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9463
Average correlation coefficient      =     0.9408
Overall figure of merit              =     0.8598
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    87686.289       8233.6914       643921.56       643961.38    


     CGMAT cycle number =      6

 Weight matrix   0.22633033    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    643896.88    

-------------------------------------------------------------------------------
             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 =     0.0402, B  =   -0.1388
Partial structure    1: scale =     0.3767, B  =   46.4865
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1597
Free R factor                        =     0.2159
Average Fourier shell correlation    =     0.9604
AverageFree Fourier shell correlation=     0.9463
Average correlation coefficient      =     0.9408
Overall figure of merit              =     0.8598
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    87683.367       8230.1729       643896.88       643921.56    


     CGMAT cycle number =      7

 Weight matrix   0.22623093    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    643874.75    

-------------------------------------------------------------------------------
             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
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.1431
Partial structure    1: scale =     0.3767, B  =   46.5256
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1596
Free R factor                        =     0.2158
Average Fourier shell correlation    =     0.9604
AverageFree Fourier shell correlation=     0.9463
Average correlation coefficient      =     0.9409
Overall figure of merit              =     0.8598
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    87681.273       8223.2305       643874.75       643896.88    


     CGMAT cycle number =      8

 Weight matrix   0.22586380    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    643926.56    

-------------------------------------------------------------------------------
             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 =     0.0402, B  =   -0.1540
Partial structure    1: scale =     0.3767, B  =   46.5589
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1597
Free R factor                        =     0.2159
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9462
Average correlation coefficient      =     0.9409
Overall figure of merit              =     0.8597
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    87691.203       8220.6191       643947.94       643874.75    

 fvalues    87691.203       8220.6191       643937.25       643944.13    
 fvalues    87691.203       8220.6191       643937.25       643944.13    


     CGMAT cycle number =      9

 Weight matrix   0.22579141    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    643928.50    

-------------------------------------------------------------------------------
             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 =     0.0402, B  =   -0.1448
Partial structure    1: scale =     0.3766, B  =   46.5624
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1597
Free R factor                        =     0.2158
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9463
Average correlation coefficient      =     0.9409
Overall figure of merit              =     0.8597
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    87689.781       8215.3164       643928.50       643944.13    


     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.= 0.949 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   0.22586885    
 Actual weight    7.2495699      is applied to the X-ray term
Norm of X_ray positional gradient                31.8
Norm of Geom. positional gradient                31.8
Norm of X_ray B-factor gradient                  106.
Norm of Geom. B-factor gradient                  111.
Product of X_ray and Geom posit. gradients     -0.976E+07
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.371E+08
 Cosine of angle between them                      -0.977


Residuals: XRAY=     0.6357E+06 GEOM=      8214.     TOTAL=     0.6439E+06
 function value    643913.63    

-------------------------------------------------------------------------------
             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     1.431     1.580
Torsion angles, period  1. refined              185     6.975     5.000
Torsion angles, period  2. refined               90    36.939    22.778
Torsion angles, period  3. refined              268    13.983    15.000
Torsion angles, period  4. refined                9    11.112    15.000
Chiral centres: refined atoms                   196     0.083     0.200
Planar groups: refined atoms                   1743     0.009     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   301     0.242     0.200
VDW repulsions.others                          1377     0.191     0.200
VDW; torsion: refined_atoms                     715     0.171     0.200
VDW; torsion.others                             787     0.083     0.200
HBOND: refined_atoms                            225     0.212     0.200
VDW repulsions: symmetry: refined_atoms           9     0.215     0.200
VDW repulsions: symmetry: others                 24     0.192     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     2.482     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     3.937     2.185
S. chain angle B values: others                1178     3.935     2.185
Long range B values: refined atoms             1849     6.569    16.954
Long range B values: others                    1753     6.275    15.595
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.1397
Partial structure    1: scale =     0.3767, B  =   46.5890
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   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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2213 100.00   481.2   485.7  0.16  0.17      98   477.5   482.2  0.20  0.22
 0.104    3735 100.00   386.2   369.1  0.16  0.15     189   387.3   362.6  0.21  0.20
 0.173    4666  99.96   247.3   242.2  0.16  0.13     276   264.9   255.5  0.22  0.19
 0.242    5503 100.00   188.6   189.2  0.16  0.13     301   190.4   190.1  0.23  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1524   0.922    689   0.821   2213   0.891  0.959  0.9634  0.9711  0.9125  0.9413
  0.1042   3040   0.885    695   0.778   3735   0.865  0.997  0.9485  0.9641  0.8793  0.9453
  0.1733   3977   0.865    689   0.767   4666   0.850  0.979  0.9457  0.9568  0.8901  0.9392
  0.2425   4801   0.867    705   0.747   5506   0.852  0.955  0.9398  0.9565  0.8639  0.9391
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16120
Percentage observed                  =    99.9823
Percentage of free reflections       =     5.0871
Overall R factor                     =     0.1597
Free R factor                        =     0.2158
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9463
Overall weighted R factor            =     0.1495
Free weighted R factor               =     0.2001
Overall weighted R2 factor           =     0.1819
Free weighted R2 factor              =     0.2414
Average correlation coefficient      =     0.9409
Overall correlation coefficient      =     0.9555
Free correlation coefficient         =     0.9140
Cruickshanks DPI for coordinate error=     0.1412
DPI based on free R factor           =     0.1408
Overall figure of merit              =     0.8597
ML based su of positional parameters =     0.0868
ML based su of thermal parameters    =     2.8884
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    87687.883       8214.1816       643913.63       643928.50    

    ****                              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.= 0.950 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_1-90A.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     1.721     1.644
Bond angles  : others                          3238     1.431     1.580
Torsion angles, period  1. refined              185     6.974     5.000
Torsion angles, period  2. refined               90    36.937    22.778
Torsion angles, period  3. refined              268    13.983    15.000
Torsion angles, period  4. refined                9    11.106    15.000
Chiral centres: refined atoms                   196     0.083     0.200
Planar groups: refined atoms                   1743     0.009     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   300     0.242     0.200
VDW repulsions.others                          1377     0.190     0.200
VDW; torsion: refined_atoms                     715     0.171     0.200
VDW; torsion.others                             789     0.082     0.200
HBOND: refined_atoms                            225     0.212     0.200
VDW repulsions: symmetry: refined_atoms           9     0.215     0.200
VDW repulsions: symmetry: others                 24     0.192     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             1848     6.571    16.958
Long range B values: others                    1752     6.277    15.597
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.1403
Partial structure    1: scale =     0.3768, B  =   46.5276
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   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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2213 100.00   481.2   485.6  0.16  0.17      98   477.4   482.2  0.20  0.22
 0.104    3735 100.00   386.2   369.1  0.16  0.15     189   387.3   362.6  0.21  0.20
 0.173    4666  99.96   247.3   242.2  0.16  0.13     276   264.9   255.4  0.22  0.19
 0.242    5503 100.00   188.6   189.2  0.16  0.13     301   190.4   190.0  0.23  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1524   0.922    689   0.821   2213   0.891  0.959  0.9635  0.9711  0.9127  0.9413
  0.1042   3040   0.885    695   0.778   3735   0.865  0.997  0.9484  0.9641  0.8792  0.9453
  0.1733   3977   0.865    689   0.767   4666   0.850  0.979  0.9457  0.9568  0.8901  0.9392
  0.2425   4801   0.867    705   0.747   5506   0.852  0.955  0.9398  0.9565  0.8639  0.9391
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16120
Percentage observed                  =    99.9823
Percentage of free reflections       =     5.0871
Overall R factor                     =     0.1597
Free R factor                        =     0.2157
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9463
Overall weighted R factor            =     0.1494
Free weighted R factor               =     0.2000
Overall weighted R2 factor           =     0.1819
Free weighted R2 factor              =     0.2413
Average correlation coefficient      =     0.9409
Overall correlation coefficient      =     0.9555
Free correlation coefficient         =     0.9140
Cruickshanks DPI for coordinate error=     0.1412
DPI based on free R factor           =     0.1407
Overall figure of merit              =     0.8598
ML based su of positional parameters =     0.0868
ML based su of thermal parameters    =     2.8884
-----------------------------------------------------------------------------
  Time in seconds: CPU =        13.50
             Elapsed =         128.00

    ****           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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1601   0.2167   0.856       87903.    4878.2   0.0111  0.824   1.711  0.995   0.083
       1   0.1600   0.2162   0.860       87712.    4875.2   0.0109  0.810   1.695  0.986   0.083
       2   0.1597   0.2161   0.860       87695.    4874.7   0.0112  0.830   1.709  0.993   0.084
       3   0.1596   0.2161   0.860       87692.    4874.8   0.0112  0.832   1.713  0.995   0.084
       4   0.1597   0.2159   0.860       87686.    4874.6   0.0112  0.833   1.715  0.996   0.084
       5   0.1597   0.2159   0.860       87683.    4874.5   0.0112  0.833   1.717  0.997   0.084
       6   0.1596   0.2158   0.860       87681.    4874.4   0.0112  0.834   1.718  0.997   0.083
       7   0.1597   0.2159   0.860       87689.    4875.2   0.0112  0.833   1.720  0.998   0.083
       8   0.1597   0.2158   0.860       87690.    4875.1   0.0112  0.833   1.720  0.998   0.083
       9   0.1597   0.2158   0.860       87688.    4874.9   0.0112  0.833   1.720  0.998   0.083
      10   0.1597   0.2157   0.860       87684.    4874.7   0.0112  0.833   1.721  0.998   0.083
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1601   0.1597
             R free    0.2167   0.2157
     Rms BondLength    0.0111   0.0112
      Rms BondAngle    1.7109   1.7207
     Rms ChirVolume    0.0833   0.0834
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      45.5s System:    0.1s Elapsed:     0:45