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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: 15:52:04 


 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 1.78     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_1-79A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-78A.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_1-78A.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       0.0789
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.7800
  Estimated number of reflections :      26299
  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  1.7800

  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_1-79A.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=   2.059 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=   2.214 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=   1.856 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=   2.200 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=   2.425 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=   2.402 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=   2.126 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       1042
Number of   all  reflections      20551
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          20551

   Current auto weighting coefficient =    6.9497814    

 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.= 0.917 id.= 3.000 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  161
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  161
 Weight matrix   0.26747200    
 Actual weight    6.9497814      is applied to the X-ray term
Norm of X_ray positional gradient                34.7
Norm of Geom. positional gradient                79.5
Norm of X_ray B-factor gradient                  115.
Norm of Geom. B-factor gradient                  118.
Product of X_ray and Geom posit. gradients     -0.117E+08
 Cosine of angle between them                      -0.437
Product of X_ray and Geom B-fact gradients     -0.400E+08
 Cosine of angle between them                      -0.908


Residuals: XRAY=     0.7201E+06 GEOM=     0.1330E+05 TOTAL=     0.7334E+06
 function value    733369.69    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.035     0.017
Bond angles  : refined atoms                   2106     1.810     1.644
Bond angles  : others                          3238     2.354     1.580
Torsion angles, period  1. refined              185     6.918     5.000
Torsion angles, period  2. refined               90    35.754    22.778
Torsion angles, period  3. refined              268    13.298    15.000
Torsion angles, period  4. refined                9    12.016    15.000
Chiral centres: refined atoms                   196     0.085     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.015     0.020
VDW repulsions: refined_atoms                   303     0.242     0.200
VDW repulsions.others                          1328     0.219     0.200
VDW; torsion: refined_atoms                     720     0.172     0.200
VDW; torsion.others                             724     0.080     0.200
HBOND: refined_atoms                            221     0.198     0.200
HBOND.others                                      1     0.055     0.200
VDW repulsions: symmetry: refined_atoms           8     0.219     0.200
VDW repulsions: symmetry: others                 21     0.206     0.200
HBOND: symmetry: refined_atoms                   24     0.188     0.200
M. chain bond B values: refined atoms           746     1.633     1.303
M. chain bond B values: others                  746     1.631     1.303
M. chain angle B values: refined atoms          929     2.567     1.940
M. chain angle B values: others                 930     2.566     1.940
S. chain bond B values: refined atoms           811     2.835     1.676
S. chain bond B values: others                  810     2.831     1.676
S. chain angle B values: refined atoms         1177     4.405     2.356
S. chain angle B values: others                1178     4.403     2.356
Long range B values: refined atoms             1852     6.850    18.108
Long range B values: others                    1757     6.536    16.659
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0416, B  =    0.0509
Partial structure    1: scale =     0.3798, B  =   43.8218
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.040    2664 100.00   469.1   477.5  0.16  0.17     123   465.2   474.4  0.20  0.22
 0.119    4488 100.00   332.6   318.4  0.16  0.15     249   328.5   304.7  0.23  0.20
 0.197    5676  99.97   220.8   208.6  0.16  0.14     306   232.3   219.0  0.21  0.17
 0.276    6675 100.00   138.7   146.1  0.20  0.15     362   140.5   148.9  0.26  0.20
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0399   1875   0.913    789   0.808   2664   0.882  0.952  0.9621  0.9697  0.9079  0.9413
  0.1187   3699   0.873    789   0.773   4488   0.855  0.994  0.9439  0.9595  0.8850  0.9427
  0.1975   4890   0.879    786   0.767   5676   0.863  1.018  0.9526  0.9601  0.9066  0.9394
  0.2762   5884   0.814    795   0.732   6679   0.804  0.891  0.9323  0.9430  0.8766  0.9230
 $$
Resolution limits                    =     41.964     1.780
Number of used reflections           =      19506
Percentage observed                  =    99.9854
Percentage of free reflections       =     5.0711
Overall R factor                     =     0.1694
Free R factor                        =     0.2206
Average Fourier shell correlation    =     0.9554
AverageFree Fourier shell correlation=     0.9445
Overall weighted R factor            =     0.1543
Free weighted R factor               =     0.1995
Overall weighted R2 factor           =     0.1868
Free weighted R2 factor              =     0.2371
Average correlation coefficient      =     0.9348
Overall correlation coefficient      =     0.9568
Free correlation coefficient         =     0.9242
Cruickshanks DPI for coordinate error=     0.1192
DPI based on free R factor           =     0.1226
Overall figure of merit              =     0.8438
ML based su of positional parameters =     0.0781
ML based su of thermal parameters    =     2.4836
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    103611.05       13295.582       733369.69      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.29862028    
 Actual weight    6.9497814      is applied to the X-ray term


 function value    725708.56    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0415, B  =   -0.0780
Partial structure    1: scale =     0.3800, B  =   44.1740
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1694
Free R factor                        =     0.2198
Average Fourier shell correlation    =     0.9585
AverageFree Fourier shell correlation=     0.9478
Average correlation coefficient      =     0.9349
Overall figure of merit              =     0.8584
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    103186.59       8584.3350       725708.56       733369.69    


     CGMAT cycle number =      3

 Weight matrix   0.30013245    
 Actual weight    6.9497814      is applied to the X-ray term


 function value    725436.56    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0415, B  =   -0.0718
Partial structure    1: scale =     0.3802, B  =   44.1941
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1691
Free R factor                        =     0.2196
Average Fourier shell correlation    =     0.9588
AverageFree Fourier shell correlation=     0.9480
Average correlation coefficient      =     0.9354
Overall figure of merit              =     0.8588
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    103116.33       8800.6084       725436.56       725708.56    


     CGMAT cycle number =      4

 Weight matrix   0.29987156    
 Actual weight    6.9497814      is applied to the X-ray term


 function value    725440.38    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0415, B  =   -0.0580
Partial structure    1: scale =     0.3803, B  =   44.1503
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1691
Free R factor                        =     0.2196
Average Fourier shell correlation    =     0.9588
AverageFree Fourier shell correlation=     0.9480
Average correlation coefficient      =     0.9355
Overall figure of merit              =     0.8588
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02

 fvalues    103105.15       8852.7559       725411.00       725436.56    


     CGMAT cycle number =      5

 Weight matrix   0.30017182    
 Actual weight    6.9497814      is applied to the X-ray term


 function value    725401.19    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0415, B  =   -0.0585
Partial structure    1: scale =     0.3803, B  =   44.1262
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1691
Free R factor                        =     0.2195
Average Fourier shell correlation    =     0.9588
AverageFree Fourier shell correlation=     0.9481
Average correlation coefficient      =     0.9355
Overall figure of merit              =     0.8589
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    103101.85       8865.8535       725401.19       725411.00    


     CGMAT cycle number =      6

 Weight matrix   0.30031073    
 Actual weight    6.9497814      is applied to the X-ray term


 function value    725390.56    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0415, B  =   -0.0627
Partial structure    1: scale =     0.3805, B  =   44.1314
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1691
Free R factor                        =     0.2194
Average Fourier shell correlation    =     0.9588
AverageFree Fourier shell correlation=     0.9481
Average correlation coefficient      =     0.9356
Overall figure of merit              =     0.8589
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    103099.93       8868.5869       725390.56       725401.19    


     CGMAT cycle number =      7

 Weight matrix   0.30028710    
 Actual weight    6.9497814      is applied to the X-ray term


 function value    725298.50    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0416, B  =   -0.0507
Partial structure    1: scale =     0.3840, B  =   44.6892
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1691
Free R factor                        =     0.2193
Average Fourier shell correlation    =     0.9588
AverageFree Fourier shell correlation=     0.9481
Average correlation coefficient      =     0.9355
Overall figure of merit              =     0.8590
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    103087.15       8865.3652       725298.50       725390.56    


     CGMAT cycle number =      8

 Weight matrix   0.29986584    
 Actual weight    6.9497814      is applied to the X-ray term


 function value    725334.63    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0416, B  =   -0.0613
Partial structure    1: scale =     0.3839, B  =   44.7041
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1692
Free R factor                        =     0.2192
Average Fourier shell correlation    =     0.9588
AverageFree Fourier shell correlation=     0.9481
Average correlation coefficient      =     0.9355
Overall figure of merit              =     0.8589
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    103092.95       8858.3701       725359.50       725298.50    

 fvalues    103092.95       8858.3701       725332.44       725331.88    
 fvalues    103092.95       8858.3701       725332.44       725331.88    


     CGMAT cycle number =      9

 Weight matrix   0.29969788    
 Actual weight    6.9497814      is applied to the X-ray term


 function value    725345.50    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0416, B  =   -0.0583
Partial structure    1: scale =     0.3839, B  =   44.6934
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1692
Free R factor                        =     0.2193
Average Fourier shell correlation    =     0.9588
AverageFree Fourier shell correlation=     0.9480
Average correlation coefficient      =     0.9355
Overall figure of merit              =     0.8588
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    103093.80       8855.3994       725318.31       725331.88    
 fvalues    103093.80       8855.3994       725318.31       725334.75    


     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.= 0.929 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        :   120  120  256
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  161
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  161
 Weight matrix   0.29988468    
 Actual weight    6.9497814      is applied to the X-ray term
Norm of X_ray positional gradient                37.8
Norm of Geom. positional gradient                37.9
Norm of X_ray B-factor gradient                  121.
Norm of Geom. B-factor gradient                  124.
Product of X_ray and Geom posit. gradients     -0.139E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.477E+08
 Cosine of angle between them                      -0.992


Residuals: XRAY=     0.7165E+06 GEOM=      8852.     TOTAL=     0.7253E+06
 function value    725321.94    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.816     1.644
Bond angles  : others                          3238     1.484     1.580
Torsion angles, period  1. refined              185     6.883     5.000
Torsion angles, period  2. refined               90    35.727    22.778
Torsion angles, period  3. refined              268    13.213    15.000
Torsion angles, period  4. refined                9    12.418    15.000
Chiral centres: refined atoms                   196     0.085     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   298     0.244     0.200
VDW repulsions.others                          1353     0.191     0.200
VDW; torsion: refined_atoms                     719     0.172     0.200
VDW; torsion.others                             786     0.084     0.200
HBOND: refined_atoms                            214     0.201     0.200
VDW repulsions: symmetry: refined_atoms           8     0.218     0.200
VDW repulsions: symmetry: others                 21     0.190     0.200
HBOND: symmetry: refined_atoms                   23     0.183     0.200
M. chain bond B values: refined atoms           746     1.640     1.314
M. chain bond B values: others                  746     1.638     1.314
M. chain angle B values: refined atoms          929     2.585     1.957
M. chain angle B values: others                 930     2.583     1.957
S. chain bond B values: refined atoms           811     2.861     1.691
S. chain bond B values: others                  810     2.856     1.691
S. chain angle B values: refined atoms         1177     4.440     2.377
S. chain angle B values: others                1178     4.438     2.377
Long range B values: refined atoms             1839     6.819    18.114
Long range B values: others                    1750     6.572    16.766
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0416, B  =   -0.0599
Partial structure    1: scale =     0.3839, B  =   44.7231
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.040    2664 100.00   469.4   477.5  0.16  0.17     123   465.5   475.3  0.20  0.21
 0.119    4488 100.00   332.8   318.3  0.17  0.15     249   328.7   305.0  0.22  0.20
 0.197    5676  99.97   221.0   208.8  0.16  0.14     306   232.4   219.0  0.21  0.17
 0.276    6675 100.00   138.8   146.1  0.20  0.15     362   140.6   148.9  0.25  0.20
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0399   1875   0.926    789   0.824   2664   0.896  0.954  0.9653  0.9723  0.9087  0.9407
  0.1187   3699   0.874    789   0.776   4488   0.857  0.994  0.9447  0.9601  0.8860  0.9424
  0.1975   4890   0.881    786   0.770   5676   0.865  1.018  0.9534  0.9608  0.9079  0.9399
  0.2762   5884   0.850    795   0.765   6679   0.840  0.901  0.9401  0.9508  0.8795  0.9249
 $$
Resolution limits                    =     41.964     1.780
Number of used reflections           =      19506
Percentage observed                  =    99.9854
Percentage of free reflections       =     5.0711
Overall R factor                     =     0.1692
Free R factor                        =     0.2192
Average Fourier shell correlation    =     0.9588
AverageFree Fourier shell correlation=     0.9481
Overall weighted R factor            =     0.1543
Free weighted R factor               =     0.1984
Overall weighted R2 factor           =     0.1869
Free weighted R2 factor              =     0.2356
Average correlation coefficient      =     0.9355
Overall correlation coefficient      =     0.9568
Free correlation coefficient         =     0.9251
Cruickshanks DPI for coordinate error=     0.1191
DPI based on free R factor           =     0.1218
Overall figure of merit              =     0.8589
ML based su of positional parameters =     0.0737
ML based su of thermal parameters    =     2.3131
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    103092.37       8852.4883       725321.94       725334.75    

    ****                              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.= 0.929 id.= 3.000 dev= -2.07 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_1-78A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.816     1.644
Bond angles  : others                          3238     1.484     1.580
Torsion angles, period  1. refined              185     6.881     5.000
Torsion angles, period  2. refined               90    35.727    22.778
Torsion angles, period  3. refined              268    13.211    15.000
Torsion angles, period  4. refined                9    12.425    15.000
Chiral centres: refined atoms                   196     0.085     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   299     0.244     0.200
VDW repulsions.others                          1349     0.192     0.200
VDW; torsion: refined_atoms                     719     0.172     0.200
VDW; torsion.others                             788     0.084     0.200
HBOND: refined_atoms                            215     0.201     0.200
VDW repulsions: symmetry: refined_atoms           8     0.218     0.200
VDW repulsions: symmetry: others                 21     0.190     0.200
HBOND: symmetry: refined_atoms                   23     0.183     0.200
M. chain bond B values: refined atoms           746     1.641     1.314
M. chain bond B values: others                  746     1.639     1.314
M. chain angle B values: refined atoms          929     2.585     1.957
M. chain angle B values: others                 930     2.584     1.957
S. chain bond B values: refined atoms           811     2.862     1.691
S. chain bond B values: others                  810     2.856     1.691
S. chain angle B values: refined atoms         1177     4.441     2.377
S. chain angle B values: others                1178     4.439     2.377
Long range B values: refined atoms             1841     6.822    18.159
Long range B values: others                    1751     6.572    16.793
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0415, B  =   -0.0550
Partial structure    1: scale =     0.3839, B  =   44.7304
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.040    2664 100.00   469.5   477.4  0.16  0.17     123   465.6   475.2  0.20  0.21
 0.119    4488 100.00   332.9   318.2  0.17  0.15     249   328.8   305.0  0.22  0.20
 0.197    5676  99.97   221.0   208.7  0.16  0.14     306   232.5   219.0  0.21  0.17
 0.276    6675 100.00   138.8   146.0  0.20  0.15     362   140.6   148.8  0.25  0.20
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0399   1875   0.926    789   0.824   2664   0.896  0.954  0.9653  0.9723  0.9086  0.9407
  0.1187   3699   0.874    789   0.776   4488   0.857  0.994  0.9447  0.9601  0.8861  0.9424
  0.1975   4890   0.881    786   0.770   5676   0.865  1.018  0.9534  0.9608  0.9079  0.9399
  0.2762   5884   0.850    795   0.765   6679   0.840  0.901  0.9400  0.9508  0.8795  0.9249
 $$
Resolution limits                    =     41.964     1.780
Number of used reflections           =      19506
Percentage observed                  =    99.9854
Percentage of free reflections       =     5.0711
Overall R factor                     =     0.1692
Free R factor                        =     0.2192
Average Fourier shell correlation    =     0.9588
AverageFree Fourier shell correlation=     0.9480
Overall weighted R factor            =     0.1544
Free weighted R factor               =     0.1984
Overall weighted R2 factor           =     0.1869
Free weighted R2 factor              =     0.2357
Average correlation coefficient      =     0.9355
Overall correlation coefficient      =     0.9568
Free correlation coefficient         =     0.9251
Cruickshanks DPI for coordinate error=     0.1191
DPI based on free R factor           =     0.1218
Overall figure of merit              =     0.8588
ML based su of positional parameters =     0.0737
ML based su of thermal parameters    =     2.3131
-----------------------------------------------------------------------------
  Time in seconds: CPU =        17.56
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1694   0.2206   0.844      103611.    5706.6   0.0124  0.921   1.810  1.045   0.085
       1   0.1694   0.2198   0.858      103187.    5696.2   0.0117  0.875   1.772  1.022   0.084
       2   0.1691   0.2196   0.859      103116.    5695.0   0.0123  0.916   1.802  1.040   0.085
       3   0.1691   0.2196   0.859      103109.    5695.0   0.0123  0.919   1.809  1.045   0.085
       4   0.1691   0.2195   0.859      103102.    5694.7   0.0124  0.919   1.812  1.046   0.085
       5   0.1691   0.2194   0.859      103100.    5694.7   0.0124  0.920   1.814  1.047   0.085
       6   0.1691   0.2193   0.859      103087.    5693.8   0.0124  0.920   1.815  1.048   0.085
       7   0.1692   0.2192   0.859      103093.    5694.1   0.0124  0.920   1.816  1.048   0.085
       8   0.1692   0.2193   0.859      103095.    5694.3   0.0124  0.920   1.816  1.048   0.085
       9   0.1692   0.2192   0.859      103092.    5694.2   0.0124  0.920   1.816  1.048   0.085
      10   0.1692   0.2192   0.859      103097.    5694.4   0.0124  0.920   1.816  1.048   0.085
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1694   0.1692
             R free    0.2206   0.2192
     Rms BondLength    0.0124   0.0124
      Rms BondAngle    1.8103   1.8155
     Rms ChirVolume    0.0850   0.0847
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      49.6s System:    0.1s Elapsed:     0:50