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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
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 User: maly  Run date: 28/ 5/2020 Run time: 10:11:01 


 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.

<!--SUMMARY_END--></FONT></B>
 $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 38.62 1.20     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 6
  Data line--- monitor MEDIum
  Data line--- free 0
  Data line--- END

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN   Filename: 1H87_dui_R.mtz 

 LABIN FP=F_FROMDIALS SIGFP=SIGF_FROMDIALS FREE=FREE

    ****                     Input and Default parameters#                      ****


Input coordinate file.  Logical name - XYZIN actual file name  - 1H87_dui_R00_1-30A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - 1H87_dui_R00_1-20A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - 1H87_dui_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - 1H87_dui_R00_1-20A.mtz

Cell from mtz :    77.243    77.243    38.656    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       0.1736
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    38.6230  1.2000
  Estimated number of reflections :      48798
  Free R exclusion - flag equals:     0
  Auto weighting. An attempt
  Refinement cycles       :     6
  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:    38.6230  1.2000

  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 :1H87_dui_R00_1-30A.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    :    1217
  Number of residues :     291
  Number of chains   :      10
  I am reading library. Please wait.
                mon_lib.cif
  INFO:     link is found (not be used) dist=   2.801 ideal_dist=   2.495
            ch:AaA  res: 284  DO3              at:N1  .->ch:AgA  res: 290  GD               at:GD  .
  INFO:     link is found (not be used) dist=   2.796 ideal_dist=   2.495
            ch:AaA  res: 284  DO3              at:N2  .->ch:AgA  res: 290  GD               at:GD  .
  INFO:     link is found (not be used) dist=   2.861 ideal_dist=   2.495
            ch:AaA  res: 284  DO3              at:N3  .->ch:AgA  res: 290  GD               at:GD  .
  INFO:     link is found (not be used) dist=   2.682 ideal_dist=   2.495
            ch:AaA  res: 284  DO3              at:N4  .->ch:AgA  res: 290  GD               at:GD  .
  INFO:     link is found (not be used) dist=   2.198 ideal_dist=   2.360
            ch:AaA  res: 284  DO3              at:O1  .->ch:AgA  res: 290  GD               at:GD  .
  INFO:     link is found (not be used) dist=   2.302 ideal_dist=   2.360
            ch:AaA  res: 284  DO3              at:O3  .->ch:AgA  res: 290  GD               at:GD  .
  INFO:     link is found (not be used) dist=   2.566 ideal_dist=   2.360
            ch:AaA  res: 284  DO3              at:O5  .->ch:AgA  res: 290  GD               at:GD  .
  INFO:     link is found (not be used) dist=   2.164 ideal_dist=   2.520
            ch:AaA  res: 284  DO3              at:O7  .->ch:AgA  res: 290  GD               at:GD  .
  INFO:     link is found (not be used) dist=   2.720 ideal_dist=   2.495
            ch:AbA  res: 285  DO3              at:N1  .->ch:AhA  res: 291  GD               at:GD  .
  INFO:     link is found (not be used) dist=   2.688 ideal_dist=   2.495
            ch:AbA  res: 285  DO3              at:N2  .->ch:AhA  res: 291  GD               at:GD  .
  INFO:     link is found (not be used) dist=   2.591 ideal_dist=   2.495
            ch:AbA  res: 285  DO3              at:N3  .->ch:AhA  res: 291  GD               at:GD  .
  INFO:     link is found (not be used) dist=   2.599 ideal_dist=   2.495
            ch:AbA  res: 285  DO3              at:N4  .->ch:AhA  res: 291  GD               at:GD  .
  INFO:     link is found (not be used) dist=   2.480 ideal_dist=   2.360
            ch:AbA  res: 285  DO3              at:O1  .->ch:AhA  res: 291  GD               at:GD  .
  INFO:     link is found (not be used) dist=   2.245 ideal_dist=   2.360
            ch:AbA  res: 285  DO3              at:O3  .->ch:AhA  res: 291  GD               at:GD  .
  INFO:     link is found (not be used) dist=   2.327 ideal_dist=   2.360
            ch:AbA  res: 285  DO3              at:O5  .->ch:AhA  res: 291  GD               at:GD  .
  INFO:     link is found (not be used) dist=   2.371 ideal_dist=   2.520
            ch:AbA  res: 285  DO3              at:O7  .->ch:AhA  res: 291  GD               at:GD  .
  --------------------------------
  --- title of input coord file ---

  PDB_code:xxxx
  PDB_name:----
  PDB_date:28-MAY-20
  --------------------------------
  Number of chains                  :      10
  Total number of monomers          :     291
  Number of atoms                   :    2543
  Number of missing atoms           :       0
  Number of rebuilt atoms           :    1018
  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   1.0555
  CL    11.4601   0.0104   7.1962   1.1662   6.2554  18.5194   1.6455  47.7784  -9.3378
  GD    25.0836   2.2534  19.0895   0.1820  13.8588  12.9331   3.5472 101.3980   1.4253


 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:      2041         0      2041
               Angles:      3684         0      3684
              Chirals:       136         0       136
               Planes:       314         0       314
             Torsions:      1098         0      1098
            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       3402
Number of   all  reflections      37125
--------------------------------------------------------------------------------
 Number of reflections in file      47969
 Number of reflections read          37125

   Current auto weighting coefficient =    5.4998202    

 mode : HKRF


######  TLS Group Definitions ######


     CGMAT cycle number =      1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   216  216  112
 Maximuum H,K,L                 :    65   65   33
 Minimum acceptable grid spacing:   140  140   70
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   216  216  112
 Maximuum H,K,L                 :    65   65   33
 Minimum acceptable grid spacing:   140  140   70
 Weight matrix    1.8683327    
 Actual weight    5.4998202      is applied to the X-ray term
Norm of X_ray positional gradient                61.3
Norm of Geom. positional gradient                89.0
Norm of X_ray B-factor gradient                  108.
Norm of Geom. B-factor gradient                  75.2
Product of X_ray and Geom posit. gradients     -0.188E+08
 Cosine of angle between them                      -0.527
Product of X_ray and Geom B-fact gradients     -0.117E+08
 Cosine of angle between them                      -0.661


Residuals: XRAY=     0.6553E+06 GEOM=      7322.     TOTAL=     0.6627E+06
 function value    662650.94    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1081     0.013     0.013
Bond distances: others                          960     0.036     0.018
Bond angles  : refined atoms                   1461     1.942     1.652
Bond angles  : others                          2223     2.353     1.582
Torsion angles, period  1. refined              128     3.265     5.000
Torsion angles, period  2. refined               61    30.122    20.656
Torsion angles, period  3. refined              166    10.916    15.000
Torsion angles, period  4. refined               11    14.089    15.000
Chiral centres: refined atoms                   136     0.100     0.200
Planar groups: refined atoms                   1211     0.009     0.020
Planar groups: others                           246     0.018     0.020
VDW repulsions: refined_atoms                   282     0.227     0.200
VDW repulsions.others                           985     0.229     0.200
VDW; torsion: refined_atoms                     542     0.179     0.200
VDW; torsion.others                             492     0.094     0.200
HBOND: refined_atoms                             93     0.169     0.200
Metal-ion: refined_atoms                          6     0.117     0.200
VDW repulsions: symmetry: refined_atoms          12     0.226     0.200
VDW repulsions: symmetry: others                 50     0.203     0.200
HBOND: symmetry: refined_atoms                    8     0.224     0.200
M. chain bond B values: refined atoms           514     0.638     1.310
M. chain bond B values: others                  514     0.638     1.310
M. chain angle B values: refined atoms          642     0.731     1.967
M. chain angle B values: others                 643     0.730     1.970
S. chain bond B values: refined atoms           566     1.032     1.441
S. chain bond B values: others                  567     1.031     1.441
S. chain angle B values: refined atoms          819     1.339     2.130
S. chain angle B values: others                 820     1.338     2.130
Long range B values: refined atoms             1360     3.354    16.881
Long range B values: others                    1335     3.148    16.538
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.9177, B  =   -0.1510
Partial structure    1: scale =     0.2324, B  =  251.5980
Overall anisotropic scale factors
   B11 =   0.03 B22 =   0.03 B33 =  -0.06 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. <Rfactor> v. resln :N:1,6,7,11,12:
:Cycle    1. <Fobs> and <Fc> v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.087    4467  99.84   326.9   324.8  0.06  0.06     445   320.8   317.4  0.07  0.07
 0.261    7720  99.95   131.0   131.5  0.06  0.04     816   136.6   137.7  0.07  0.05
 0.434    9848  99.67    60.0    58.1  0.20  0.16    1000    59.4    58.3  0.21  0.18
 0.608    6581  56.37    50.1    34.2  0.40  0.39     620    49.7    33.5  0.40  0.39
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle    1. FSC and  Fom(<cos(DelPhi)>-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0874   3500   0.978    967   0.929   4467   0.967  0.997  0.9928  0.9914  0.9860  0.9799
  0.2608   6753   0.959    967   0.904   7720   0.952  0.990  0.9931  0.9929  0.9908  0.9916
  0.4343   8878   0.805    970   0.743   9848   0.799  0.908  0.9071  0.9116  0.8828  0.8974
  0.6077   6140   0.448    441   0.440   6581   0.447  0.671  0.5110  0.5302  0.3441  0.3721
 $$
Resolution limits                    =     38.623     1.200
Number of used reflections           =      28616
Percentage observed                  =    84.8404
Percentage of free reflections       =     9.1469
Overall R factor                     =     0.1186
Free R factor                        =     0.1235
Average Fourier shell correlation    =     0.8583
AverageFree Fourier shell correlation=     0.8595
Overall weighted R factor            =     0.0760
Free weighted R factor               =     0.0810
Overall weighted R2 factor           =     0.1188
Free weighted R2 factor              =     0.0931
Average correlation coefficient      =     0.8149
Overall correlation coefficient      =     0.9859
Free correlation coefficient         =     0.9878
Cruickshanks DPI for coordinate error=     0.0351
DPI based on free R factor           =     0.0333
Overall figure of merit              =     0.7856
ML based su of positional parameters =     0.0257
ML based su of thermal parameters    =     0.7652
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    119154.69       7321.5405       662650.94      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix    1.8633269    
 Actual weight    5.4998202      is applied to the X-ray term


 function value    659706.00    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1081     0.013     0.013
Bond distances: others                          960     0.002     0.018
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.9175, B  =    0.0094
Partial structure    1: scale =     0.2330, B  =  257.1029
Overall anisotropic scale factors
   B11 =   0.03 B22 =   0.03 B33 =  -0.06 B12 =  -0.00 B13 =  -0.00 B23 =  -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1186
Free R factor                        =     0.1238
Average Fourier shell correlation    =     0.8535
AverageFree Fourier shell correlation=     0.8548
Average correlation coefficient      =     0.8152
Overall figure of merit              =     0.7792
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    119157.93       4358.8145       659706.00       662650.94    


     CGMAT cycle number =      3

 Weight matrix    1.6730030    
 Actual weight    4.9998364      is applied to the X-ray term


 function value    600250.81    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1081     0.013     0.013
Bond distances: others                          960     0.001     0.018
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.9174, B  =   -0.0030
Partial structure    1: scale =     0.2331, B  =  258.1660
Overall anisotropic scale factors
   B11 =   0.03 B22 =   0.03 B33 =  -0.06 B12 =  -0.00 B13 =  -0.00 B23 =  -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1185
Free R factor                        =     0.1239
Average Fourier shell correlation    =     0.8494
AverageFree Fourier shell correlation=     0.8510
Average correlation coefficient      =     0.8153
Overall figure of merit              =     0.7743
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    119180.85       4366.0317       600250.81       659706.00    


     CGMAT cycle number =      4

 Weight matrix    1.5142298    
 Actual weight    4.5453057      is applied to the X-ray term


 function value    546200.75    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1081     0.013     0.013
Bond distances: others                          960     0.001     0.018
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.9173, B  =   -0.0014
Partial structure    1: scale =     0.2331, B  =  259.1918
Overall anisotropic scale factors
   B11 =   0.03 B22 =   0.03 B33 =  -0.06 B12 =  -0.00 B13 =  -0.00 B23 =  -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1186
Free R factor                        =     0.1240
Average Fourier shell correlation    =     0.8472
AverageFree Fourier shell correlation=     0.8488
Average correlation coefficient      =     0.8153
Overall figure of merit              =     0.7715
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    119225.88       4282.6895       546200.75       600250.81    


     CGMAT cycle number =      5

 Weight matrix    1.5086466    
 Actual weight    4.5453057      is applied to the X-ray term


 function value    546278.50    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1081     0.013     0.013
Bond distances: others                          960     0.001     0.018
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.9173, B  =   -0.0008
Partial structure    1: scale =     0.2331, B  =  259.4722
Overall anisotropic scale factors
   B11 =   0.03 B22 =   0.03 B33 =  -0.06 B12 =  -0.00 B13 =  -0.00 B23 =  -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1188
Free R factor                        =     0.1241
Average Fourier shell correlation    =     0.8458
AverageFree Fourier shell correlation=     0.8475
Average correlation coefficient      =     0.8152
Overall figure of merit              =     0.7697
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03


 fvalues    119268.98       4182.3525       546328.44       546200.75    

 fvalues    119268.98       4182.3525       546308.50       546296.38    
 fvalues    119268.98       4182.3525       546308.50       546296.38    


     CGMAT cycle number =      6

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   216  216  112
 Maximuum H,K,L                 :    65   65   33
 Minimum acceptable grid spacing:   140  140   70
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   216  216  112
 Maximuum H,K,L                 :    65   65   33
 Minimum acceptable grid spacing:   140  140   70
 Weight matrix    1.5072201    
 Actual weight    4.5453057      is applied to the X-ray term
Norm of X_ray positional gradient                47.2
Norm of Geom. positional gradient                48.0
Norm of X_ray B-factor gradient                  75.4
Norm of Geom. B-factor gradient                  75.8
Product of X_ray and Geom posit. gradients     -0.148E+08
 Cosine of angle between them                      -0.998
Product of X_ray and Geom B-fact gradients     -0.122E+08
 Cosine of angle between them                      -0.981


Residuals: XRAY=     0.5421E+06 GEOM=      4174.     TOTAL=     0.5463E+06
 function value    546291.69    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1081     0.013     0.013
Bond distances: others                          960     0.001     0.018
Bond angles  : refined atoms                   1461     1.907     1.652
Bond angles  : others                          2223     1.588     1.582
Torsion angles, period  1. refined              128     3.329     5.000
Torsion angles, period  2. refined               61    30.099    20.656
Torsion angles, period  3. refined              166    10.928    15.000
Torsion angles, period  4. refined               11    14.131    15.000
Chiral centres: refined atoms                   136     0.098     0.200
Planar groups: refined atoms                   1211     0.008     0.020
Planar groups: others                           246     0.002     0.020
VDW repulsions: refined_atoms                   285     0.227     0.200
VDW repulsions.others                           995     0.202     0.200
VDW; torsion: refined_atoms                     541     0.179     0.200
VDW; torsion.others                             472     0.106     0.200
HBOND: refined_atoms                             94     0.170     0.200
Metal-ion: refined_atoms                          6     0.121     0.200
VDW repulsions: symmetry: refined_atoms          12     0.229     0.200
VDW repulsions: symmetry: others                 49     0.195     0.200
HBOND: symmetry: refined_atoms                   10     0.202     0.200
M. chain bond B values: refined atoms           514     0.622     1.296
M. chain bond B values: others                  514     0.622     1.296
M. chain angle B values: refined atoms          642     0.722     1.946
M. chain angle B values: others                 643     0.722     1.948
S. chain bond B values: refined atoms           566     1.005     1.426
S. chain bond B values: others                  567     1.004     1.427
S. chain angle B values: refined atoms          819     1.312     2.108
S. chain angle B values: others                 820     1.311     2.108
Long range B values: refined atoms             1363     3.434    16.797
Long range B values: others                    1336     3.209    16.409
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.9172, B  =   -0.0001
Partial structure    1: scale =     0.2332, B  =  260.0208
Overall anisotropic scale factors
   B11 =   0.03 B22 =   0.03 B33 =  -0.06 B12 =  -0.00 B13 =  -0.00 B23 =  -0.00
-----------------------------------------------------------------------------

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

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle    6. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    6. <Rfactor> v. resln :N:1,6,7,11,12:
:Cycle    6. <Fobs> and <Fc> v. resln :N:1,4,5,9,10:
:Cycle    6. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.087    4467  99.84   327.1   325.2  0.06  0.07     445   321.0   318.0  0.07  0.07
 0.261    7720  99.95   131.1   131.6  0.06  0.04     816   136.6   137.9  0.07  0.05
 0.434    9848  99.67    60.1    58.0  0.20  0.16    1000    59.5    58.2  0.22  0.18
 0.608    6581  56.37    50.2    34.2  0.40  0.39     620    49.8    33.5  0.40  0.39
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle    6. FSC and  Fom(<cos(DelPhi)>-acentric, centric, overall v resln:
 $GRAPHS:Cycle    6. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0874   3500   0.978    967   0.930   4467   0.968  0.997  0.9929  0.9916  0.9859  0.9801
  0.2608   6753   0.959    967   0.905   7720   0.952  0.990  0.9930  0.9928  0.9906  0.9916
  0.4343   8878   0.796    970   0.736   9848   0.791  0.903  0.9046  0.9091  0.8819  0.8979
  0.6077   6140   0.388    441   0.379   6581   0.387  0.595  0.4580  0.4787  0.3456  0.3725
 $$
Resolution limits                    =     38.623     1.200
Number of used reflections           =      28616
Percentage observed                  =    84.8404
Percentage of free reflections       =     9.1469
Overall R factor                     =     0.1188
Free R factor                        =     0.1241
Average Fourier shell correlation    =     0.8456
AverageFree Fourier shell correlation=     0.8472
Overall weighted R factor            =     0.0764
Free weighted R factor               =     0.0813
Overall weighted R2 factor           =     0.1183
Free weighted R2 factor              =     0.0935
Average correlation coefficient      =     0.8152
Overall correlation coefficient      =     0.9860
Free correlation coefficient         =     0.9877
Cruickshanks DPI for coordinate error=     0.0352
DPI based on free R factor           =     0.0335
Overall figure of merit              =     0.7691
ML based su of positional parameters =     0.0260
ML based su of thermal parameters    =     0.7778
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    119269.68       4174.4795       546291.69       546296.38    

 LABOUT FREE=FREE F_FROMDIALS=F_FROMDIALS SIGF_FROMDIALS=SIGF_FROMDIALS 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: 1H87_dui_R00_1-20A.mtz 


-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1081     0.013     0.013
Bond distances: others                          960     0.001     0.018
Bond angles  : refined atoms                   1461     1.904     1.652
Bond angles  : others                          2223     1.587     1.582
Torsion angles, period  1. refined              128     3.334     5.000
Torsion angles, period  2. refined               61    30.100    20.656
Torsion angles, period  3. refined              166    10.928    15.000
Torsion angles, period  4. refined               11    14.131    15.000
Chiral centres: refined atoms                   136     0.098     0.200
Planar groups: refined atoms                   1211     0.008     0.020
Planar groups: others                           246     0.002     0.020
VDW repulsions: refined_atoms                   285     0.227     0.200
VDW repulsions.others                           999     0.201     0.200
VDW; torsion: refined_atoms                     542     0.179     0.200
VDW; torsion.others                             476     0.105     0.200
HBOND: refined_atoms                             95     0.170     0.200
Metal-ion: refined_atoms                          6     0.121     0.200
VDW repulsions: symmetry: refined_atoms          12     0.229     0.200
VDW repulsions: symmetry: others                 50     0.193     0.200
HBOND: symmetry: refined_atoms                   10     0.202     0.200
M. chain bond B values: refined atoms           514     0.621     1.296
M. chain bond B values: others                  514     0.621     1.296
M. chain angle B values: refined atoms          642     0.722     1.946
M. chain angle B values: others                 643     0.721     1.948
S. chain bond B values: refined atoms           566     1.003     1.426
S. chain bond B values: others                  567     1.002     1.426
S. chain angle B values: refined atoms          819     1.309     2.108
S. chain angle B values: others                 820     1.309     2.108
Long range B values: refined atoms             1365     3.454    16.828
Long range B values: others                    1337     3.207    16.423
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.9172, B  =   -0.0001
Partial structure    1: scale =     0.2332, B  =  260.0923
Overall anisotropic scale factors
   B11 =   0.03 B22 =   0.03 B33 =  -0.06 B12 =  -0.00 B13 =  -0.00 B23 =  -0.00
-----------------------------------------------------------------------------

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

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle    7. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    7. <Rfactor> v. resln :N:1,6,7,11,12:
:Cycle    7. <Fobs> and <Fc> v. resln :N:1,4,5,9,10:
:Cycle    7. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.087    4467  99.84   327.1   325.2  0.06  0.07     445   321.0   318.0  0.07  0.07
 0.261    7720  99.95   131.1   131.7  0.06  0.04     816   136.6   137.9  0.07  0.05
 0.434    9848  99.67    60.1    58.0  0.20  0.16    1000    59.5    58.3  0.22  0.18
 0.608    6581  56.37    50.2    34.2  0.40  0.39     620    49.8    33.5  0.40  0.39
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle    7. FSC and  Fom(<cos(DelPhi)>-acentric, centric, overall v resln:
 $GRAPHS:Cycle    7. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0874   3500   0.978    967   0.930   4467   0.968  0.997  0.9929  0.9916  0.9859  0.9801
  0.2608   6753   0.959    967   0.905   7720   0.952  0.990  0.9930  0.9928  0.9906  0.9916
  0.4343   8878   0.796    970   0.736   9848   0.791  0.903  0.9046  0.9091  0.8818  0.8979
  0.6077   6140   0.390    441   0.381   6581   0.389  0.601  0.4595  0.4804  0.3457  0.3724
 $$
Resolution limits                    =     38.623     1.200
Number of used reflections           =      28616
Percentage observed                  =    84.8404
Percentage of free reflections       =     9.1469
Overall R factor                     =     0.1188
Free R factor                        =     0.1242
Average Fourier shell correlation    =     0.8460
AverageFree Fourier shell correlation=     0.8475
Overall weighted R factor            =     0.0764
Free weighted R factor               =     0.0814
Overall weighted R2 factor           =     0.1183
Free weighted R2 factor              =     0.0936
Average correlation coefficient      =     0.8152
Overall correlation coefficient      =     0.9860
Free correlation coefficient         =     0.9877
Cruickshanks DPI for coordinate error=     0.0352
DPI based on free R factor           =     0.0335
Overall figure of merit              =     0.7695
ML based su of positional parameters =     0.0260
ML based su of thermal parameters    =     0.7778
-----------------------------------------------------------------------------
  Time in seconds: CPU =        15.79
             Elapsed =         128.00

    ****           Things for loggraph, R factor and others vs cycle            ****


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS:<Rfactor> 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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1186   0.1235   0.786      119155.   12094.4   0.0130  1.025   1.942  1.160   0.100
       1   0.1186   0.1238   0.779      119158.   12100.7   0.0131  1.040   1.933  1.155   0.101
       2   0.1185   0.1239   0.774      119181.   12105.9   0.0134  1.063   1.944  1.163   0.102
       3   0.1186   0.1240   0.772      119226.   12109.9   0.0130  1.025   1.932  1.155   0.100
       4   0.1188   0.1241   0.770      119265.   12112.3   0.0126  0.989   1.910  1.141   0.098
       5   0.1188   0.1241   0.769      119270.   12112.8   0.0126  0.988   1.907  1.140   0.098
       6   0.1188   0.1242   0.769      119281.   12114.4   0.0125  0.986   1.904  1.138   0.098
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1186   0.1188
             R free    0.1235   0.1242
     Rms BondLength    0.0130   0.0125
      Rms BondAngle    1.9417   1.9041
     Rms ChirVolume    0.0996   0.0976
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
 Refmac:  End of Refmac_5.8.0258   
Times: User:      46.9s System:    0.2s Elapsed:     0:47  
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