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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: 10:01:04 


 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.

<!--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 1.50     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_1-60A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - 1H87_dui_R00_1-50A.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_1-50A.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       0.1111
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    38.6230  1.5000
  Estimated number of reflections :      24606
  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  1.5000

  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_1-60A.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=   2.798 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=   2.800 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=   2.858 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=   2.687 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=   2.205 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=   2.305 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=   2.578 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=   2.156 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=   2.715 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=   2.689 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=   2.586 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=   2.611 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=   2.251 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=   2.330 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=   2.378 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       1781
Number of   all  reflections      19284
--------------------------------------------------------------------------------
 Number of reflections in file      47969
 Number of reflections read          19284

   Current auto weighting coefficient =    6.2497344    

 mode : HKRF


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


     CGMAT cycle number =      1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   176  176   88
 Maximuum H,K,L                 :    52   52   26
 Minimum acceptable grid spacing:   116  116   58
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   176  176   88
 Maximuum H,K,L                 :    52   52   26
 Minimum acceptable grid spacing:   116  116   58
 Weight matrix    2.5669525    
 Actual weight    6.2497344      is applied to the X-ray term
Norm of X_ray positional gradient                69.7
Norm of Geom. positional gradient                89.4
Norm of X_ray B-factor gradient                  135.
Norm of Geom. B-factor gradient                  77.7
Product of X_ray and Geom posit. gradients     -0.213E+08
 Cosine of angle between them                      -0.523
Product of X_ray and Geom B-fact gradients     -0.126E+08
 Cosine of angle between them                      -0.552


Residuals: XRAY=     0.4483E+06 GEOM=      7373.     TOTAL=     0.4556E+06
 function value    455629.28    

-------------------------------------------------------------------------------
             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     1.936     1.652
Bond angles  : others                          2223     2.360     1.582
Torsion angles, period  1. refined              128     3.301     5.000
Torsion angles, period  2. refined               61    30.006    20.656
Torsion angles, period  3. refined              166    10.972    15.000
Torsion angles, period  4. refined               11    14.225    15.000
Chiral centres: refined atoms                   136     0.103     0.200
Planar groups: refined atoms                   1211     0.009     0.020
Planar groups: others                           246     0.018     0.020
VDW repulsions: refined_atoms                   283     0.226     0.200
VDW repulsions.others                           978     0.230     0.200
VDW; torsion: refined_atoms                     538     0.179     0.200
VDW; torsion.others                             486     0.094     0.200
HBOND: refined_atoms                             97     0.167     0.200
Metal-ion: refined_atoms                          6     0.117     0.200
VDW repulsions: symmetry: refined_atoms          12     0.221     0.200
VDW repulsions: symmetry: others                 53     0.197     0.200
HBOND: symmetry: refined_atoms                    9     0.212     0.200
M. chain bond B values: refined atoms           514     0.675     1.320
M. chain bond B values: others                  514     0.675     1.320
M. chain angle B values: refined atoms          642     0.772     1.982
M. chain angle B values: others                 643     0.772     1.985
S. chain bond B values: refined atoms           566     1.060     1.452
S. chain bond B values: others                  567     1.059     1.452
S. chain angle B values: refined atoms          819     1.353     2.146
S. chain angle B values: others                 820     1.352     2.147
Long range B values: refined atoms             1360     3.454    17.034
Long range B values: others                    1331     3.198    16.631
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.9278, B  =    0.0555
Partial structure    1: scale =     0.2385, B  =  211.8764
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    2351  99.85   405.6   400.8  0.07  0.08     247   394.6   387.8  0.07  0.08
 0.167    4029  99.91   208.3   209.7  0.04  0.03     408   203.7   205.1  0.05  0.05
 0.278    5100  99.95   116.5   115.8  0.07  0.05     530   121.6   121.8  0.08  0.06
 0.389    6005  99.83    68.0    67.3  0.16  0.12     591    68.6    68.4  0.17  0.14
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   1743   0.982    608   0.940   2351   0.971  1.000  0.9936  0.9908  0.9860  0.9744
  0.1671   3391   0.973    638   0.909   4029   0.963  0.992  0.9929  0.9951  0.9838  0.9949
  0.2780   4487   0.957    613   0.901   5100   0.950  1.001  0.9918  0.9909  0.9886  0.9877
  0.3890   5380   0.873    626   0.806   6006   0.866  0.955  0.9491  0.9486  0.9263  0.9310
 $$
Resolution limits                    =     38.623     1.500
Number of used reflections           =      17486
Percentage observed                  =    99.8807
Percentage of free reflections       =     9.2202
Overall R factor                     =     0.0738
Free R factor                        =     0.0815
Average Fourier shell correlation    =     0.9773
AverageFree Fourier shell correlation=     0.9781
Overall weighted R factor            =     0.0603
Free weighted R factor               =     0.0671
Overall weighted R2 factor           =     0.1119
Free weighted R2 factor              =     0.0891
Average correlation coefficient      =     0.9681
Overall correlation coefficient      =     0.9889
Free correlation coefficient         =     0.9907
Cruickshanks DPI for coordinate error=     0.0355
DPI based on free R factor           =     0.0333
Overall figure of merit              =     0.9270
ML based su of positional parameters =     0.0234
ML based su of thermal parameters    =     0.7201
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    71724.078       7372.8389       455629.28      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix    2.5869043    
 Actual weight    6.2497344      is applied to the X-ray term


 function value    452091.09    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1081     0.014     0.013
Bond distances: others                          960     0.002     0.018
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.9276, B  =    0.0250
Partial structure    1: scale =     0.2383, B  =  211.3628
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                     =     0.0734
Free R factor                        =     0.0812
Average Fourier shell correlation    =     0.9776
AverageFree Fourier shell correlation=     0.9782
Average correlation coefficient      =     0.9688
Overall figure of merit              =     0.9275
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    71627.508       4438.1787       452091.09       455629.28    


     CGMAT cycle number =      3

 Weight matrix    2.3593149    
 Actual weight    5.6815767      is applied to the X-ray term


 function value    411236.81    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1081     0.014     0.013
Bond distances: others                          960     0.001     0.018
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.9273, B  =   -0.0001
Partial structure    1: scale =     0.2384, B  =  211.8506
Overall anisotropic scale factors
   B11 =   0.03 B22 =   0.03 B33 =  -0.05 B12 =  -0.00 B13 =  -0.00 B23 =  -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.0731
Free R factor                        =     0.0811
Average Fourier shell correlation    =     0.9777
AverageFree Fourier shell correlation=     0.9782
Average correlation coefficient      =     0.9691
Overall figure of merit              =     0.9276
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    71593.969       4470.1865       411236.81       452091.09    


     CGMAT cycle number =      4

 Weight matrix    2.1510143    
 Actual weight    5.1650696      is applied to the X-ray term


 function value    374202.38    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1081     0.014     0.013
Bond distances: others                          960     0.001     0.018
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.9272, B  =    0.0040
Partial structure    1: scale =     0.2383, B  =  212.5911
Overall anisotropic scale factors
   B11 =   0.03 B22 =   0.03 B33 =  -0.05 B12 =  -0.00 B13 =  -0.00 B23 =  -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.0731
Free R factor                        =     0.0811
Average Fourier shell correlation    =     0.9777
AverageFree Fourier shell correlation=     0.9782
Average correlation coefficient      =     0.9693
Overall figure of merit              =     0.9277
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    71592.781       4420.6836       374202.38       411236.81    


     CGMAT cycle number =      5

 Weight matrix    2.1555028    
 Actual weight    5.1650696      is applied to the X-ray term


 function value    374176.03    

-------------------------------------------------------------------------------
             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 =     0.9272, B  =    0.0048
Partial structure    1: scale =     0.2383, B  =  212.1910
Overall anisotropic scale factors
   B11 =   0.03 B22 =   0.03 B33 =  -0.05 B12 =  -0.00 B13 =  -0.00 B23 =  -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.0732
Free R factor                        =     0.0810
Average Fourier shell correlation    =     0.9778
AverageFree Fourier shell correlation=     0.9782
Average correlation coefficient      =     0.9693
Overall figure of merit              =     0.9277
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    71603.633       4338.2705       374176.03       374202.38    


     CGMAT cycle number =      6

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   176  176   88
 Maximuum H,K,L                 :    52   52   26
 Minimum acceptable grid spacing:   116  116   58
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   176  176   88
 Maximuum H,K,L                 :    52   52   26
 Minimum acceptable grid spacing:   116  116   58
 Weight matrix    2.1556427    
 Actual weight    5.1650696      is applied to the X-ray term
Norm of X_ray positional gradient                51.7
Norm of Geom. positional gradient                51.9
Norm of X_ray B-factor gradient                  82.0
Norm of Geom. B-factor gradient                  78.3
Product of X_ray and Geom posit. gradients     -0.175E+08
 Cosine of angle between them                      -0.996
Product of X_ray and Geom B-fact gradients     -0.133E+08
 Cosine of angle between them                      -0.952


Residuals: XRAY=     0.3699E+06 GEOM=      4315.     TOTAL=     0.3742E+06
 function value    374195.31    

-------------------------------------------------------------------------------
             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     1.947     1.652
Bond angles  : others                          2223     1.596     1.582
Torsion angles, period  1. refined              128     3.291     5.000
Torsion angles, period  2. refined               61    30.061    20.656
Torsion angles, period  3. refined              166    10.941    15.000
Torsion angles, period  4. refined               11    14.212    15.000
Chiral centres: refined atoms                   136     0.100     0.200
Planar groups: refined atoms                   1211     0.008     0.020
Planar groups: others                           246     0.002     0.020
VDW repulsions: refined_atoms                   282     0.228     0.200
VDW repulsions.others                           989     0.202     0.200
VDW; torsion: refined_atoms                     542     0.179     0.200
VDW; torsion.others                             482     0.105     0.200
HBOND: refined_atoms                             94     0.169     0.200
Metal-ion: refined_atoms                          6     0.118     0.200
VDW repulsions: symmetry: refined_atoms          12     0.224     0.200
VDW repulsions: symmetry: others                 51     0.190     0.200
HBOND: symmetry: refined_atoms                    9     0.212     0.200
M. chain bond B values: refined atoms           514     0.664     1.326
M. chain bond B values: others                  514     0.664     1.326
M. chain angle B values: refined atoms          642     0.762     1.990
M. chain angle B values: others                 643     0.762     1.993
S. chain bond B values: refined atoms           566     1.064     1.456
S. chain bond B values: others                  567     1.063     1.457
S. chain angle B values: refined atoms          819     1.358     2.153
S. chain angle B values: others                 820     1.357     2.154
Long range B values: refined atoms             1360     3.389    17.059
Long range B values: others                    1333     3.149    16.677
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.9273, B  =    0.0063
Partial structure    1: scale =     0.2384, B  =  211.7712
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    2351  99.85   405.9   401.2  0.07  0.08     247   394.8   388.2  0.07  0.08
 0.167    4029  99.91   208.4   209.9  0.04  0.03     408   203.8   205.3  0.05  0.05
 0.278    5100  99.95   116.5   116.0  0.07  0.05     530   121.7   122.0  0.08  0.06
 0.389    6005  99.83    68.1    67.2  0.15  0.12     591    68.7    68.4  0.17  0.14
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   1743   0.982    608   0.942   2351   0.972  1.000  0.9937  0.9908  0.9862  0.9743
  0.1671   3391   0.974    638   0.911   4029   0.964  0.992  0.9931  0.9953  0.9841  0.9948
  0.2780   4487   0.957    613   0.903   5100   0.950  1.001  0.9919  0.9909  0.9887  0.9875
  0.3890   5380   0.874    626   0.809   6006   0.867  0.955  0.9493  0.9498  0.9262  0.9350
 $$
Resolution limits                    =     38.623     1.500
Number of used reflections           =      17486
Percentage observed                  =    99.8807
Percentage of free reflections       =     9.2202
Overall R factor                     =     0.0733
Free R factor                        =     0.0811
Average Fourier shell correlation    =     0.9778
AverageFree Fourier shell correlation=     0.9782
Overall weighted R factor            =     0.0600
Free weighted R factor               =     0.0666
Overall weighted R2 factor           =     0.1119
Free weighted R2 factor              =     0.0884
Average correlation coefficient      =     0.9694
Overall correlation coefficient      =     0.9890
Free correlation coefficient         =     0.9908
Cruickshanks DPI for coordinate error=     0.0353
DPI based on free R factor           =     0.0331
Overall figure of merit              =     0.9277
ML based su of positional parameters =     0.0231
ML based su of thermal parameters    =     0.7154
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    71611.727       4314.6030       374253.78       374176.03    

 fvalues    71611.727       4314.6030       374221.06       374194.16    
 fvalues    71611.727       4314.6030       374221.06       374194.16    

 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_1-50A.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     1.946     1.652
Bond angles  : others                          2223     1.596     1.582
Torsion angles, period  1. refined              128     3.292     5.000
Torsion angles, period  2. refined               61    30.063    20.656
Torsion angles, period  3. refined              166    10.940    15.000
Torsion angles, period  4. refined               11    14.210    15.000
Chiral centres: refined atoms                   136     0.100     0.200
Planar groups: refined atoms                   1211     0.008     0.020
Planar groups: others                           246     0.002     0.020
VDW repulsions: refined_atoms                   282     0.228     0.200
VDW repulsions.others                           991     0.201     0.200
VDW; torsion: refined_atoms                     542     0.179     0.200
VDW; torsion.others                             482     0.105     0.200
HBOND: refined_atoms                             94     0.169     0.200
Metal-ion: refined_atoms                          6     0.118     0.200
VDW repulsions: symmetry: refined_atoms          12     0.224     0.200
VDW repulsions: symmetry: others                 51     0.190     0.200
HBOND: symmetry: refined_atoms                    9     0.212     0.200
M. chain bond B values: refined atoms           514     0.664     1.326
M. chain bond B values: others                  514     0.664     1.326
M. chain angle B values: refined atoms          642     0.762     1.990
M. chain angle B values: others                 643     0.761     1.993
S. chain bond B values: refined atoms           566     1.064     1.456
S. chain bond B values: others                  567     1.063     1.457
S. chain angle B values: refined atoms          819     1.358     2.153
S. chain angle B values: others                 820     1.357     2.154
Long range B values: refined atoms             1360     3.389    17.060
Long range B values: others                    1333     3.148    16.677
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.9273, B  =    0.0069
Partial structure    1: scale =     0.2383, B  =  211.6480
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    2351  99.85   405.9   401.2  0.07  0.08     247   394.8   388.2  0.07  0.08
 0.167    4029  99.91   208.4   209.9  0.04  0.03     408   203.8   205.3  0.05  0.05
 0.278    5100  99.95   116.5   116.0  0.07  0.05     530   121.7   122.0  0.08  0.06
 0.389    6005  99.83    68.1    67.2  0.15  0.12     591    68.6    68.4  0.17  0.14
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   1743   0.982    608   0.942   2351   0.972  1.000  0.9937  0.9908  0.9862  0.9743
  0.1671   3391   0.974    638   0.911   4029   0.964  0.992  0.9931  0.9952  0.9841  0.9948
  0.2780   4487   0.957    613   0.903   5100   0.950  1.001  0.9918  0.9909  0.9887  0.9875
  0.3890   5380   0.874    626   0.809   6006   0.867  0.955  0.9493  0.9498  0.9261  0.9350
 $$
Resolution limits                    =     38.623     1.500
Number of used reflections           =      17486
Percentage observed                  =    99.8807
Percentage of free reflections       =     9.2202
Overall R factor                     =     0.0733
Free R factor                        =     0.0811
Average Fourier shell correlation    =     0.9777
AverageFree Fourier shell correlation=     0.9782
Overall weighted R factor            =     0.0601
Free weighted R factor               =     0.0666
Overall weighted R2 factor           =     0.1119
Free weighted R2 factor              =     0.0884
Average correlation coefficient      =     0.9694
Overall correlation coefficient      =     0.9890
Free correlation coefficient         =     0.9908
Cruickshanks DPI for coordinate error=     0.0353
DPI based on free R factor           =     0.0331
Overall figure of merit              =     0.9277
ML based su of positional parameters =     0.0231
ML based su of thermal parameters    =     0.7154
-----------------------------------------------------------------------------
  Time in seconds: CPU =         8.43
             Elapsed =           0.00

    ****           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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.0738   0.0815   0.927       71724.    7395.0   0.0132  1.038   1.936  1.157   0.103
       1   0.0734   0.0812   0.928       71628.    7389.7   0.0136  1.078   1.951  1.166   0.104
       2   0.0731   0.0811   0.928       71594.    7388.4   0.0138  1.099   1.969  1.178   0.104
       3   0.0731   0.0811   0.928       71593.    7386.8   0.0136  1.074   1.966  1.176   0.103
       4   0.0732   0.0810   0.928       71604.    7385.8   0.0132  1.040   1.952  1.166   0.101
       5   0.0733   0.0811   0.928       71612.    7386.2   0.0131  1.037   1.947  1.163   0.100
       6   0.0733   0.0811   0.928       71615.    7386.4   0.0131  1.036   1.946  1.163   0.100
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.0738   0.0733
             R free    0.0815   0.0811
     Rms BondLength    0.0132   0.0131
      Rms BondAngle    1.9355   1.9460
     Rms ChirVolume    0.1026   0.1004
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
 Refmac:  End of Refmac_5.8.0258   
Times: User:      36.4s System:    0.1s Elapsed:     0:37  
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