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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 28/ 5/2020 Run time: 10:03:48 


 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 1.40     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_1-50A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - 1H87_dui_R00_1-40A.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_1-40A.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       0.1276
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    38.6230  1.4000
  Estimated number of reflections :      30732
  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  1.4000

  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_1-50A.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=   2.797 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=   2.794 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=   2.681 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=   2.202 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=   2.573 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=   2.159 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=   2.717 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=   2.685 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=   2.588 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=   2.601 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=   2.482 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=   2.246 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=   2.329 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=   2.372 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       2214
Number of   all  reflections      23633
--------------------------------------------------------------------------------
 Number of reflections in file      47969
 Number of reflections read          23633

   Current auto weighting coefficient =    5.9997506    

 mode : HKRF


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


     CGMAT cycle number =      1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   192  192   96
 Maximuum H,K,L                 :    56   56   28
 Minimum acceptable grid spacing:   123  123   62
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   192  192   96
 Maximuum H,K,L                 :    56   56   28
 Minimum acceptable grid spacing:   123  123   62
 Weight matrix    2.4850509    
 Actual weight    5.9997506      is applied to the X-ray term
Norm of X_ray positional gradient                66.1
Norm of Geom. positional gradient                89.7
Norm of X_ray B-factor gradient                  124.
Norm of Geom. B-factor gradient                  76.0
Product of X_ray and Geom posit. gradients     -0.217E+08
 Cosine of angle between them                      -0.559
Product of X_ray and Geom B-fact gradients     -0.121E+08
 Cosine of angle between them                      -0.588


Residuals: XRAY=     0.5266E+06 GEOM=      7378.     TOTAL=     0.5340E+06
 function value    533960.25    

-------------------------------------------------------------------------------
             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     1.947     1.652
Bond angles  : others                          2223     2.358     1.582
Torsion angles, period  1. refined              128     3.289     5.000
Torsion angles, period  2. refined               61    30.065    20.656
Torsion angles, period  3. refined              166    10.937    15.000
Torsion angles, period  4. refined               11    14.193    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                   284     0.227     0.200
VDW repulsions.others                           984     0.230     0.200
VDW; torsion: refined_atoms                     542     0.179     0.200
VDW; torsion.others                             495     0.093     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     0.201     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             1362     3.387    17.085
Long range B values: others                    1335     3.147    16.703
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.9276, B  =   -0.0194
Partial structure    1: scale =     0.2409, B  =  198.1051
Overall anisotropic scale factors
   B11 =   0.03 B22 =   0.03 B33 =  -0.05 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.064    2863  99.87   379.4   375.4  0.07  0.07     290   376.5   370.1  0.07  0.07
 0.192    4912  99.93   185.4   186.5  0.04  0.03     528   185.5   186.8  0.06  0.05
 0.319    6277  99.94    93.6    93.0  0.09  0.07     623    93.6    93.7  0.11  0.08
 0.447    7330  99.67    56.5    53.2  0.22  0.19     765    55.2    52.9  0.23  0.20
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0644   2163   0.983    700   0.940   2863   0.972  1.000  0.9940  0.9918  0.9870  0.9784
  0.1917   4188   0.972    724   0.916   4912   0.963  0.993  0.9929  0.9944  0.9847  0.9936
  0.3191   5563   0.932    714   0.861   6277   0.924  0.992  0.9819  0.9830  0.9732  0.9795
  0.4465   6625   0.797    709   0.738   7334   0.791  0.920  0.8876  0.8951  0.8511  0.8655
 $$
Resolution limits                    =     38.623     1.400
Number of used reflections           =      21386
Percentage observed                  =    99.8307
Percentage of free reflections       =     9.3583
Overall R factor                     =     0.0851
Free R factor                        =     0.0938
Average Fourier shell correlation    =     0.9566
AverageFree Fourier shell correlation=     0.9534
Overall weighted R factor            =     0.0644
Free weighted R factor               =     0.0714
Overall weighted R2 factor           =     0.1095
Free weighted R2 factor              =     0.0887
Average correlation coefficient      =     0.9435
Overall correlation coefficient      =     0.9892
Free correlation coefficient         =     0.9905
Cruickshanks DPI for coordinate error=     0.0334
DPI based on free R factor           =     0.0324
Overall figure of merit              =     0.8939
ML based su of positional parameters =     0.0233
ML based su of thermal parameters    =     0.7075
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    87767.328       7378.1851       533960.25      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix    2.4887729    
 Actual weight    5.9997506      is applied to the X-ray term


 function value    530886.44    

-------------------------------------------------------------------------------
             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 =     0.9272, B  =    0.0154
Partial structure    1: scale =     0.2384, B  =  201.0967
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                     =     0.0848
Free R factor                        =     0.0938
Average Fourier shell correlation    =     0.9560
AverageFree Fourier shell correlation=     0.9525
Average correlation coefficient      =     0.9442
Overall figure of merit              =     0.8920
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    87743.906       4444.8677       530886.44       533960.25    


     CGMAT cycle number =      3

 Weight matrix    2.2616138    
 Actual weight    5.4543185      is applied to the X-ray term


 function value    483012.38    

-------------------------------------------------------------------------------
             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 =     0.9267, B  =   -0.0071
Partial structure    1: scale =     0.2402, B  =  198.9747
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                     =     0.0847
Free R factor                        =     0.0938
Average Fourier shell correlation    =     0.9560
AverageFree Fourier shell correlation=     0.9523
Average correlation coefficient      =     0.9446
Overall figure of merit              =     0.8916
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    87736.805       4467.9180       483012.38       530886.44    


     CGMAT cycle number =      4

 Weight matrix    2.0592525    
 Actual weight    4.9584713      is applied to the X-ray term


 function value    439494.06    

-------------------------------------------------------------------------------
             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 =     0.9267, B  =    0.0000
Partial structure    1: scale =     0.2402, B  =  198.9687
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                     =     0.0847
Free R factor                        =     0.0938
Average Fourier shell correlation    =     0.9560
AverageFree Fourier shell correlation=     0.9524
Average correlation coefficient      =     0.9447
Overall figure of merit              =     0.8917
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    87745.969       4408.1953       439494.06       483012.38    


     CGMAT cycle number =      5

 Weight matrix    2.0603027    
 Actual weight    4.9584713      is applied to the X-ray term


 function value    439496.91    

-------------------------------------------------------------------------------
             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 =     0.9267, B  =    0.0009
Partial structure    1: scale =     0.2403, B  =  198.7523
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                     =     0.0848
Free R factor                        =     0.0937
Average Fourier shell correlation    =     0.9560
AverageFree Fourier shell correlation=     0.9523
Average correlation coefficient      =     0.9447
Overall figure of merit              =     0.8917
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03


 fvalues    87765.211       4317.9229       439541.25       439494.06    

 fvalues    87765.211       4317.9229       439519.19       439499.22    
 fvalues    87765.211       4317.9229       439519.19       439499.22    


     CGMAT cycle number =      6

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   192  192   96
 Maximuum H,K,L                 :    56   56   28
 Minimum acceptable grid spacing:   123  123   62
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   192  192   96
 Maximuum H,K,L                 :    56   56   28
 Minimum acceptable grid spacing:   123  123   62
 Weight matrix    2.0594218    
 Actual weight    4.9584713      is applied to the X-ray term
Norm of X_ray positional gradient                51.0
Norm of Geom. positional gradient                51.7
Norm of X_ray B-factor gradient                  75.8
Norm of Geom. B-factor gradient                  77.1
Product of X_ray and Geom posit. gradients     -0.172E+08
 Cosine of angle between them                      -0.997
Product of X_ray and Geom B-fact gradients     -0.126E+08
 Cosine of angle between them                      -0.987


Residuals: XRAY=     0.4352E+06 GEOM=      4311.     TOTAL=     0.4395E+06
 function value    439509.63    

-------------------------------------------------------------------------------
             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     1.951     1.652
Bond angles  : others                          2223     1.598     1.582
Torsion angles, period  1. refined              128     3.268     5.000
Torsion angles, period  2. refined               61    30.095    20.656
Torsion angles, period  3. refined              166    10.934    15.000
Torsion angles, period  4. refined               11    14.119    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                   281     0.228     0.200
VDW repulsions.others                           987     0.203     0.200
VDW; torsion: refined_atoms                     542     0.179     0.200
VDW; torsion.others                             482     0.106     0.200
HBOND: refined_atoms                             93     0.170     0.200
Metal-ion: refined_atoms                          6     0.117     0.200
VDW repulsions: symmetry: refined_atoms          12     0.225     0.200
VDW repulsions: symmetry: others                 50     0.192     0.200
HBOND: symmetry: refined_atoms                    9     0.212     0.200
M. chain bond B values: refined atoms           514     0.646     1.323
M. chain bond B values: others                  514     0.646     1.323
M. chain angle B values: refined atoms          642     0.746     1.986
M. chain angle B values: others                 643     0.746     1.989
S. chain bond B values: refined atoms           566     1.050     1.454
S. chain bond B values: others                  567     1.049     1.454
S. chain angle B values: refined atoms          819     1.348     2.149
S. chain angle B values: others                 820     1.347     2.150
Long range B values: refined atoms             1358     3.369    17.009
Long range B values: others                    1332     3.144    16.645
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.9267, B  =    0.0015
Partial structure    1: scale =     0.2404, B  =  198.5232
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.064    2863  99.87   379.8   375.9  0.07  0.07     290   376.9   370.6  0.07  0.07
 0.192    4912  99.93   185.6   186.8  0.04  0.03     528   185.7   187.3  0.06  0.05
 0.319    6277  99.94    93.7    93.1  0.09  0.07     623    93.7    93.9  0.11  0.08
 0.447    7330  99.67    56.5    53.2  0.22  0.19     765    55.3    52.9  0.23  0.20
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0644   2163   0.983    700   0.942   2863   0.973  1.000  0.9940  0.9918  0.9871  0.9784
  0.1917   4188   0.972    724   0.917   4912   0.964  0.993  0.9931  0.9945  0.9847  0.9935
  0.3191   5563   0.932    714   0.861   6277   0.924  0.992  0.9818  0.9829  0.9730  0.9794
  0.4465   6625   0.790    709   0.732   7334   0.784  0.917  0.8846  0.8932  0.8506  0.8692
 $$
Resolution limits                    =     38.623     1.400
Number of used reflections           =      21386
Percentage observed                  =    99.8307
Percentage of free reflections       =     9.3583
Overall R factor                     =     0.0848
Free R factor                        =     0.0938
Average Fourier shell correlation    =     0.9560
AverageFree Fourier shell correlation=     0.9523
Overall weighted R factor            =     0.0644
Free weighted R factor               =     0.0712
Overall weighted R2 factor           =     0.1096
Free weighted R2 factor              =     0.0886
Average correlation coefficient      =     0.9447
Overall correlation coefficient      =     0.9892
Free correlation coefficient         =     0.9905
Cruickshanks DPI for coordinate error=     0.0333
DPI based on free R factor           =     0.0324
Overall figure of merit              =     0.8917
ML based su of positional parameters =     0.0232
ML based su of thermal parameters    =     0.7073
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    87768.797       4310.8169       439535.31       439499.22    

 fvalues    87768.797       4310.8169       439522.88       439509.88    
 fvalues    87768.797       4310.8169       439522.88       439509.88    

 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_1-40A.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     1.950     1.652
Bond angles  : others                          2223     1.597     1.582
Torsion angles, period  1. refined              128     3.269     5.000
Torsion angles, period  2. refined               61    30.095    20.656
Torsion angles, period  3. refined              166    10.934    15.000
Torsion angles, period  4. refined               11    14.118    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                   281     0.228     0.200
VDW repulsions.others                           988     0.202     0.200
VDW; torsion: refined_atoms                     542     0.179     0.200
VDW; torsion.others                             483     0.106     0.200
HBOND: refined_atoms                             93     0.170     0.200
Metal-ion: refined_atoms                          6     0.117     0.200
VDW repulsions: symmetry: refined_atoms          12     0.225     0.200
VDW repulsions: symmetry: others                 50     0.192     0.200
HBOND: symmetry: refined_atoms                    9     0.212     0.200
M. chain bond B values: refined atoms           514     0.646     1.323
M. chain bond B values: others                  514     0.646     1.323
M. chain angle B values: refined atoms          642     0.746     1.986
M. chain angle B values: others                 643     0.746     1.989
S. chain bond B values: refined atoms           566     1.049     1.454
S. chain bond B values: others                  567     1.048     1.454
S. chain angle B values: refined atoms          819     1.348     2.149
S. chain angle B values: others                 820     1.347     2.150
Long range B values: refined atoms             1358     3.369    17.009
Long range B values: others                    1332     3.144    16.645
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.9267, B  =    0.0009
Partial structure    1: scale =     0.2404, B  =  198.5019
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.064    2863  99.87   379.8   375.9  0.07  0.07     290   376.9   370.6  0.07  0.07
 0.192    4912  99.93   185.6   186.8  0.04  0.03     528   185.7   187.3  0.06  0.05
 0.319    6277  99.94    93.7    93.2  0.09  0.07     623    93.7    93.9  0.11  0.08
 0.447    7330  99.67    56.5    53.2  0.22  0.19     765    55.3    52.9  0.23  0.20
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0644   2163   0.983    700   0.942   2863   0.973  1.000  0.9940  0.9918  0.9871  0.9784
  0.1917   4188   0.972    724   0.917   4912   0.964  0.993  0.9931  0.9945  0.9847  0.9935
  0.3191   5563   0.932    714   0.861   6277   0.924  0.992  0.9818  0.9830  0.9730  0.9794
  0.4465   6625   0.790    709   0.732   7334   0.784  0.917  0.8846  0.8932  0.8506  0.8692
 $$
Resolution limits                    =     38.623     1.400
Number of used reflections           =      21386
Percentage observed                  =    99.8307
Percentage of free reflections       =     9.3583
Overall R factor                     =     0.0848
Free R factor                        =     0.0938
Average Fourier shell correlation    =     0.9560
AverageFree Fourier shell correlation=     0.9523
Overall weighted R factor            =     0.0644
Free weighted R factor               =     0.0712
Overall weighted R2 factor           =     0.1096
Free weighted R2 factor              =     0.0886
Average correlation coefficient      =     0.9447
Overall correlation coefficient      =     0.9892
Free correlation coefficient         =     0.9905
Cruickshanks DPI for coordinate error=     0.0333
DPI based on free R factor           =     0.0324
Overall figure of merit              =     0.8917
ML based su of positional parameters =     0.0232
ML based su of thermal parameters    =     0.7073
-----------------------------------------------------------------------------
  Time in seconds: CPU =        11.72
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.0851   0.0938   0.894       87767.    9170.4   0.0131  1.037   1.947  1.164   0.100
       1   0.0848   0.0938   0.892       87744.    9172.6   0.0136  1.081   1.956  1.169   0.103
       2   0.0847   0.0938   0.892       87737.    9174.6   0.0139  1.101   1.974  1.180   0.103
       3   0.0847   0.0938   0.892       87746.    9173.9   0.0136  1.074   1.969  1.177   0.102
       4   0.0848   0.0937   0.892       87765.    9173.8   0.0132  1.039   1.953  1.166   0.100
       5   0.0848   0.0938   0.892       87769.    9174.2   0.0132  1.038   1.951  1.165   0.100
       6   0.0848   0.0938   0.892       87770.    9174.4   0.0132  1.037   1.950  1.165   0.100
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.0851   0.0848
             R free    0.0938   0.0938
     Rms BondLength    0.0131   0.0132
      Rms BondAngle    1.9469   1.9503
     Rms ChirVolume    0.1005   0.0997
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
 Refmac:  End of Refmac_5.8.0258   
Times: User:      40.3s System:    0.1s Elapsed:     0:41  
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