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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: 10:07:06 


 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 1.30     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_1-40A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - 1H87_dui_R00_1-30A.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_1-30A.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       0.1479
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    38.6230  1.3000
  Estimated number of reflections :      37800
  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  1.3000

  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_1-40A.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=   2.800 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=   2.860 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=   2.680 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=   2.571 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=   2.165 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=   2.719 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=   2.590 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=   2.330 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=   2.371 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       2713
Number of   all  reflections      29352
--------------------------------------------------------------------------------
 Number of reflections in file      47969
 Number of reflections read          29352

   Current auto weighting coefficient =    5.7496696    

 mode : HKRF


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


     CGMAT cycle number =      1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   200  200  112
 Maximuum H,K,L                 :    60   60   30
 Minimum acceptable grid spacing:   131  131   66
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   200  200  112
 Maximuum H,K,L                 :    60   60   30
 Minimum acceptable grid spacing:   131  131   66
 Weight matrix    2.2255104    
 Actual weight    5.7496696      is applied to the X-ray term
Norm of X_ray positional gradient                64.6
Norm of Geom. positional gradient                89.4
Norm of X_ray B-factor gradient                  137.
Norm of Geom. B-factor gradient                  74.9
Product of X_ray and Geom posit. gradients     -0.215E+08
 Cosine of angle between them                      -0.571
Product of X_ray and Geom B-fact gradients     -0.123E+08
 Cosine of angle between them                      -0.552


Residuals: XRAY=     0.6231E+06 GEOM=      7359.     TOTAL=     0.6304E+06
 function value    630412.44    

-------------------------------------------------------------------------------
             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     1.950     1.652
Bond angles  : others                          2223     2.358     1.582
Torsion angles, period  1. refined              128     3.271     5.000
Torsion angles, period  2. refined               61    30.086    20.656
Torsion angles, period  3. refined              166    10.931    15.000
Torsion angles, period  4. refined               11    14.125    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     0.228     0.200
VDW repulsions.others                           986     0.229     0.200
VDW; torsion: refined_atoms                     542     0.179     0.200
VDW; torsion.others                             495     0.094     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     0.203     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             1359     3.368    17.024
Long range B values: others                    1333     3.143    16.661
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.9229, B  =   -0.1316
Partial structure    1: scale =     0.2322, B  =  222.5415
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.075    3545  99.80   354.1   351.0  0.06  0.07     365   346.7   342.0  0.07  0.07
 0.222    6087  99.99   159.3   160.1  0.05  0.04     642   161.1   162.4  0.06  0.05
 0.370    7836  99.85    74.5    74.3  0.14  0.10     769    74.3    74.7  0.15  0.11
 0.518    8797  96.10    50.0    41.3  0.30  0.28     890    49.1    41.3  0.31  0.29
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0746   2728   0.984    817   0.943   3545   0.974  0.999  0.9939  0.9916  0.9874  0.9790
  0.2223   5252   0.968    835   0.906   6087   0.959  0.995  0.9920  0.9934  0.9852  0.9925
  0.3701   7006   0.892    830   0.826   7836   0.885  0.960  0.9627  0.9632  0.9493  0.9533
  0.5178   8057   0.656    744   0.612   8801   0.653  0.843  0.7584  0.7642  0.6987  0.7028
 $$
Resolution limits                    =     38.623     1.300
Number of used reflections           =      26269
Percentage observed                  =    98.5760
Percentage of free reflections       =     9.2138
Overall R factor                     =     0.1049
Free R factor                        =     0.1110
Average Fourier shell correlation    =     0.9074
AverageFree Fourier shell correlation=     0.9058
Overall weighted R factor            =     0.0717
Free weighted R factor               =     0.0772
Overall weighted R2 factor           =     0.1158
Free weighted R2 factor              =     0.0910
Average correlation coefficient      =     0.8819
Overall correlation coefficient      =     0.9875
Free correlation coefficient         =     0.9893
Cruickshanks DPI for coordinate error=     0.0337
DPI based on free R factor           =     0.0322
Overall figure of merit              =     0.8362
ML based su of positional parameters =     0.0241
ML based su of thermal parameters    =     0.7268
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    108363.40       7358.6768       630412.44      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix    2.2019227    
 Actual weight    5.7496696      is applied to the X-ray term


 function value    627710.56    

-------------------------------------------------------------------------------
             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 =     0.9224, B  =    0.0026
Partial structure    1: scale =     0.2325, B  =  227.3877
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                     =     0.1046
Free R factor                        =     0.1111
Average Fourier shell correlation    =     0.9013
AverageFree Fourier shell correlation=     0.8997
Average correlation coefficient      =     0.8825
Overall figure of merit              =     0.8262
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    108400.19       4445.2993       627710.56       630412.44    


     CGMAT cycle number =      3

 Weight matrix    1.9977152    
 Actual weight    5.2269721      is applied to the X-ray term


 function value    571078.69    

-------------------------------------------------------------------------------
             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 =     0.9221, B  =   -0.0083
Partial structure    1: scale =     0.2324, B  =  228.2124
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                     =     0.1045
Free R factor                        =     0.1111
Average Fourier shell correlation    =     0.9014
AverageFree Fourier shell correlation=     0.8998
Average correlation coefficient      =     0.8826
Overall figure of merit              =     0.8266
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    108403.41       4457.0508       571078.69       627710.56    


     CGMAT cycle number =      4

 Weight matrix    1.8118827    
 Actual weight    4.7517929      is applied to the X-ray term


 function value    519643.97    

-------------------------------------------------------------------------------
             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 =     0.9220, B  =   -0.0020
Partial structure    1: scale =     0.2324, B  =  228.4812
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                     =     0.1046
Free R factor                        =     0.1112
Average Fourier shell correlation    =     0.9005
AverageFree Fourier shell correlation=     0.8988
Average correlation coefficient      =     0.8826
Overall figure of merit              =     0.8250
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    108434.49       4385.7085       519643.97       571078.69    


     CGMAT cycle number =      5

 Weight matrix    1.8100966    
 Actual weight    4.7517929      is applied to the X-ray term


 function value    519705.78    

-------------------------------------------------------------------------------
             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 =     0.9219, B  =   -0.0018
Partial structure    1: scale =     0.2325, B  =  228.6797
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                     =     0.1047
Free R factor                        =     0.1112
Average Fourier shell correlation    =     0.9001
AverageFree Fourier shell correlation=     0.8985
Average correlation coefficient      =     0.8826
Overall figure of merit              =     0.8243
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03


 fvalues    108469.12       4288.7773       519759.97       519643.97    

 fvalues    108469.12       4288.7773       519737.66       519711.56    
 fvalues    108469.12       4288.7773       519737.66       519711.56    


     CGMAT cycle number =      6

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   200  200  112
 Maximuum H,K,L                 :    60   60   30
 Minimum acceptable grid spacing:   131  131   66
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   200  200  112
 Maximuum H,K,L                 :    60   60   30
 Minimum acceptable grid spacing:   131  131   66
 Weight matrix    1.8092606    
 Actual weight    4.7517929      is applied to the X-ray term
Norm of X_ray positional gradient                50.0
Norm of Geom. positional gradient                50.7
Norm of X_ray B-factor gradient                  75.5
Norm of Geom. B-factor gradient                  77.5
Product of X_ray and Geom posit. gradients     -0.165E+08
 Cosine of angle between them                      -0.998
Product of X_ray and Geom B-fact gradients     -0.127E+08
 Cosine of angle between them                      -0.994


Residuals: XRAY=     0.5154E+06 GEOM=      4282.     TOTAL=     0.5197E+06
 function value    519727.16    

-------------------------------------------------------------------------------
             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     1.942     1.652
Bond angles  : others                          2223     1.594     1.582
Torsion angles, period  1. refined              128     3.264     5.000
Torsion angles, period  2. refined               61    30.123    20.656
Torsion angles, period  3. refined              166    10.919    15.000
Torsion angles, period  4. refined               11    14.083    15.000
Chiral centres: refined atoms                   136     0.099     0.200
Planar groups: refined atoms                   1211     0.008     0.020
Planar groups: others                           246     0.002     0.020
VDW repulsions: refined_atoms                   282     0.227     0.200
VDW repulsions.others                           986     0.203     0.200
VDW; torsion: refined_atoms                     543     0.179     0.200
VDW; torsion.others                             476     0.106     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                 49     0.194     0.200
HBOND: symmetry: refined_atoms                    9     0.211     0.200
M. chain bond B values: refined atoms           514     0.639     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     0.731     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             1361     3.353    16.885
Long range B values: others                    1336     3.147    16.543
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.9218, B  =   -0.0017
Partial structure    1: scale =     0.2325, B  =  228.8362
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    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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.075    3545  99.80   354.5   351.5  0.06  0.07     365   347.1   342.7  0.07  0.07
 0.222    6087  99.99   159.5   160.4  0.05  0.04     642   161.3   162.8  0.06  0.05
 0.370    7836  99.85    74.6    74.3  0.14  0.10     769    74.4    74.7  0.15  0.11
 0.518    8797  96.10    50.1    41.3  0.30  0.28     890    49.1    41.3  0.31  0.29
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0746   2728   0.984    817   0.945   3545   0.975  0.999  0.9940  0.9916  0.9874  0.9789
  0.2223   5252   0.968    835   0.906   6087   0.959  0.994  0.9921  0.9935  0.9852  0.9925
  0.3701   7006   0.893    830   0.828   7836   0.886  0.960  0.9628  0.9635  0.9490  0.9536
  0.5178   8057   0.619    744   0.574   8801   0.616  0.813  0.7362  0.7422  0.6985  0.7045
 $$
Resolution limits                    =     38.623     1.300
Number of used reflections           =      26269
Percentage observed                  =    98.5760
Percentage of free reflections       =     9.2138
Overall R factor                     =     0.1047
Free R factor                        =     0.1112
Average Fourier shell correlation    =     0.9001
AverageFree Fourier shell correlation=     0.8985
Overall weighted R factor            =     0.0716
Free weighted R factor               =     0.0773
Overall weighted R2 factor           =     0.1161
Free weighted R2 factor              =     0.0910
Average correlation coefficient      =     0.8826
Overall correlation coefficient      =     0.9875
Free correlation coefficient         =     0.9894
Cruickshanks DPI for coordinate error=     0.0337
DPI based on free R factor           =     0.0323
Overall figure of merit              =     0.8244
ML based su of positional parameters =     0.0242
ML based su of thermal parameters    =     0.7350
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    108474.40       4281.5879       519757.78       519711.56    

 fvalues    108474.40       4281.5879       519744.47       519729.47    
 fvalues    108474.40       4281.5879       519744.47       519729.47    

 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_1-30A.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     1.941     1.652
Bond angles  : others                          2223     1.594     1.582
Torsion angles, period  1. refined              128     3.265     5.000
Torsion angles, period  2. refined               61    30.123    20.656
Torsion angles, period  3. refined              166    10.919    15.000
Torsion angles, period  4. refined               11    14.082    15.000
Chiral centres: refined atoms                   136     0.099     0.200
Planar groups: refined atoms                   1211     0.008     0.020
Planar groups: others                           246     0.002     0.020
VDW repulsions: refined_atoms                   282     0.227     0.200
VDW repulsions.others                           986     0.202     0.200
VDW; torsion: refined_atoms                     543     0.179     0.200
VDW; torsion.others                             476     0.106     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                 49     0.194     0.200
HBOND: symmetry: refined_atoms                    9     0.211     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     0.731     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     1.338     2.130
S. chain angle B values: others                 820     1.338     2.130
Long range B values: refined atoms             1361     3.353    16.885
Long range B values: others                    1336     3.147    16.543
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.9218, B  =   -0.0029
Partial structure    1: scale =     0.2325, B  =  228.8591
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    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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.075    3545  99.80   354.6   351.5  0.06  0.07     365   347.1   342.8  0.07  0.07
 0.222    6087  99.99   159.5   160.4  0.05  0.04     642   161.3   162.8  0.06  0.05
 0.370    7836  99.85    74.6    74.4  0.14  0.10     769    74.4    74.7  0.15  0.11
 0.518    8797  96.10    50.1    41.3  0.30  0.28     890    49.1    41.3  0.31  0.29
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0746   2728   0.984    817   0.945   3545   0.975  0.999  0.9940  0.9916  0.9874  0.9789
  0.2223   5252   0.968    835   0.906   6087   0.959  0.994  0.9921  0.9935  0.9852  0.9925
  0.3701   7006   0.893    830   0.828   7836   0.886  0.960  0.9628  0.9635  0.9490  0.9536
  0.5178   8057   0.619    744   0.574   8801   0.616  0.813  0.7362  0.7422  0.6985  0.7045
 $$
Resolution limits                    =     38.623     1.300
Number of used reflections           =      26269
Percentage observed                  =    98.5760
Percentage of free reflections       =     9.2138
Overall R factor                     =     0.1047
Free R factor                        =     0.1112
Average Fourier shell correlation    =     0.9001
AverageFree Fourier shell correlation=     0.8985
Overall weighted R factor            =     0.0717
Free weighted R factor               =     0.0773
Overall weighted R2 factor           =     0.1161
Free weighted R2 factor              =     0.0910
Average correlation coefficient      =     0.8826
Overall correlation coefficient      =     0.9875
Free correlation coefficient         =     0.9894
Cruickshanks DPI for coordinate error=     0.0337
DPI based on free R factor           =     0.0323
Overall figure of merit              =     0.8244
ML based su of positional parameters =     0.0242
ML based su of thermal parameters    =     0.7350
-----------------------------------------------------------------------------
  Time in seconds: CPU =        13.31
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1049   0.1110   0.836      108363.   11099.9   0.0131  1.037   1.950  1.164   0.100
       1   0.1046   0.1111   0.826      108400.   11110.5   0.0136  1.079   1.958  1.170   0.103
       2   0.1045   0.1111   0.827      108403.   11113.4   0.0138  1.095   1.973  1.180   0.103
       3   0.1046   0.1112   0.825      108434.   11115.3   0.0134  1.063   1.963  1.174   0.102
       4   0.1047   0.1112   0.824      108468.   11116.9   0.0130  1.027   1.944  1.162   0.100
       5   0.1047   0.1112   0.824      108474.   11117.5   0.0130  1.026   1.942  1.161   0.099
       6   0.1047   0.1112   0.824      108477.   11117.9   0.0130  1.025   1.941  1.160   0.099
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1049   0.1047
             R free    0.1110   0.1112
     Rms BondLength    0.0131   0.0130
      Rms BondAngle    1.9496   1.9415
     Rms ChirVolume    0.0996   0.0994
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
 Refmac:  End of Refmac_5.8.0258   
Times: User:      41.9s System:    0.1s Elapsed:     0:42  
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