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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: 09:58:57 


 Please reference: Collaborative Computational Project, Number 4. 2011.
 "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242.
 as well as any specific reference in the program write-up.


 $TEXT:Reference1: $$ Primary reference $$ 
   "Overview of refinement procedures within REFMAC5: utilizing data from different sources"
   O.Kovalevskiy, R.A.Nicholls, F.Long, G.N.Murshudov,(2018) 
   Acta Crystallogr. D74, 492-505

 $$
 $SUMMARY :Reference1:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference1: $$ Primary reference for EM $$ 
   "Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM
   R.A. Nicholls, M. Tykac, O.Kovalevskiy, G.N.Murshudov,(2018) 
   Acta Crystallogr. D74, 215-227

 $$
 $SUMMARY :Reference2:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference1: $$ Secondary reference $$ 
   "REFMAC5 for the refinement of macromolecular crystal structures:"
   G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011) 
   Acta Crystallogr. D67, 355-367

 $$
 $SUMMARY :Reference3:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference2: $$ Secondary reference $$ 
   "Refinement of Macromolecular Structures by the  Maximum-Likelihood Method:"
   G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
   Acta Crystallogr. D53, 240-255
   EU  Validation contract: BIO2CT-92-0524

 $$
 $SUMMARY :Reference4:  $$ Refmac: $$
 :TEXT:Reference2: $$

  Data line--- make     check NONE
  Data line--- refi     type REST reso 38.62 1.60     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_1-72A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - 1H87_dui_R00_1-60A.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_1-60A.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       0.0977
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    38.6230  1.6000
  Estimated number of reflections :      21008
  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  1.6000

  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_1-72A.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=   2.812 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=   2.815 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=   2.848 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=   2.701 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=   2.208 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=   2.306 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=   2.145 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=   2.725 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=   2.708 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=   2.589 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=   2.621 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=   2.485 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=   2.260 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=   2.346 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=   2.373 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       1484
Number of   all  reflections      15970
--------------------------------------------------------------------------------
 Number of reflections in file      47969
 Number of reflections read          15970

   Current auto weighting coefficient =    6.4999743    

 mode : HKRF


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



     CGMAT cycle number =      1

    ****                          Bond angle outliers                           ****

Bond angle deviations from the ideal >10.000Sigma will be monitored

A     80 CYS HA    - A     80 CYS CB    mod.=  87.40 id.= 108.44 dev= 21.039 sig.=  1.500

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   168  168   88
 Maximuum H,K,L                 :    49   49   25
 Minimum acceptable grid spacing:   111  111   56
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   168  168   88
 Maximuum H,K,L                 :    49   49   25
 Minimum acceptable grid spacing:   111  111   56
 Weight matrix    2.5583680    
 Actual weight    6.4999743      is applied to the X-ray term
Norm of X_ray positional gradient                90.3
Norm of Geom. positional gradient                87.1
Norm of X_ray B-factor gradient                  189.
Norm of Geom. B-factor gradient                  75.5
Product of X_ray and Geom posit. gradients     -0.192E+08
 Cosine of angle between them                      -0.375
Product of X_ray and Geom B-fact gradients     -0.106E+08
 Cosine of angle between them                      -0.341


Residuals: XRAY=     0.3880E+06 GEOM=      7301.     TOTAL=     0.3953E+06
 function value    395276.41    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1081     0.012     0.013
Bond distances: others                          960     0.036     0.018
Bond angles  : refined atoms                   1461     1.915     1.652
Bond angles  : others                          2223     2.394     1.582
Torsion angles, period  1. refined              128     3.524     5.000
Torsion angles, period  2. refined               61    29.966    20.656
Torsion angles, period  3. refined              166    11.087    15.000
Torsion angles, period  4. refined               11    14.248    15.000
Chiral centres: refined atoms                   136     0.131     0.200
Planar groups: refined atoms                   1211     0.008     0.020
Planar groups: others                           246     0.016     0.020
VDW repulsions: refined_atoms                   288     0.224     0.200
VDW repulsions.others                           968     0.230     0.200
VDW; torsion: refined_atoms                     538     0.177     0.200
VDW; torsion.others                             494     0.091     0.200
HBOND: refined_atoms                             95     0.168     0.200
Metal-ion: refined_atoms                          6     0.118     0.200
VDW repulsions: symmetry: refined_atoms          14     0.207     0.200
VDW repulsions: symmetry: others                 51     0.204     0.200
HBOND: symmetry: refined_atoms                   10     0.201     0.200
M. chain bond B values: refined atoms           514     0.673     1.321
M. chain bond B values: others                  514     0.672     1.321
M. chain angle B values: refined atoms          642     0.792     1.984
M. chain angle B values: others                 643     0.791     1.986
S. chain bond B values: refined atoms           566     1.037     1.452
S. chain bond B values: others                  567     1.036     1.452
S. chain angle B values: refined atoms          819     1.332     2.147
S. chain angle B values: others                 820     1.331     2.147
Long range B values: refined atoms             1364     3.431    17.095
Long range B values: others                    1335     3.157    16.678
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.9255, B  =    0.0052
Partial structure    1: scale =     0.2368, B  =  218.8315
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.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    1961  99.86   423.7   417.4  0.08  0.09     202   418.2   408.3  0.08  0.08
 0.147    3334  99.86   233.6   235.3  0.04  0.04     327   230.2   231.8  0.06  0.05
 0.244    4213  99.98   142.0   141.8  0.05  0.04     469   146.7   147.6  0.06  0.05
 0.342    4967  99.94    82.8    82.4  0.12  0.09     483    83.7    83.7  0.13  0.10
$$

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

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0494   1425   0.980    536   0.935   1961   0.968  1.002  0.9930  0.9897  0.9848  0.9707
  0.1469   2777   0.972    557   0.903   3334   0.960  0.990  0.9929  0.9954  0.9840  0.9955
  0.2444   3670   0.968    543   0.922   4213   0.962  1.000  0.9941  0.9943  0.9901  0.9922
  0.3419   4418   0.915    551   0.846   4969   0.907  0.984  0.9733  0.9730  0.9587  0.9618
 $$
Resolution limits                    =     38.623     1.600
Number of used reflections           =      14475
Percentage observed                  =    99.9186
Percentage of free reflections       =     9.2818
Overall R factor                     =     0.0671
Free R factor                        =     0.0759
Average Fourier shell correlation    =     0.9866
AverageFree Fourier shell correlation=     0.9869
Overall weighted R factor            =     0.0582
Free weighted R factor               =     0.0657
Overall weighted R2 factor           =     0.1129
Free weighted R2 factor              =     0.0903
Average correlation coefficient      =     0.9796
Overall correlation coefficient      =     0.9884
Free correlation coefficient         =     0.9903
Cruickshanks DPI for coordinate error=     0.0395
DPI based on free R factor           =     0.0364
Overall figure of merit              =     0.9437
ML based su of positional parameters =     0.0239
ML based su of thermal parameters    =     0.7487
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    59688.789       7300.8047       395276.41      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix    2.6059849    
 Actual weight    6.4999743      is applied to the X-ray term


 function value    390850.09    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.9251, B  =    0.0153
Partial structure    1: scale =     0.2374, B  =  220.8528
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                     =     0.0658
Free R factor                        =     0.0750
Average Fourier shell correlation    =     0.9869
AverageFree Fourier shell correlation=     0.9871
Average correlation coefficient      =     0.9805
Overall figure of merit              =     0.9443
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    59456.188       4386.4053       390850.09       395276.41    


     CGMAT cycle number =      3

 Weight matrix    2.3857167    
 Actual weight    5.9090672      is applied to the X-ray term


 function value    355311.88    

-------------------------------------------------------------------------------
             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 =     0.9248, B  =   -0.0009
Partial structure    1: scale =     0.2372, B  =  219.5976
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                     =     0.0654
Free R factor                        =     0.0746
Average Fourier shell correlation    =     0.9871
AverageFree Fourier shell correlation=     0.9871
Average correlation coefficient      =     0.9809
Overall figure of merit              =     0.9446
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    59380.949       4425.8384       355311.88       390850.09    


     CGMAT cycle number =      4

 Weight matrix    2.1802995    
 Actual weight    5.3718791      is applied to the X-ray term


 function value    323237.38    

-------------------------------------------------------------------------------
             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 =     0.9249, B  =    0.0044
Partial structure    1: scale =     0.2372, B  =  219.4132
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                     =     0.0653
Free R factor                        =     0.0745
Average Fourier shell correlation    =     0.9871
AverageFree Fourier shell correlation=     0.9872
Average correlation coefficient      =     0.9810
Overall figure of merit              =     0.9448
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    59353.996       4394.8740       323237.38       355311.88    


     CGMAT cycle number =      5

 Weight matrix    2.1854413    
 Actual weight    5.3718791      is applied to the X-ray term


 function value    323164.19    

-------------------------------------------------------------------------------
             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 =     0.9250, B  =    0.0065
Partial structure    1: scale =     0.2373, B  =  220.1461
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                     =     0.0653
Free R factor                        =     0.0744
Average Fourier shell correlation    =     0.9871
AverageFree Fourier shell correlation=     0.9872
Average correlation coefficient      =     0.9811
Overall figure of merit              =     0.9449
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    59353.586       4323.8994       323164.19       323237.38    


     CGMAT cycle number =      6

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   168  168   88
 Maximuum H,K,L                 :    49   49   25
 Minimum acceptable grid spacing:   111  111   56
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   168  168   88
 Maximuum H,K,L                 :    49   49   25
 Minimum acceptable grid spacing:   111  111   56
 Weight matrix    2.1856961    
 Actual weight    5.3718791      is applied to the X-ray term
Norm of X_ray positional gradient                52.2
Norm of Geom. positional gradient                51.8
Norm of X_ray B-factor gradient                  83.3
Norm of Geom. B-factor gradient                  80.0
Product of X_ray and Geom posit. gradients     -0.175E+08
 Cosine of angle between them                      -0.988
Product of X_ray and Geom B-fact gradients     -0.140E+08
 Cosine of angle between them                      -0.964


Residuals: XRAY=     0.3189E+06 GEOM=      4309.     TOTAL=     0.3232E+06
 function value    323161.34    

-------------------------------------------------------------------------------
             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     1.937     1.652
Bond angles  : others                          2223     1.591     1.582
Torsion angles, period  1. refined              128     3.304     5.000
Torsion angles, period  2. refined               61    29.992    20.656
Torsion angles, period  3. refined              166    10.973    15.000
Torsion angles, period  4. refined               11    14.239    15.000
Chiral centres: refined atoms                   136     0.103     0.200
Planar groups: refined atoms                   1211     0.008     0.020
Planar groups: others                           246     0.002     0.020
VDW repulsions: refined_atoms                   284     0.226     0.200
VDW repulsions.others                           985     0.202     0.200
VDW; torsion: refined_atoms                     537     0.179     0.200
VDW; torsion.others                             473     0.106     0.200
HBOND: refined_atoms                             97     0.167     0.200
Metal-ion: refined_atoms                          6     0.118     0.200
VDW repulsions: symmetry: refined_atoms          12     0.221     0.200
VDW repulsions: symmetry: others                 52     0.188     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     1.984
S. chain bond B values: refined atoms           566     1.061     1.451
S. chain bond B values: others                  567     1.060     1.452
S. chain angle B values: refined atoms          819     1.353     2.146
S. chain angle B values: others                 820     1.353     2.147
Long range B values: refined atoms             1361     3.454    17.046
Long range B values: others                    1332     3.198    16.645
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.9251, B  =    0.0076
Partial structure    1: scale =     0.2373, B  =  219.7448
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.  v. resln :N:1,6,7,11,12:
:Cycle    6.  and  v. resln :N:1,4,5,9,10:
:Cycle    6. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    1961  99.86   423.9   417.9  0.08  0.09     202   418.4   409.2  0.08  0.08
 0.147    3334  99.86   233.7   235.3  0.04  0.03     327   230.3   232.2  0.06  0.05
 0.244    4213  99.98   142.0   142.0  0.05  0.04     469   146.7   147.8  0.06  0.05
 0.342    4967  99.94    82.9    82.4  0.11  0.08     483    83.7    83.7  0.13  0.10
$$

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

 $TABLE: Cycle    6. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    6. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0494   1425   0.981    536   0.938   1961   0.969  1.002  0.9931  0.9898  0.9850  0.9707
  0.1469   2777   0.974    557   0.908   3334   0.963  0.990  0.9933  0.9957  0.9847  0.9956
  0.2444   3670   0.969    543   0.926   4213   0.964  0.999  0.9944  0.9944  0.9906  0.9923
  0.3419   4418   0.915    551   0.846   4969   0.907  0.984  0.9735  0.9742  0.9592  0.9661
 $$
Resolution limits                    =     38.623     1.600
Number of used reflections           =      14475
Percentage observed                  =    99.9186
Percentage of free reflections       =     9.2818
Overall R factor                     =     0.0653
Free R factor                        =     0.0744
Average Fourier shell correlation    =     0.9871
AverageFree Fourier shell correlation=     0.9872
Overall weighted R factor            =     0.0568
Free weighted R factor               =     0.0642
Overall weighted R2 factor           =     0.1123
Free weighted R2 factor              =     0.0891
Average correlation coefficient      =     0.9811
Overall correlation coefficient      =     0.9885
Free correlation coefficient         =     0.9905
Cruickshanks DPI for coordinate error=     0.0385
DPI based on free R factor           =     0.0357
Overall figure of merit              =     0.9449
ML based su of positional parameters =     0.0234
ML based su of thermal parameters    =     0.7377
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    59355.781       4309.2500       323161.34       323164.19    

 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_1-60A.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     1.936     1.652
Bond angles  : others                          2223     1.590     1.582
Torsion angles, period  1. refined              128     3.304     5.000
Torsion angles, period  2. refined               61    29.999    20.656
Torsion angles, period  3. refined              166    10.970    15.000
Torsion angles, period  4. refined               11    14.236    15.000
Chiral centres: refined atoms                   136     0.102     0.200
Planar groups: refined atoms                   1211     0.008     0.020
Planar groups: others                           246     0.002     0.020
VDW repulsions: refined_atoms                   283     0.227     0.200
VDW repulsions.others                           993     0.200     0.200
VDW; torsion: refined_atoms                     540     0.179     0.200
VDW; torsion.others                             480     0.105     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                 52     0.188     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     0.773     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             1361     3.453    17.039
Long range B values: others                    1332     3.197    16.637
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.9253, B  =    0.0083
Partial structure    1: scale =     0.2373, B  =  219.0583
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.  v. resln :N:1,6,7,11,12:
:Cycle    7.  and  v. resln :N:1,4,5,9,10:
:Cycle    7. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    1961  99.86   423.8   417.9  0.08  0.09     202   418.3   409.2  0.08  0.08
 0.147    3334  99.86   233.7   235.3  0.04  0.03     327   230.3   232.2  0.06  0.05
 0.244    4213  99.98   142.0   142.0  0.05  0.04     469   146.7   147.7  0.06  0.05
 0.342    4967  99.94    82.9    82.4  0.11  0.08     483    83.7    83.6  0.13  0.10
$$

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

 $TABLE: Cycle    7. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    7. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0494   1425   0.981    536   0.938   1961   0.969  1.002  0.9931  0.9898  0.9850  0.9707
  0.1469   2777   0.974    557   0.908   3334   0.963  0.990  0.9933  0.9957  0.9848  0.9955
  0.2444   3670   0.969    543   0.926   4213   0.964  0.999  0.9944  0.9944  0.9906  0.9922
  0.3419   4418   0.915    551   0.845   4969   0.907  0.984  0.9734  0.9741  0.9590  0.9661
 $$
Resolution limits                    =     38.623     1.600
Number of used reflections           =      14475
Percentage observed                  =    99.9186
Percentage of free reflections       =     9.2818
Overall R factor                     =     0.0654
Free R factor                        =     0.0745
Average Fourier shell correlation    =     0.9871
AverageFree Fourier shell correlation=     0.9872
Overall weighted R factor            =     0.0569
Free weighted R factor               =     0.0643
Overall weighted R2 factor           =     0.1123
Free weighted R2 factor              =     0.0891
Average correlation coefficient      =     0.9811
Overall correlation coefficient      =     0.9885
Free correlation coefficient         =     0.9905
Cruickshanks DPI for coordinate error=     0.0385
DPI based on free R factor           =     0.0357
Overall figure of merit              =     0.9448
ML based su of positional parameters =     0.0234
ML based su of thermal parameters    =     0.7377
-----------------------------------------------------------------------------
  Time in seconds: CPU =         5.95
             Elapsed =           0.00

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


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS: vs cycle :N:1,2,3:
:FOM vs cycle :N:1,4:
:-LL vs cycle :N:1,5:
:-LLfree vs cycle :N:1,6:
:Geometry vs cycle:N:1,7,8,9,10,11:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.0671   0.0759   0.944       59689.    6213.9   0.0121  0.942   1.915  1.147   0.131
       1   0.0658   0.0750   0.944       59456.    6200.2   0.0135  1.063   1.927  1.154   0.115
       2   0.0654   0.0746   0.945       59381.    6195.1   0.0138  1.090   1.948  1.166   0.109
       3   0.0653   0.0745   0.945       59354.    6191.4   0.0136  1.071   1.950  1.167   0.107
       4   0.0653   0.0744   0.945       59354.    6189.7   0.0132  1.040   1.940  1.160   0.104
       5   0.0653   0.0744   0.945       59356.    6189.7   0.0132  1.038   1.937  1.158   0.103
       6   0.0654   0.0745   0.945       59366.    6190.9   0.0132  1.037   1.936  1.158   0.102
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.0671   0.0654
             R free    0.0759   0.0745
     Rms BondLength    0.0121   0.0132
      Rms BondAngle    1.9147   1.9362
     Rms ChirVolume    0.1310   0.1024
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      33.3s System:    0.2s Elapsed:     0:33