Index results for dntr_1

Symmetry and refined cell parameters

Image Symmetry a b c alpha beta gamma
1 P3 107.093 107.093 296.616 90.000 90.000 120.000
2 H3 107.267 107.267 894.683 90.000 90.000 120.000
1+2 P3 107.092 107.092 296.674 90.000 90.000 120.000

Spots found, rejected, RMS spot deviation, beamcentre shift

Image Spots found Spots rejected Fraction RMS spot deviation Beam shift x Beam shift y
1 274 1 0.004 0.040 0.080 -0.065
2 173 0 0.000 0.650 0.110 0.035
1+2 447 1 0.002 0.050 0.080 -0.065

Image 1: /scisoft/pxsoft/data/dna_061202/ref-dntr_1_001.img

Image 2: /scisoft/pxsoft/data/dna_061202/ref-dntr_1_002.img

MOSFLM log



 ************ Version 6.2.3 (beta test 1.6) for Image plate and CCD data 4th November 2002  ***********
 A.G.W. Leslie, MRC Laboratory Of Molecular Biology, HILLS ROAD, CAMBRIDGE CB2 2QH, UK
 E-mail andrew@mrc-lmb.cam.ac.uk
 New auto-indexing using DPS due to Ingo Steller Robert Bolotovsky and Michael Rossmann
 (1998) J. Appl. Cryst. 30, 1036-1040
 Original auto-indexing using REFIX due to Wolfgang Kabsch (Kabsch,W. (1993),
J.Appl.Cryst. 24,795-800.)
 X-windows interface using xdl_view due to John Campbell (Daresbury Laboratory, UK.)
 (Campbell,J.W. (1995) J. Appl. Cryst. 28, 236-242.


 ===> newmat autoindex.mat
 ===> template ref-dntr_1_###.img
 ===> directory /scisoft/pxsoft/data/dna_061202
 ===> detector adsc
 ===> beam 93.630000 95.185000
 ===> autoindex threshold 10 dps image 1
Using DPS code for background indexing
 ===> mosaic estimate
 ===> go

  (Q)QOPEN: file opened on unit  1      Status: READONLY

 Logical Name: /scisoft/pxsoft/data/dna_061202/ref-dntr_1_001.img      Filename: /scisoft/pxsoft/data/dna_061202/ref-dntr_1_001.img



 Crystal to detector distance of  249.99mm taken from image header

 Wavelength of 0.93400A taken from image header

 Pixel size of 0.0816mm taken from image header.
 IBEAM =  2 it should be 2

 Input beam coordinates   93.63mm   95.18mm will be used


 Autoindexing image    1
 =======================

 image FILENAME: /scisoft/pxsoft/data/dna_061202/ref-dntr_1_001.img

  (Q)QOPEN: file opened on unit  1      Status: READONLY

 Logical Name: /scisoft/pxsoft/data/dna_061202/ref-dntr_1_001.img      Filename: /scisoft/pxsoft/data/dna_061202/ref-dntr_1_001.img


 Determining best threshold for spot finding.
 Default parameters may be reset with SPOTS keyword.
 Minimum radius   9.4mm, maximum radius 37.60mm, minimum number of spots 10

 Background strip overlaps gap between detector tiles, so YOFFSET changed to   4.2mm
 sorting  82 spots
 Threshold set to    4.3
 sorting  87 spots
 Threshold set to    4.2


 Finding spots on image     1 (Midpoint of phi   0.250 degrees)
 Calculating radial background..... 
 The background is radial along the X (slow) direction
 The average of  51 pixels, excluding outliers, is used
 The scan is offset by 4.7mm from the image centre in Y to avoid any
 backstop shadow
 Radial Background calculation complete
 RADIUS   9.4   9.7  10.0  10.4  10.7  11.0  11.3  11.7  12.0  12.3  12.6  13.0
 BACKG    163   163   163   163   164   163   164   163   163   166   166   166
 SIGMA     12    12    12    12    12    12    12    12    12    12    12    12
 NREJ       0     0     0     0     0     0     0     0     0     0     0     2
 RADIUS  13.3  13.6  14.0  14.3  14.6  14.9  15.3  15.6  15.9  16.2  16.6  16.9
 BACKG    167   165   164   164   166   163   164   165   165   166   165   166
 SIGMA     12    12    12    12    12    12    12    12    12    12    12    12
 NREJ       2     0     0     0     0     0     0     0     0     0     0     0
 RADIUS  17.2  17.5  17.9  18.2  18.5  18.8  19.2  19.5  19.8  20.2  20.5  20.8
 BACKG    164   166   167   166   166   166   166   166   164   162   163   163
 SIGMA     12    12    12    12    12    12    12    12    12    12    12    12
 NREJ       0     0     0     0     0     0     0     0     1     0     0     0
 RADIUS  21.1  21.5  21.8  22.1  22.4  22.8  23.1  23.4  23.7  24.1  24.4  24.7
 BACKG    162   163   164   163   161   162   159   158   158   159   157   157
 SIGMA     12    12    12    12    12    12    12    12    12    12    12    12
 NREJ       0     0     0     0     0     0     0     0     0     0     0     0
 RADIUS  25.1  25.4  25.7  26.0  26.4  26.7  27.0  27.3  27.7  28.0  28.3  28.6
 BACKG    156   156   156   156   153   154   154   153   153   151   154   150
 SIGMA     12    12    12    12    12    12    12    12    12    12    12    12
 NREJ       0     0     0     0     0     0     0     0     0     0     0     0
 RADIUS  29.0  29.3  29.6  29.9  30.3  30.6  30.9  31.3  31.6  31.9  32.2  32.6
 BACKG    149   151   151   148   148   148   148   147   147   148   146   144
 SIGMA     12    12    12    12    12    12    12    12    12    12    12    12
 NREJ       0     0     1     0     0     0     0     0     0     0     0     0
 RADIUS  32.9  33.2  33.5  33.9  34.2  34.5  34.8  35.2  35.5  35.8  36.1  36.5
 BACKG    145   146   144   144   144   142   143   143   142   141   143   144
 SIGMA     12    12    12    12    12    11    11    11    11    11    11    11
 NREJ       0     0     0     1     0     0     0     0     0     0     1     0
 RADIUS  36.8  37.1  37.5  37.8  38.1  38.4  38.8  39.1  39.4  39.7  40.1  40.4
 BACKG    142   141   140   142   141   141   140   139   140   140   139   139
 SIGMA     11    11    11    11    11    11    11    11    11    11    11    11
 NREJ       0     0     0     0     0     0     0     0     0     0     0     0
 RADIUS  40.7  41.0  41.4  41.7  42.0  42.4  42.7  43.0  43.3  43.7  44.0  44.3
 BACKG    138   139   139   139   139   138   139   139   137   137   139   140
 SIGMA     11    11    11    11    11    11    11    11    11    11    11    11
 NREJ       0     0     0     0     0     0     0     0     0     0     0     0
 RADIUS  44.6  45.0  45.3  45.6  45.9  46.3  46.6  46.9  47.2  47.6  47.9  48.2
 BACKG    139   140   139   141   138   139   140   139   141   141   140   141
 SIGMA     11    11    11    11    11    11    11    11    11    11    11    11
 NREJ       0     0     0     0     1     0     0     1     0     0     0     0
 RADIUS  48.6  48.9  49.2  49.5  49.9  50.2  50.5  50.8  51.2  51.5  51.8  52.1
 BACKG    143   143   144   143   144   145   145   147   149   149   150   151
 SIGMA     11    11    12    11    11    12    12    12    12    12    12    12
 NREJ       0     0     0     1     0     0     1     0     0     0     1     0
 RADIUS  52.5  52.8  53.1  53.4  53.8  54.1  54.4  54.8  55.1  55.4  55.7  56.1
 BACKG    152   152   155   158   158   160   160   159   159   158   158   159
 SIGMA     12    12    12    12    12    12    12    12    12    12    12    12
 NREJ       0     0     0     0     0     0     1     1     0     2     0     0
 RADIUS  56.4  56.7  57.0  57.4  57.7  58.0  58.3  58.7  59.0  59.3  59.6  60.0
 BACKG    158   158   157   158   158   158   159   158   161   158   158   158
 SIGMA     12    12    12    12    12    12    12    12    12    12    12    12
 NREJ       0     0     0     1     0     2     0     0     0     0     0     0
 RADIUS  60.3  60.6  61.0  61.3  61.6  61.9  62.3  62.6  62.9  63.2  63.6  63.9
 BACKG    160   163   163   161   164   164   167   165   166   166   166   168
 SIGMA     12    12    12    12    12    12    12    12    12    12    12    12
 NREJ       0     1     4     2     1     1     0     0     2     0     0     0
 RADIUS  64.2  64.5  64.9  65.2  65.5  65.9  66.2  66.5  66.8  67.2  67.5  67.8
 BACKG    168   166   167   166   165   164   162   163   161   158   158   157
 SIGMA     12    12    12    12    12    12    12    12    12    12    12    12
 NREJ       0     0     0     0     0     0     2     0     1     0     0     0
 RADIUS  68.1  68.5  68.8  69.1  69.4  69.8  70.1  70.4  70.7  71.1  71.4  71.7
 BACKG    158   156   152   152   151   152   150   149   147   145   147   146
 SIGMA     12    12    12    12    12    12    12    12    12    12    12    12
 NREJ       0     0     0     0     0     0     0     0     0     1     0     0
 RADIUS  72.1  72.4  72.7  73.0  73.4  73.7  74.0  74.3  74.7  75.0  75.3  75.6
 BACKG    143   144   142   144   141   142   141   139   139   136   135   135
 SIGMA     11    12    11    11    11    11    11    11    11    11    11    11
 NREJ       0     0     1     0     0     0     0     0     0     2     0     0
 RADIUS  76.0  76.3  76.6  76.9  77.3  77.6  77.9  78.3  78.6  78.9  79.2  79.6
 BACKG    137   134   134   134   131   131   130   129   129   127   128   126
 SIGMA     11    11    11    11    11    11    11    11    11    11    11    11
 NREJ       0     0     0     0     0     0     0     0     0     0     0     0
 RADIUS  79.9  80.2  80.5  80.9  81.2  81.5  81.8  82.2  82.5  82.8  83.2  83.5
 BACKG    127   126   125   125   126   124   123   123   122   121   119   119
 SIGMA     11    11    11    11    11    11    11    11    11    11    10    10
 NREJ       0     1     0     0     0     0     0     0     0     0     0     0
 RADIUS  83.8  84.1  84.5
 BACKG    119   118    58
 SIGMA     10    10     5
 NREJ       0     0     0

 Starting spot search...
 sorting  274 spots

  Median spot size is   3 x   3 pixels

  Total number of spots found: 274
  Number rejected as too small on X:   0
  Number rejected as too small on Y:   0
  Number rejected as too big on X:   1
  Number rejected as too big on Y:   0
  Number too close (SEPARATION keyword):   0
  Number stored as OK: 273



             Number of spots found in each bin
              14   8   6   8  10   7   7  17
              13   8   8   9  14   3   6  12
              12   5  12  12  12  14   7   9
               5   4   7   3   4   3   4   4
               0   0   3   0   0   0   2   1

 Determining average spot size for spots in centre of image.
 ==========================================================
 Finding spot size around direct beam position
 Default parameters may be reset with SPOTS keyword.
 Minimum radius   9.4mm, maximum radius 37.60mm, minimum number of spots 10
 sorting  88 spots

 Based on a median spot size of  4 by  4 pixels in X and Y, the measurement box 
 parameters have been set to  15  15   9   5   5
 The overall size of the box has been fixed.
 To prevent this use keywords PROFILE NOFIXBOX.
 ***** WARNING ***** Lattice type not specified, so assumed primitive

 Based on a median spot size of  4 by  4 pixels in X and Y, the spot separation 
 parameters (in X and Y) have been set to  0.48  0.48mm.
 Closest possible spot separation is  0.00mm.

 Because the minimum possible spot separation is less than the estimated spot
 size plus a safety margin of 2 pixels (set by keywords SPOTS SAFE) the
 "CLOSE" option for integration has been set.
 ****************************************************
 ****************************************************
 It is advisable to ensure that all images for this dataset are also
 processed using the "CLOSE" option by explicitly including keywords:
 SEPARATION CLOSE
 ****************************************************
 ****************************************************

 FORMATTED      UNKNOWN file opened on unit  10

 Logical name: ref-dntr_1.spt, Filename: ref-dntr_1.spt


   273 spots written for image    1
 A total of   273 spots were written to file

 FORMATTED      OLD     file opened on unit  10

 Logical name: ref-dntr_1.spt, Filename: ref-dntr_1.spt


DPS Indexing at Two-theta =    0.00 with  225 reflections (minimum spot separation = 0.33mm. Maximum expected cell edge  306.54, Beam position is   93.63   95.18
Generating direct lattice vectors (This may take some time):
|-----------------|
..................
 Refining  30 direct space vectors:
|----------------------------|
..............................
selected 11
 List of possible Laue groups, sorted on penalty index.
 The lower the PENALTY, the better
 No PENALTY LATT     a        b        c     alpha  beta gamma  Possible spacegroups

  44 999    cI   314.72   107.89   315.88    80.2  34.3  80.3   I23,I213,I432,I4132
  43 995    hR   350.74   315.04   107.27    80.6  90.2  50.4   H3,H32 (hexagonal settings of R3 and R32)
  42 940    cF   315.73   349.03   315.35   142.6  40.0 142.8   F23,F432,F4132
  41 937    tI   315.04   315.35   107.27    80.5  99.4 145.5   I4,I41,I422,I4122
  40 890    tI   314.72   107.89   315.88    80.2  34.3  80.3   I4,I41,I422,I4122
  39 890    hP   107.27   296.53   107.64    89.8 119.7  90.3   P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
                                                                P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
  38 841    tI   315.88   314.72   107.89    80.3  80.2  34.3   I4,I41,I422,I4122
  37 837    oI   107.89   314.72   315.88    34.3  80.2  80.3   I222,I212121
  36 832    oI   107.27   315.04   315.35    34.5  80.5  80.6   I222,I212121
  35 785    tP   107.64   296.53   107.27    90.3 119.7  89.8   P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
  34 785    cP   107.27   107.64   296.53    89.8  90.3 119.7   P23,P213,P432,P4232,P4332,P4132
  33 785    hR   185.86   314.72   315.73   145.6  90.2 106.8   H3,H32 (hexagonal settings of R3 and R32)
  32 783    oC   315.88   315.04   107.27    80.6 100.1  39.9   C222,C2221
  31 780    hR   107.89   314.72   350.88   129.9  90.0  99.7   H3,H32 (hexagonal settings of R3 and R32)
  30 780    mC   315.88   315.04   107.27    80.6 100.1  39.9   C2
  29 779    mC   315.88   315.04   107.27    99.4 100.1 140.1   C2
  28 214    hR   107.27   107.89   907.72    90.2  99.9 120.0   H3,H32 (hexagonal settings of R3 and R32)
  27 211    oF   107.27   186.93   602.04    89.9  99.9  90.2   F222
  26 176    tI   107.27   107.64   602.98    94.9  95.5 119.7   I4,I41,I422,I4122
  25 175    oI   107.27   107.64   602.59    84.6  85.2 119.7   I222,I212121
  24 163    mI   107.64   602.59   107.27    85.2 119.7  84.6   C2
  23 163    oC   107.27   602.04   107.64    85.2 119.7  99.9   C222,C2221
  22 163    oC   107.27   602.04   107.64    85.2 119.7  99.9   C222,C2221
  21 162    mC   602.04   107.27   107.64   119.7  94.8  80.1   C2
  20 161    mC   602.04   107.27   107.64   119.7  94.8  80.1   C2
  19 158    mC   107.64   602.30   107.27    94.7 119.7  79.9   C2
  18 158    mC   107.27   602.04   107.64    94.8 119.7  80.1   C2
  17 115    oF   107.89   185.86   602.59    90.4 100.2  89.8   F222
  16 112    mC   185.86   107.89   314.72    80.3 106.8  89.8   C2
  15  63    mC   186.30   107.64   349.47    90.4 122.0  89.6   C2
  14  60    tP   107.27   107.64   296.53    89.8  90.3 119.7   P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
  13  59    oP   107.27   107.64   296.53    89.8  90.3 119.7   P222,P2221,P21212,P212121
  12  58    mP   107.64   107.27   296.53    90.3  89.8 119.7   P2,P21
  11  57    mP   107.27   107.64   296.53    89.8  90.3 119.7   P2,P21
  10   6    hP   107.27   107.64   296.53    89.8  90.3 119.7   P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
                                                                P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
   9   5    oC   107.89   185.86   296.53    89.7  90.1  89.8   C222,C2221
   8   5    mC   107.89   185.86   296.53    89.7  90.1  89.8   C2
   7   5    oC   107.27   186.93   296.53    90.1  90.3  90.2   C222,C2221
   6   4    mC   186.93   107.27   296.53    90.3  89.9  89.8   C2
   5   4    mP   107.27   296.53   107.64    89.8 119.7  90.3   P2,P21
   4   1    mC   107.27   186.93   296.53    89.9  90.3  89.8   C2
   3   1    mC   185.86   107.89   296.53    90.1  90.3  90.2   C2
   2   1    aP   107.27   107.64   296.53    89.8  90.3 119.7   P1
   1   0    aP   107.27   107.64   296.53    89.8  89.7  60.3   P1
 No PENALTY SDCELL FRACN LATT      a        b        c     alpha  beta gamma  Possible spacegroups

The solution and direct beam position will now be refined; reflections which deviate by more
than the sigma cutoff from their calculated position will be excluded from the refinement.

Refining solution #10 with P3     (number 143) symmetry imposed

Initial cell (before refinement) is  107.4513  107.4513  296.5257  90.000  90.000 120.000
Using  218 indexed reflections (out of  225 spots found, {delta(XY) <= 2.5 sigma}),
final sd in spot positions is 0.04mm and in phi 0.11 degrees
Refined cell parameters  107.09  107.09  296.62  90.00  90.00 120.00
Beam coordinates of  93.63  95.18 have been refined to  93.71  95.12
This is a shift of  0.10mm or  0.129 times the minimum spot separation of ca  0.79mm.
  Final cell (after refinement) is   107.0925  107.0925  296.6158  90.000  90.000 120.000

 FORMATTED      UNKNOWN file opened on unit  12

 Logical name: autoindex.mat, Filename: autoindex.mat


Updating the stored central beam position from   9363.000  9518.500 to   9430.001  9511.762

 ****** INFORMATION *****
 ****** INFORMATION *****
 ****** INFORMATION *****
 The cell derived from autoindexing will override that given on the CELL keyword.
 To force the program to use the input cell, add the keyword KEEP. eg:
 CELL KEEP 74.2 74.2 35.1 90 90 90


 **** WARNING ****
 Because input wavelength ( 0.9340) is not CuKa (1.5418) or Mo (0.7107),
 source is assumed to be a synchrotron and synchrotron defaults for polarisation and beam divergence
 will be used if these have not been defined explicitly (SYNCH POLAR and DIVH/DIVV keywords.


  (Q)QOPEN: file opened on unit  1      Status: UNKNOWN

 Logical Name: ref-dntr_1.gen      Filename: ref-dntr_1.gen




 Title for MTZ and GENERATE Files (TITLE):
 .
 Crystal identifier (IDENT): ref-dntr_1

********************************************************************************
 Warning!! No PROTEIN NAME GIVEN by KeyWord PNAME
 It has been set to be "Unspecified"
********************************************************************************

********************************************************************************
 Warning!! No DATA SET NAME GIVEN by KeyWord DNAME
 It has been set to be "Unspecified"
********************************************************************************
  PSIX changed by  0.00 Degrees and CCOMEGA set to 0.000

  MAX. No. of Active Reflections=    81

 Beam divergence refinement

 Refining DIV  with stepsize  0.01 Degrees
 Divergence      0.000 0.050 0.100 0.150 0.200 0.250 0.300 0.350 0.400 0.450 0.500 0.550 0.600 0.650 0.700 0.750 0.800 0.850 0.900
 Divergence      0.950 1.000
 No gained           0   400   393   421   376   394   395   402   396   387   375   392   400   394   420   399   370   377   382
 No gained         366   386
 Total intensity 82400 89521 93788 96642 97399 97863 98418 98680 98851 99184 99497 99467 99507 99638 99608 99769 99860 99910 99991
 Total intensity 99951 99789
 SD of intensity   464   484   504   525   545   555   575   585   605   615   625   646   656   666   686   696   706   716   726
 SD of intensity   736   746
 The mosaicity has been estimated as ---> 0.24 <--- for this image only; 
This value can be used cautiously as an initial estimate.
Storing space group from DPS autoindexing: P3         number 143



 *********** END OF PROCESSING *****************


 ************ Version 6.2.3 (beta test 1.6) for Image plate and CCD data 4th November 2002  ***********
 A.G.W. Leslie, MRC Laboratory Of Molecular Biology, HILLS ROAD, CAMBRIDGE CB2 2QH, UK
 E-mail andrew@mrc-lmb.cam.ac.uk
 New auto-indexing using DPS due to Ingo Steller Robert Bolotovsky and Michael Rossmann
 (1998) J. Appl. Cryst. 30, 1036-1040
 Original auto-indexing using REFIX due to Wolfgang Kabsch (Kabsch,W. (1993),
J.Appl.Cryst. 24,795-800.)
 X-windows interface using xdl_view due to John Campbell (Daresbury Laboratory, UK.)
 (Campbell,J.W. (1995) J. Appl. Cryst. 28, 236-242.


 ===> newmat autoindex.mat
 ===> template ref-dntr_1_###.img
 ===> directory /scisoft/pxsoft/data/dna_061202
 ===> detector adsc
 ===> beam 93.630000 95.185000
 ===> autoindex threshold 10 dps image 2
Using DPS code for background indexing
 ===> mosaic estimate
 ===> go

  (Q)QOPEN: file opened on unit  1      Status: READONLY

 Logical Name: /scisoft/pxsoft/data/dna_061202/ref-dntr_1_002.img      Filename: /scisoft/pxsoft/data/dna_061202/ref-dntr_1_002.img



 Crystal to detector distance of  249.99mm taken from image header

 Wavelength of 0.93400A taken from image header

 Pixel size of 0.0816mm taken from image header.
 IBEAM =  2 it should be 2

 Input beam coordinates   93.63mm   95.18mm will be used


 Autoindexing image    2
 =======================

 image FILENAME: /scisoft/pxsoft/data/dna_061202/ref-dntr_1_002.img

  (Q)QOPEN: file opened on unit  1      Status: READONLY

 Logical Name: /scisoft/pxsoft/data/dna_061202/ref-dntr_1_002.img      Filename: /scisoft/pxsoft/data/dna_061202/ref-dntr_1_002.img


 Determining best threshold for spot finding.
 Default parameters may be reset with SPOTS keyword.
 Minimum radius   9.4mm, maximum radius 37.60mm, minimum number of spots 10

 Background strip overlaps gap between detector tiles, so YOFFSET changed to   4.2mm
 sorting  74 spots
 Threshold set to    4.2
 sorting  85 spots
 Threshold set to    4.1


 Finding spots on image     2 (Midpoint of phi  89.750 degrees)
 Calculating radial background..... 
 The background is radial along the X (slow) direction
 The average of  51 pixels, excluding outliers, is used
 The scan is offset by 4.7mm from the image centre in Y to avoid any
 backstop shadow
 Radial Background calculation complete
 RADIUS   9.4   9.7  10.0  10.4  10.7  11.0  11.3  11.7  12.0  12.3  12.6  13.0
 BACKG    161   161   161   164   163   163   162   161   163   163   163   163
 SIGMA     12    12    12    12    12    12    12    12    12    12    12    12
 NREJ       0     0     0     0     0     0     0     0     0     0     0     0
 RADIUS  13.3  13.6  14.0  14.3  14.6  14.9  15.3  15.6  15.9  16.2  16.6  16.9
 BACKG    163   162   163   165   165   165   163   163   163   167   164   164
 SIGMA     12    12    12    12    12    12    12    12    12    12    12    12
 NREJ       0     0     0     0     4     0     0     0     0     0     0     0
 RADIUS  17.2  17.5  17.9  18.2  18.5  18.8  19.2  19.5  19.8  20.2  20.5  20.8
 BACKG    165   164   164   164   163   166   165   163   164   162   164   163
 SIGMA     12    12    12    12    12    12    12    12    12    12    12    12
 NREJ       0     0     0     0     0     0     0     0     0     0     0     0
 RADIUS  21.1  21.5  21.8  22.1  22.4  22.8  23.1  23.4  23.7  24.1  24.4  24.7
 BACKG    163   161   161   161   159   159   158   157   157   158   159   156
 SIGMA     12    12    12    12    12    12    12    12    12    12    12    12
 NREJ       0     0     0     0     0     1     0     0     0     0     0     0
 RADIUS  25.1  25.4  25.7  26.0  26.4  26.7  27.0  27.3  27.7  28.0  28.3  28.6
 BACKG    155   156   155   152   153   152   153   151   151   151   150   148
 SIGMA     12    12    12    12    12    12    12    12    12    12    12    12
 NREJ       0     2     2     0     0     0     0     0     1     0     0     0
 RADIUS  29.0  29.3  29.6  29.9  30.3  30.6  30.9  31.3  31.6  31.9  32.2  32.6
 BACKG    149   148   148   148   148   147   148   147   145   146   144   145
 SIGMA     12    12    12    12    12    12    12    12    12    12    12    12
 NREJ       0     0     0     0     0     0     1     0     0     0     0     0
 RADIUS  32.9  33.2  33.5  33.9  34.2  34.5  34.8  35.2  35.5  35.8  36.1  36.5
 BACKG    145   143   144   144   143   142   143   142   142   141   141   140
 SIGMA     12    11    12    11    11    11    11    11    11    11    11    11
 NREJ       0     0     0     0     0     0     0     0     0     1     0     0
 RADIUS  36.8  37.1  37.5  37.8  38.1  38.4  38.8  39.1  39.4  39.7  40.1  40.4
 BACKG    141   142   141   140   141   141   140   140   138   137   139   140
 SIGMA     11    11    11    11    11    11    11    11    11    11    11    11
 NREJ       0     0     0     1     0     0     0     0     0     0     0     0
 RADIUS  40.7  41.0  41.4  41.7  42.0  42.4  42.7  43.0  43.3  43.7  44.0  44.3
 BACKG    139   137   140   138   138   140   139   140   138   138   139   140
 SIGMA     11    11    11    11    11    11    11    11    11    11    11    11
 NREJ       0     0     0     0     2     0     0     0     0     1     1     0
 RADIUS  44.6  45.0  45.3  45.6  45.9  46.3  46.6  46.9  47.2  47.6  47.9  48.2
 BACKG    140   141   140   140   140   143   143   141   141   142   144   144
 SIGMA     11    11    11    11    11    11    11    11    11    11    11    12
 NREJ       2     2     0     0     0     0     2     0     0     0     0     0
 RADIUS  48.6  48.9  49.2  49.5  49.9  50.2  50.5  50.8  51.2  51.5  51.8  52.1
 BACKG    146   145   147   145   147   150   152   152   154   156   161   162
 SIGMA     12    12    12    12    12    12    12    12    12    12    12    12
 NREJ       0     0     0     0     0     0     0     1     0     0     0     1
 RADIUS  52.5  52.8  53.1  53.4  53.8  54.1  54.4  54.8  55.1  55.4  55.7  56.1
 BACKG    164   169   173   179   180   178   178   180   178   175   174   171
 SIGMA     12    13    13    13    13    13    13    13    13    13    13    13
 NREJ       0     0     0     0     0     0     1     0     0     0     0     0
 RADIUS  56.4  56.7  57.0  57.4  57.7  58.0  58.3  58.7  59.0  59.3  59.6  60.0
 BACKG    172   168   167   167   167   168   167   166   168   169   167   168
 SIGMA     13    12    12    12    12    12    12    12    12    12    12    12
 NREJ       0     0     0     0     0     0     0     0     0     0     0     0
 RADIUS  60.3  60.6  61.0  61.3  61.6  61.9  62.3  62.6  62.9  63.2  63.6  63.9
 BACKG    170   171   174   175   175   177   181   182   183   184   185   185
 SIGMA     13    13    13    13    13    13    13    13    13    13    13    13
 NREJ       0     0     2     0     0     0     0     0     0     0     0     0
 RADIUS  64.2  64.5  64.9  65.2  65.5  65.9  66.2  66.5  66.8  67.2  67.5  67.8
 BACKG    184   183   183   184   181   179   177   174   170   170   168   167
 SIGMA     13    13    13    13    13    13    13    13    13    13    12    12
 NREJ       0     1     1     0     0     2     0     0     0     0     0     0
 RADIUS  68.1  68.5  68.8  69.1  69.4  69.8  70.1  70.4  70.7  71.1  71.4  71.7
 BACKG    162   162   161   159   157   153   153   153   150   150   149   148
 SIGMA     12    12    12    12    12    12    12    12    12    12    12    12
 NREJ       0     0     1     0     0     1     0     1     0     0     0     0
 RADIUS  72.1  72.4  72.7  73.0  73.4  73.7  74.0  74.3  74.7  75.0  75.3  75.6
 BACKG    147   145   144   143   143   142   141   140   138   137   138   137
 SIGMA     12    12    12    11    11    11    11    11    11    11    11    11
 NREJ       0     1     0     0     0     1     0     0     0     0     0     0
 RADIUS  76.0  76.3  76.6  76.9  77.3  77.6  77.9  78.3  78.6  78.9  79.2  79.6
 BACKG    135   134   134   134   132   132   130   131   131   129   127   127
 SIGMA     11    11    11    11    11    11    11    11    11    11    11    11
 NREJ       0     0     0     0     1     0     0     0     0     0     1     0
 RADIUS  79.9  80.2  80.5  80.9  81.2  81.5  81.8  82.2  82.5  82.8  83.2  83.5
 BACKG    127   126   126   125   124   124   121   122   121   119   119   120
 SIGMA     11    11    11    11    11    11    11    11    10    10    10    10
 NREJ       0     0     0     0     0     0     0     1     0     0     0     0
 RADIUS  83.8  84.1  84.5
 BACKG    118   116    59
 SIGMA     10    10     5
 NREJ       0     0     0

 Starting spot search...
 sorting  173 spots

  Median spot size is   4 x   3 pixels

  Total number of spots found: 173
  Number rejected as too small on X:   0
  Number rejected as too small on Y:   0
  Number rejected as too big on X:   0
  Number rejected as too big on Y:   0
  Number too close (SEPARATION keyword):   0
  Number stored as OK: 173



             Number of spots found in each bin
              12  10   5   8  10   2   6  15
               5   4   5   2   4   5   8   6
               4   8   6   4   5   4   6   4
               2   0   3   2   4   3   4   2
               0   2   1   0   1   0   0   1

 Determining average spot size for spots in centre of image.
 ==========================================================
 Finding spot size around direct beam position
 Default parameters may be reset with SPOTS keyword.
 Minimum radius   9.4mm, maximum radius 37.60mm, minimum number of spots 10
 sorting  85 spots

 Based on a median spot size of  4 by  4 pixels in X and Y, the measurement box 
 parameters have been set to  15  15   9   5   5
 The overall size of the box has been fixed.
 To prevent this use keywords PROFILE NOFIXBOX.
 ***** WARNING ***** Lattice type not specified, so assumed primitive

 Based on a median spot size of  4 by  4 pixels in X and Y, the spot separation 
 parameters (in X and Y) have been set to  0.48  0.48mm.
 Closest possible spot separation is  0.00mm.

 Because the minimum possible spot separation is less than the estimated spot
 size plus a safety margin of 2 pixels (set by keywords SPOTS SAFE) the
 "CLOSE" option for integration has been set.
 ****************************************************
 ****************************************************
 It is advisable to ensure that all images for this dataset are also
 processed using the "CLOSE" option by explicitly including keywords:
 SEPARATION CLOSE
 ****************************************************
 ****************************************************

 FORMATTED      UNKNOWN file opened on unit  10

 Logical name: ref-dntr_1.spt, Filename: ref-dntr_1.spt


   173 spots written for image    2
 A total of   173 spots were written to file

 FORMATTED      OLD     file opened on unit  10

 Logical name: ref-dntr_1.spt, Filename: ref-dntr_1.spt


DPS Indexing at Two-theta =    0.00 with  140 reflections (minimum spot separation = 0.33mm. Maximum expected cell edge  267.65, Beam position is   93.63   95.18
Generating direct lattice vectors (This may take some time):
|-----------------|
..................
 Refining  30 direct space vectors:
|----------------------------|
..............................
selected 15
 List of possible Laue groups, sorted on penalty index.
 The lower the PENALTY, the better
 No PENALTY LATT     a        b        c     alpha  beta gamma  Possible spacegroups

  44 999    cI   316.57   106.93   313.44    80.3  33.6  80.4   I23,I213,I432,I4132
  43 987    hR   350.68   313.60   105.67    81.5  90.4  49.7   H3,H32 (hexagonal settings of R3 and R32)
  42 930    cF   315.35   345.49   315.69   143.1  39.6 143.1   F23,F432,F4132
  41 920    tI   313.44   315.69   105.64    81.0  98.6 145.9   I4,I41,I422,I4122
  40 893    tI   313.44   106.93   316.57    80.4  33.6  80.3   I4,I41,I422,I4122
  39 891    hP   105.67   296.85   105.64    89.1 119.2  91.0   P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
                                                                P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
  38 856    tI   313.44   316.57   106.93    80.4  80.3  33.6   I4,I41,I422,I4122
  37 846    oI   106.93   316.57   313.44    33.6  80.3  80.4   I222,I212121
  36 833    oI   105.67   313.60   315.35    34.1  81.0  81.5   I222,I212121
  35 800    tP   105.67   296.85   105.64    89.1 119.2  91.0   P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
  34 800    cP   105.64   105.67   296.85    91.0  89.1 119.2   P23,P213,P432,P4232,P4332,P4132
  33 795    oC   313.44   316.75   105.64    79.8  98.6  39.2   C222,C2221
  32 795    hR   182.27   313.60   315.35   145.9  91.0 105.9   H3,H32 (hexagonal settings of R3 and R32)
  31 785    mC   316.57   313.60   105.67    81.5 100.3  39.2   C2
  30 781    mC   316.57   313.60   105.67    98.5 100.3 140.8   C2
  29 781    hR   106.93   313.60   351.18   130.9  89.9  99.9   H3,H32 (hexagonal settings of R3 and R32)
  28 197    hR   105.64   106.93   905.74    89.9  99.1 120.4   H3,H32 (hexagonal settings of R3 and R32)
  27 187    oF   105.64   184.50   601.47    89.3  99.3  90.8   F222
  26 169    tI   105.64   106.93   601.30    95.0  94.1 120.4   I4,I41,I422,I4122
  25 166    oI   105.64   106.93   601.30    85.0  85.9 120.4   I222,I212121
  24 157    mI   105.64   603.08   105.67    85.8 119.2  84.0   C2
  23 157    oC   105.67   601.30   105.64    85.9 119.2  99.2   C222,C2221
  22 157    oC   105.67   601.30   105.64    85.9 119.2  99.2   C222,C2221
  21 153    mC   601.30   105.67   105.64   119.2  94.1  80.8   C2
  20 153    mC   601.30   105.67   105.64   119.2  94.1  80.8   C2
  19 140    mC   105.67   601.30   105.64    94.1 119.2  80.8   C2
  18 139    mC   105.64   601.47   105.67    94.0 119.2  80.7   C2
  17 122    oF   106.93   182.27   603.08    89.0 100.1  90.0   F222
  16 113    mC   182.27   106.93   316.57    80.4 107.8  90.0   C2
  15  66    oP   105.64   105.67   296.85    91.0  89.1 119.2   P222,P2221,P21212,P212121
  14  66    tP   105.64   105.67   296.85    91.0  89.1 119.2   P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
  13  61    mP   105.67   105.64   296.85    89.1  91.0 119.2   P2,P21
  12  61    mP   105.67   105.64   296.85    89.1  91.0 119.2   P2,P21
  11  51    mC   182.27   106.93   345.49    89.9 120.8  90.0   C2
  10  17    hP   105.64   105.67   296.85    91.0  89.1 119.2   P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
                                                                P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
   9  16    oC   105.64   184.50   296.85    89.4  89.1  90.8   C222,C2221
   8  14    oC   106.93   182.27   296.85    91.0  90.1  90.0   C222,C2221
   7  14    mC   106.93   182.27   296.85    91.0  90.1  90.0   C2
   6  14    mP   105.64   296.85   105.67    91.0 119.2  89.1   P2,P21
   5  11    mC   184.50   105.64   296.85    89.1  90.6  89.2   C2
   4   7    mC   105.67   184.45   296.85    89.6  91.0  89.2   C2
   3   4    aP   105.64   105.67   296.85    91.0  89.1 119.2   P1
   2   1    mC   182.27   106.93   296.85    89.9  91.0  90.0   C2
   1   0    aP   105.64   105.67   296.85    89.0  89.1  60.8   P1
 No PENALTY SDCELL FRACN LATT      a        b        c     alpha  beta gamma  Possible spacegroups

The solution and direct beam position will now be refined; reflections which deviate by more
than the sigma cutoff from their calculated position will be excluded from the refinement.

Refining solution #28 with H3     (number 146) symmetry imposed

Initial cell (before refinement) is  106.2866  106.2866  905.7405  90.000  90.000 120.000
Using  140 indexed reflections (out of  140 spots found, {delta(XY) <= 2.5 sigma}),
final sd in spot positions is 0.65mm and in phi 0.96 degrees
Refined cell parameters  107.27  107.27  894.68  90.00  90.00 120.00
Beam coordinates of  93.63  95.18 have been refined to  93.74  95.22
***** WARNING ***** WARNING ***** WARNING ***** WARNING ***** WARNING ***** WARNING 
This is a shift of  0.12mm or  0.452 times the minimum spot separation of ca  0.26mm.
  Final cell (after refinement) is   107.2668  107.2668  894.6829  90.000  90.000 120.000

 FORMATTED      UNKNOWN file opened on unit  12

 Logical name: autoindex.mat, Filename: autoindex.mat


Updating the stored central beam position from   9363.000  9518.500 to   9426.329  9521.846

 ****** INFORMATION *****
 ****** INFORMATION *****
 ****** INFORMATION *****
 The cell derived from autoindexing will override that given on the CELL keyword.
 To force the program to use the input cell, add the keyword KEEP. eg:
 CELL KEEP 74.2 74.2 35.1 90 90 90


 **** WARNING ****
 Because input wavelength ( 0.9340) is not CuKa (1.5418) or Mo (0.7107),
 source is assumed to be a synchrotron and synchrotron defaults for polarisation and beam divergence
 will be used if these have not been defined explicitly (SYNCH POLAR and DIVH/DIVV keywords.


  (Q)QOPEN: file opened on unit  1      Status: UNKNOWN

 Logical Name: ref-dntr_1.gen      Filename: ref-dntr_1.gen




 Title for MTZ and GENERATE Files (TITLE):
 .
 Crystal identifier (IDENT): ref-dntr_1

********************************************************************************
 Warning!! No PROTEIN NAME GIVEN by KeyWord PNAME
 It has been set to be "Unspecified"
********************************************************************************

********************************************************************************
 Warning!! No DATA SET NAME GIVEN by KeyWord DNAME
 It has been set to be "Unspecified"
********************************************************************************
  PSIX changed by  0.00 Degrees and CCOMEGA set to 0.000

  MAX. No. of Active Reflections=    80

 Beam divergence refinement

 Beam divergence refinement

 Beam divergence refinement


 More than 1000 Reflections LOST/GAINED per STEP
 RERUN with smaller STEP SIZE


 ************ Version 6.2.3 (beta test 1.6) for Image plate and CCD data 4th November 2002  ***********
 A.G.W. Leslie, MRC Laboratory Of Molecular Biology, HILLS ROAD, CAMBRIDGE CB2 2QH, UK
 E-mail andrew@mrc-lmb.cam.ac.uk
 New auto-indexing using DPS due to Ingo Steller Robert Bolotovsky and Michael Rossmann
 (1998) J. Appl. Cryst. 30, 1036-1040
 Original auto-indexing using REFIX due to Wolfgang Kabsch (Kabsch,W. (1993),
J.Appl.Cryst. 24,795-800.)
 X-windows interface using xdl_view due to John Campbell (Daresbury Laboratory, UK.)
 (Campbell,J.W. (1995) J. Appl. Cryst. 28, 236-242.


 ===> newmat autoindex.mat
 ===> template ref-dntr_1_###.img
 ===> directory /scisoft/pxsoft/data/dna_061202
 ===> detector adsc
 ===> beam 93.630000 95.185000
 ===> autoindex threshold 10 dps image 1
Using DPS code for background indexing
 ===> autoindex threshold 10 dps image 2
Using DPS code for background indexing
 ===> mosaic estimate
 ===> go

  (Q)QOPEN: file opened on unit  1      Status: READONLY

 Logical Name: /scisoft/pxsoft/data/dna_061202/ref-dntr_1_001.img      Filename: /scisoft/pxsoft/data/dna_061202/ref-dntr_1_001.img



 Crystal to detector distance of  249.99mm taken from image header

 Wavelength of 0.93400A taken from image header

 Pixel size of 0.0816mm taken from image header.
 IBEAM =  2 it should be 2

 Input beam coordinates   93.63mm   95.18mm will be used


 Autoindexing using  2 images
 Image numbers:     1    2
 image FILENAME: /scisoft/pxsoft/data/dna_061202/ref-dntr_1_001.img

  (Q)QOPEN: file opened on unit  1      Status: READONLY

 Logical Name: /scisoft/pxsoft/data/dna_061202/ref-dntr_1_001.img      Filename: /scisoft/pxsoft/data/dna_061202/ref-dntr_1_001.img


 Determining best threshold for spot finding.
 Default parameters may be reset with SPOTS keyword.
 Minimum radius   9.4mm, maximum radius 37.60mm, minimum number of spots 10

 Background strip overlaps gap between detector tiles, so YOFFSET changed to   4.2mm
 sorting  82 spots
 Threshold set to    4.3
 sorting  87 spots
 Threshold set to    4.2


 Finding spots on image     1 (Midpoint of phi   0.250 degrees)
 Calculating radial background..... 
 The background is radial along the X (slow) direction
 The average of  51 pixels, excluding outliers, is used
 The scan is offset by 4.7mm from the image centre in Y to avoid any
 backstop shadow
 Radial Background calculation complete
 RADIUS   9.4   9.7  10.0  10.4  10.7  11.0  11.3  11.7  12.0  12.3  12.6  13.0
 BACKG    163   163   163   163   164   163   164   163   163   166   166   166
 SIGMA     12    12    12    12    12    12    12    12    12    12    12    12
 NREJ       0     0     0     0     0     0     0     0     0     0     0     2
 RADIUS  13.3  13.6  14.0  14.3  14.6  14.9  15.3  15.6  15.9  16.2  16.6  16.9
 BACKG    167   165   164   164   166   163   164   165   165   166   165   166
 SIGMA     12    12    12    12    12    12    12    12    12    12    12    12
 NREJ       2     0     0     0     0     0     0     0     0     0     0     0
 RADIUS  17.2  17.5  17.9  18.2  18.5  18.8  19.2  19.5  19.8  20.2  20.5  20.8
 BACKG    164   166   167   166   166   166   166   166   164   162   163   163
 SIGMA     12    12    12    12    12    12    12    12    12    12    12    12
 NREJ       0     0     0     0     0     0     0     0     1     0     0     0
 RADIUS  21.1  21.5  21.8  22.1  22.4  22.8  23.1  23.4  23.7  24.1  24.4  24.7
 BACKG    162   163   164   163   161   162   159   158   158   159   157   157
 SIGMA     12    12    12    12    12    12    12    12    12    12    12    12
 NREJ       0     0     0     0     0     0     0     0     0     0     0     0
 RADIUS  25.1  25.4  25.7  26.0  26.4  26.7  27.0  27.3  27.7  28.0  28.3  28.6
 BACKG    156   156   156   156   153   154   154   153   153   151   154   150
 SIGMA     12    12    12    12    12    12    12    12    12    12    12    12
 NREJ       0     0     0     0     0     0     0     0     0     0     0     0
 RADIUS  29.0  29.3  29.6  29.9  30.3  30.6  30.9  31.3  31.6  31.9  32.2  32.6
 BACKG    149   151   151   148   148   148   148   147   147   148   146   144
 SIGMA     12    12    12    12    12    12    12    12    12    12    12    12
 NREJ       0     0     1     0     0     0     0     0     0     0     0     0
 RADIUS  32.9  33.2  33.5  33.9  34.2  34.5  34.8  35.2  35.5  35.8  36.1  36.5
 BACKG    145   146   144   144   144   142   143   143   142   141   143   144
 SIGMA     12    12    12    12    12    11    11    11    11    11    11    11
 NREJ       0     0     0     1     0     0     0     0     0     0     1     0
 RADIUS  36.8  37.1  37.5  37.8  38.1  38.4  38.8  39.1  39.4  39.7  40.1  40.4
 BACKG    142   141   140   142   141   141   140   139   140   140   139   139
 SIGMA     11    11    11    11    11    11    11    11    11    11    11    11
 NREJ       0     0     0     0     0     0     0     0     0     0     0     0
 RADIUS  40.7  41.0  41.4  41.7  42.0  42.4  42.7  43.0  43.3  43.7  44.0  44.3
 BACKG    138   139   139   139   139   138   139   139   137   137   139   140
 SIGMA     11    11    11    11    11    11    11    11    11    11    11    11
 NREJ       0     0     0     0     0     0     0     0     0     0     0     0
 RADIUS  44.6  45.0  45.3  45.6  45.9  46.3  46.6  46.9  47.2  47.6  47.9  48.2
 BACKG    139   140   139   141   138   139   140   139   141   141   140   141
 SIGMA     11    11    11    11    11    11    11    11    11    11    11    11
 NREJ       0     0     0     0     1     0     0     1     0     0     0     0
 RADIUS  48.6  48.9  49.2  49.5  49.9  50.2  50.5  50.8  51.2  51.5  51.8  52.1
 BACKG    143   143   144   143   144   145   145   147   149   149   150   151
 SIGMA     11    11    12    11    11    12    12    12    12    12    12    12
 NREJ       0     0     0     1     0     0     1     0     0     0     1     0
 RADIUS  52.5  52.8  53.1  53.4  53.8  54.1  54.4  54.8  55.1  55.4  55.7  56.1
 BACKG    152   152   155   158   158   160   160   159   159   158   158   159
 SIGMA     12    12    12    12    12    12    12    12    12    12    12    12
 NREJ       0     0     0     0     0     0     1     1     0     2     0     0
 RADIUS  56.4  56.7  57.0  57.4  57.7  58.0  58.3  58.7  59.0  59.3  59.6  60.0
 BACKG    158   158   157   158   158   158   159   158   161   158   158   158
 SIGMA     12    12    12    12    12    12    12    12    12    12    12    12
 NREJ       0     0     0     1     0     2     0     0     0     0     0     0
 RADIUS  60.3  60.6  61.0  61.3  61.6  61.9  62.3  62.6  62.9  63.2  63.6  63.9
 BACKG    160   163   163   161   164   164   167   165   166   166   166   168
 SIGMA     12    12    12    12    12    12    12    12    12    12    12    12
 NREJ       0     1     4     2     1     1     0     0     2     0     0     0
 RADIUS  64.2  64.5  64.9  65.2  65.5  65.9  66.2  66.5  66.8  67.2  67.5  67.8
 BACKG    168   166   167   166   165   164   162   163   161   158   158   157
 SIGMA     12    12    12    12    12    12    12    12    12    12    12    12
 NREJ       0     0     0     0     0     0     2     0     1     0     0     0
 RADIUS  68.1  68.5  68.8  69.1  69.4  69.8  70.1  70.4  70.7  71.1  71.4  71.7
 BACKG    158   156   152   152   151   152   150   149   147   145   147   146
 SIGMA     12    12    12    12    12    12    12    12    12    12    12    12
 NREJ       0     0     0     0     0     0     0     0     0     1     0     0
 RADIUS  72.1  72.4  72.7  73.0  73.4  73.7  74.0  74.3  74.7  75.0  75.3  75.6
 BACKG    143   144   142   144   141   142   141   139   139   136   135   135
 SIGMA     11    12    11    11    11    11    11    11    11    11    11    11
 NREJ       0     0     1     0     0     0     0     0     0     2     0     0
 RADIUS  76.0  76.3  76.6  76.9  77.3  77.6  77.9  78.3  78.6  78.9  79.2  79.6
 BACKG    137   134   134   134   131   131   130   129   129   127   128   126
 SIGMA     11    11    11    11    11    11    11    11    11    11    11    11
 NREJ       0     0     0     0     0     0     0     0     0     0     0     0
 RADIUS  79.9  80.2  80.5  80.9  81.2  81.5  81.8  82.2  82.5  82.8  83.2  83.5
 BACKG    127   126   125   125   126   124   123   123   122   121   119   119
 SIGMA     11    11    11    11    11    11    11    11    11    11    10    10
 NREJ       0     1     0     0     0     0     0     0     0     0     0     0
 RADIUS  83.8  84.1  84.5
 BACKG    119   118    58
 SIGMA     10    10     5
 NREJ       0     0     0

 Starting spot search...
 sorting  274 spots

  Median spot size is   3 x   3 pixels

  Total number of spots found: 274
  Number rejected as too small on X:   0
  Number rejected as too small on Y:   0
  Number rejected as too big on X:   1
  Number rejected as too big on Y:   0
  Number too close (SEPARATION keyword):   0
  Number stored as OK: 273



             Number of spots found in each bin
              14   8   6   8  10   7   7  17
              13   8   8   9  14   3   6  12
              12   5  12  12  12  14   7   9
               5   4   7   3   4   3   4   4
               0   0   3   0   0   0   2   1

 Determining average spot size for spots in centre of image.
 ==========================================================
 Finding spot size around direct beam position
 Default parameters may be reset with SPOTS keyword.
 Minimum radius   9.4mm, maximum radius 37.60mm, minimum number of spots 10
 sorting  88 spots

 Based on a median spot size of  4 by  4 pixels in X and Y, the measurement box 
 parameters have been set to  15  15   9   5   5
 The overall size of the box has been fixed.
 To prevent this use keywords PROFILE NOFIXBOX.
 ***** WARNING ***** Lattice type not specified, so assumed primitive

 Based on a median spot size of  4 by  4 pixels in X and Y, the spot separation 
 parameters (in X and Y) have been set to  0.48  0.48mm.
 Closest possible spot separation is  0.00mm.

 Because the minimum possible spot separation is less than the estimated spot
 size plus a safety margin of 2 pixels (set by keywords SPOTS SAFE) the
 "CLOSE" option for integration has been set.
 ****************************************************
 ****************************************************
 It is advisable to ensure that all images for this dataset are also
 processed using the "CLOSE" option by explicitly including keywords:
 SEPARATION CLOSE
 ****************************************************
 ****************************************************
 image FILENAME: /scisoft/pxsoft/data/dna_061202/ref-dntr_1_002.img

  (Q)QOPEN: file opened on unit  1      Status: READONLY

 Logical Name: /scisoft/pxsoft/data/dna_061202/ref-dntr_1_002.img      Filename: /scisoft/pxsoft/data/dna_061202/ref-dntr_1_002.img




 Finding spots on image     2 (Midpoint of phi  89.750 degrees)
 Calculating radial background..... 
 The background is radial along the X (slow) direction
 The average of  51 pixels, excluding outliers, is used
 The scan is offset by 4.7mm from the image centre in Y to avoid any
 backstop shadow
 Radial Background calculation complete
 RADIUS   9.4   9.7  10.0  10.4  10.7  11.0  11.3  11.7  12.0  12.3  12.6  13.0
 BACKG    161   161   161   164   163   163   162   161   163   163   163   163
 SIGMA     12    12    12    12    12    12    12    12    12    12    12    12
 NREJ       0     0     0     0     0     0     0     0     0     0     0     0
 RADIUS  13.3  13.6  14.0  14.3  14.6  14.9  15.3  15.6  15.9  16.2  16.6  16.9
 BACKG    163   162   163   165   165   165   163   163   163   167   164   164
 SIGMA     12    12    12    12    12    12    12    12    12    12    12    12
 NREJ       0     0     0     0     4     0     0     0     0     0     0     0
 RADIUS  17.2  17.5  17.9  18.2  18.5  18.8  19.2  19.5  19.8  20.2  20.5  20.8
 BACKG    165   164   164   164   163   166   165   163   164   162   164   163
 SIGMA     12    12    12    12    12    12    12    12    12    12    12    12
 NREJ       0     0     0     0     0     0     0     0     0     0     0     0
 RADIUS  21.1  21.5  21.8  22.1  22.4  22.8  23.1  23.4  23.7  24.1  24.4  24.7
 BACKG    163   161   161   161   159   159   158   157   157   158   159   156
 SIGMA     12    12    12    12    12    12    12    12    12    12    12    12
 NREJ       0     0     0     0     0     1     0     0     0     0     0     0
 RADIUS  25.1  25.4  25.7  26.0  26.4  26.7  27.0  27.3  27.7  28.0  28.3  28.6
 BACKG    155   156   155   152   153   152   153   151   151   151   150   148
 SIGMA     12    12    12    12    12    12    12    12    12    12    12    12
 NREJ       0     2     2     0     0     0     0     0     1     0     0     0
 RADIUS  29.0  29.3  29.6  29.9  30.3  30.6  30.9  31.3  31.6  31.9  32.2  32.6
 BACKG    149   148   148   148   148   147   148   147   145   146   144   145
 SIGMA     12    12    12    12    12    12    12    12    12    12    12    12
 NREJ       0     0     0     0     0     0     1     0     0     0     0     0
 RADIUS  32.9  33.2  33.5  33.9  34.2  34.5  34.8  35.2  35.5  35.8  36.1  36.5
 BACKG    145   143   144   144   143   142   143   142   142   141   141   140
 SIGMA     12    11    12    11    11    11    11    11    11    11    11    11
 NREJ       0     0     0     0     0     0     0     0     0     1     0     0
 RADIUS  36.8  37.1  37.5  37.8  38.1  38.4  38.8  39.1  39.4  39.7  40.1  40.4
 BACKG    141   142   141   140   141   141   140   140   138   137   139   140
 SIGMA     11    11    11    11    11    11    11    11    11    11    11    11
 NREJ       0     0     0     1     0     0     0     0     0     0     0     0
 RADIUS  40.7  41.0  41.4  41.7  42.0  42.4  42.7  43.0  43.3  43.7  44.0  44.3
 BACKG    139   137   140   138   138   140   139   140   138   138   139   140
 SIGMA     11    11    11    11    11    11    11    11    11    11    11    11
 NREJ       0     0     0     0     2     0     0     0     0     1     1     0
 RADIUS  44.6  45.0  45.3  45.6  45.9  46.3  46.6  46.9  47.2  47.6  47.9  48.2
 BACKG    140   141   140   140   140   143   143   141   141   142   144   144
 SIGMA     11    11    11    11    11    11    11    11    11    11    11    12
 NREJ       2     2     0     0     0     0     2     0     0     0     0     0
 RADIUS  48.6  48.9  49.2  49.5  49.9  50.2  50.5  50.8  51.2  51.5  51.8  52.1
 BACKG    146   145   147   145   147   150   152   152   154   156   161   162
 SIGMA     12    12    12    12    12    12    12    12    12    12    12    12
 NREJ       0     0     0     0     0     0     0     1     0     0     0     1
 RADIUS  52.5  52.8  53.1  53.4  53.8  54.1  54.4  54.8  55.1  55.4  55.7  56.1
 BACKG    164   169   173   179   180   178   178   180   178   175   174   171
 SIGMA     12    13    13    13    13    13    13    13    13    13    13    13
 NREJ       0     0     0     0     0     0     1     0     0     0     0     0
 RADIUS  56.4  56.7  57.0  57.4  57.7  58.0  58.3  58.7  59.0  59.3  59.6  60.0
 BACKG    172   168   167   167   167   168   167   166   168   169   167   168
 SIGMA     13    12    12    12    12    12    12    12    12    12    12    12
 NREJ       0     0     0     0     0     0     0     0     0     0     0     0
 RADIUS  60.3  60.6  61.0  61.3  61.6  61.9  62.3  62.6  62.9  63.2  63.6  63.9
 BACKG    170   171   174   175   175   177   181   182   183   184   185   185
 SIGMA     13    13    13    13    13    13    13    13    13    13    13    13
 NREJ       0     0     2     0     0     0     0     0     0     0     0     0
 RADIUS  64.2  64.5  64.9  65.2  65.5  65.9  66.2  66.5  66.8  67.2  67.5  67.8
 BACKG    184   183   183   184   181   179   177   174   170   170   168   167
 SIGMA     13    13    13    13    13    13    13    13    13    13    12    12
 NREJ       0     1     1     0     0     2     0     0     0     0     0     0
 RADIUS  68.1  68.5  68.8  69.1  69.4  69.8  70.1  70.4  70.7  71.1  71.4  71.7
 BACKG    162   162   161   159   157   153   153   153   150   150   149   148
 SIGMA     12    12    12    12    12    12    12    12    12    12    12    12
 NREJ       0     0     1     0     0     1     0     1     0     0     0     0
 RADIUS  72.1  72.4  72.7  73.0  73.4  73.7  74.0  74.3  74.7  75.0  75.3  75.6
 BACKG    147   145   144   143   143   142   141   140   138   137   138   137
 SIGMA     12    12    12    11    11    11    11    11    11    11    11    11
 NREJ       0     1     0     0     0     1     0     0     0     0     0     0
 RADIUS  76.0  76.3  76.6  76.9  77.3  77.6  77.9  78.3  78.6  78.9  79.2  79.6
 BACKG    135   134   134   134   132   132   130   131   131   129   127   127
 SIGMA     11    11    11    11    11    11    11    11    11    11    11    11
 NREJ       0     0     0     0     1     0     0     0     0     0     1     0
 RADIUS  79.9  80.2  80.5  80.9  81.2  81.5  81.8  82.2  82.5  82.8  83.2  83.5
 BACKG    127   126   126   125   124   124   121   122   121   119   119   120
 SIGMA     11    11    11    11    11    11    11    11    10    10    10    10
 NREJ       0     0     0     0     0     0     0     1     0     0     0     0
 RADIUS  83.8  84.1  84.5
 BACKG    118   116    59
 SIGMA     10    10     5
 NREJ       0     0     0

 Starting spot search...
 sorting  173 spots

  Median spot size is   4 x   3 pixels

  Total number of spots found: 173
  Number rejected as too small on X:   0
  Number rejected as too small on Y:   0
  Number rejected as too big on X:   0
  Number rejected as too big on Y:   0
  Number too close (SEPARATION keyword):   0
  Number stored as OK: 173



             Number of spots found in each bin
              12  10   5   8  10   2   6  15
               5   4   5   2   4   5   8   6
               4   8   6   4   5   4   6   4
               2   0   3   2   4   3   4   2
               0   2   1   0   1   0   0   1

 FORMATTED      UNKNOWN file opened on unit  10

 Logical name: ref-dntr_1.spt, Filename: ref-dntr_1.spt


   273 spots written for image    1
   173 spots written for image    2
 A total of   446 spots were written to file

 FORMATTED      OLD     file opened on unit  10

 Logical name: ref-dntr_1.spt, Filename: ref-dntr_1.spt


DPS Indexing at Two-theta =    0.00 with  364 reflections (minimum spot separation = 0.24mm. Maximum expected cell edge  306.54, Beam position is   93.63   95.18
Generating direct lattice vectors (This may take some time):
|-----------------|
..................
 Refining  30 direct space vectors:
|----------------------------|
..............................
selected 0
 List of possible Laue groups, sorted on penalty index.
 The lower the PENALTY, the better
 No PENALTY LATT     a        b        c     alpha  beta gamma  Possible spacegroups

  44 999    cI   315.17   107.32   315.42    80.2  34.1  80.4   I23,I213,I432,I4132
  43 999    hR   350.03   315.55   106.71    80.4  90.0  50.2   H3,H32 (hexagonal settings of R3 and R32)
  42 945    cF   315.42   349.46   315.55   142.8  39.7 143.0   F23,F432,F4132
  41 943    tI   315.31   315.55   106.71    80.4  99.7 145.7   I4,I41,I422,I4122
  40 892    tI   315.17   107.32   315.42    80.2  34.1  80.4   I4,I41,I422,I4122
  39 892    hP   107.32   296.70   106.71    89.9 119.9  90.1   P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
                                                                P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
  38 839    tI   315.42   315.17   107.32    80.4  80.2  34.1   I4,I41,I422,I4122
  37 838    oI   106.71   315.55   315.31    34.3  80.3  80.4   I222,I212121
  36 837    oI   106.71   315.31   315.55    34.3  80.4  80.3   I222,I212121
  35 785    cP   106.71   107.25   296.70    90.0  90.1 119.8   P23,P213,P432,P4232,P4332,P4132
  34 784    tP   107.25   296.70   106.71    90.1 119.8  90.0   P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
  33 784    hR   107.25   315.17   350.07   130.1  89.8  99.7   H3,H32 (hexagonal settings of R3 and R32)
  32 784    hR   185.10   315.44   315.31   145.8  89.9 107.0   H3,H32 (hexagonal settings of R3 and R32)
  31 783    mC   315.71   315.31   106.71    99.7  99.8 140.2   C2
  30 783    oC   315.42   315.55   106.71    80.4  99.8  39.7   C222,C2221
  29 783    mC   315.42   315.55   106.71    80.4  99.8  39.7   C2
  28 216    hR   106.71   107.25   908.81    90.0 100.1 119.8   H3,H32 (hexagonal settings of R3 and R32)
  27 214    oF   106.71   186.16   602.77    89.9 100.1  90.0   F222
  26 167    tI   106.71   107.25   602.81    95.1  95.0 119.8   I4,I41,I422,I4122
  25 165    oI   106.71   107.25   602.81    84.9  85.0 119.8   I222,I212121
  24 163    mC   602.77   106.71   107.25   119.8  95.1  79.9   C2
  23 163    oC   106.71   602.77   107.25    84.9 119.8 100.1   C222,C2221
  22 162    mC   106.71   602.77   107.32    94.9 119.9  79.9   C2
  21 162    mI   107.25   602.77   107.32    85.1 120.4  84.9   C2
  20 162    oC   106.71   602.77   107.25    84.9 119.8 100.1   C222,C2221
  19 162    mC   602.77   106.71   107.25   119.8  95.1  79.9   C2
  18 161    mC   106.71   602.77   107.32    94.9 119.9  79.9   C2
  17 110    oF   107.32   185.10   602.81    90.1 100.1  89.7   F222
  16 109    mC   186.16   106.71   315.31    80.3 107.1  90.0   C2
  15  56    tP   106.71   107.25   296.70    90.0  90.1 119.8   P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
  14  56    mC   186.16   106.71   350.03    90.0 122.0  90.0   C2
  13  55    oP   106.71   107.25   296.70    90.0  90.1 119.8   P222,P2221,P21212,P212121
  12  55    mP   107.25   106.71   296.70    90.1  90.0 119.8   P2,P21
  11  54    mP   106.71   107.25   296.70    90.0  90.1 119.8   P2,P21
  10   2    oC   107.32   185.10   296.70    90.0  90.1  89.7   C222,C2221
   9   2    hP   106.71   107.25   296.70    90.0  90.1 119.8   P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
                                                                P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
   8   2    mC   185.22   107.25   296.70    90.0  90.1  90.4   C2
   7   1    mC   107.32   185.10   296.70    90.0  90.1  89.7   C2
   6   1    mP   106.71   296.70   107.25    90.0 119.8  90.1   P2,P21
   5   1    mC   106.71   186.16   296.70    89.9  90.1  90.0   C2
   4   1    mC   186.16   106.71   296.70    90.1  90.1  90.0   C2
   3   1    oC   106.71   186.16   296.70    89.9  90.1  90.0   C222,C2221
   2   0    aP   106.71   107.32   296.70    89.9  89.9  60.1   P1
   1   0    aP   106.71   107.25   296.70    90.0  90.1 119.8   P1
 No PENALTY SDCELL FRACN LATT      a        b        c     alpha  beta gamma  Possible spacegroups

The solution and direct beam position will now be refined; reflections which deviate by more
than the sigma cutoff from their calculated position will be excluded from the refinement.

Refining solution # 9 with P3     (number 143) symmetry imposed

Initial cell (before refinement) is  106.9813  106.9813  296.6982  90.000  90.000 120.000
Using  341 indexed reflections (out of  364 spots found, {delta(XY) <= 2.5 sigma}),
final sd in spot positions is 0.05mm and in phi 0.13 degrees
Refined cell parameters  107.09  107.09  296.67  90.00  90.00 120.00
Beam coordinates of  93.63  95.18 have been refined to  93.71  95.12
This is a shift of  0.11mm or  0.136 times the minimum spot separation of ca  0.79mm.
  Final cell (after refinement) is   107.0922  107.0922  296.6736  90.000  90.000 120.000

 FORMATTED      UNKNOWN file opened on unit  12

 Logical name: autoindex.mat, Filename: autoindex.mat


Updating the stored central beam position from   9363.000  9518.500 to   9429.460  9511.583

 ****** INFORMATION *****
 ****** INFORMATION *****
 ****** INFORMATION *****
 The cell derived from autoindexing will override that given on the CELL keyword.
 To force the program to use the input cell, add the keyword KEEP. eg:
 CELL KEEP 74.2 74.2 35.1 90 90 90


 **** WARNING ****
 Because input wavelength ( 0.9340) is not CuKa (1.5418) or Mo (0.7107),
 source is assumed to be a synchrotron and synchrotron defaults for polarisation and beam divergence
 will be used if these have not been defined explicitly (SYNCH POLAR and DIVH/DIVV keywords.


  (Q)QOPEN: file opened on unit  1      Status: UNKNOWN

 Logical Name: ref-dntr_1.gen      Filename: ref-dntr_1.gen




 Title for MTZ and GENERATE Files (TITLE):
 .
 Crystal identifier (IDENT): ref-dntr_1

********************************************************************************
 Warning!! No PROTEIN NAME GIVEN by KeyWord PNAME
 It has been set to be "Unspecified"
********************************************************************************

********************************************************************************
 Warning!! No DATA SET NAME GIVEN by KeyWord DNAME
 It has been set to be "Unspecified"
********************************************************************************
  PSIX changed by  0.00 Degrees and CCOMEGA set to 0.000

  MAX. No. of Active Reflections=    81

 Beam divergence refinement

 Refining DIV  with stepsize  0.01 Degrees
 Divergence      0.000 0.050 0.100 0.150 0.200 0.250 0.300 0.350 0.400 0.450 0.500 0.550 0.600 0.650 0.700 0.750 0.800 0.850 0.900
 Divergence      0.950 1.000
 No gained           0   406   387   361   412   395   428   365   399   426   417   390   394   398   402   394   355   406   428
 No gained         370   400
 Total intensity 74330 82904 88849 94556 96417 97689 99018 99732 99997 99704 99760 99676 99396 99746 99788 99774 99592 99368 99368
 Total intensity 99368 99200
 SD of intensity   587   629   657   685   713   727   755   769   797   811   839   853   881   895   909   937   951   965   979
 SD of intensity   993  1021
 The mosaicity has been estimated as ---> 0.21 <--- for this image only; 
This value can be used cautiously as an initial estimate.
Storing space group from DPS autoindexing: P3         number 143
Storing space group from DPS autoindexing: P3         number 143



 *********** END OF PROCESSING *****************
/n/n