Index results for ntest1_1

Symmetry and refined cell parameters

Image Symmetry a b c alpha beta gamma
1 P222 54.775 58.060 67.294 90.000 90.000 90.000
2 P4 54.837 54.837 67.286 90.000 90.000 90.000
1+2 P222 54.787 58.068 67.200 90.000 90.000 90.000

Spots found, rejected, RMS spot deviation, beamcentre shift

Image Spots found Spots rejected Fraction RMS spot deviation Beam shift x Beam shift y
1 236 37 0.157 0.090 0.015 -0.265
2 218 25 0.115 0.100 0.025 -0.195
1+2 454 62 0.137 0.100 0.005 -0.285

Image 1: /scisoft/pxsoft/data/dna_040402/ref-ntest1_1_001.img

Image 2: /scisoft/pxsoft/data/dna_040402/ref-ntest1_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-ntest1_1_###.img
 ===> directory /scisoft/pxsoft/data/dna_040402
 ===> 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_040402/ref-ntest1_1_001.img      Filename: /scisoft/pxsoft/data/dna_040402/ref-ntest1_1_001.img



 Crystal to detector distance of  249.95mm taken from image header

 Wavelength of 0.93300A taken from image header

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

***** WARNING *****
***** WARNING *****
***** WARNING *****
***** WARNING *****
 Input beam coordinates   93.63mm   95.18mm DO NOT agree with 
 those calculated from the image header (  93.58mm   92.24mm)


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

 image FILENAME: /scisoft/pxsoft/data/dna_040402/ref-ntest1_1_001.img

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

 Logical Name: /scisoft/pxsoft/data/dna_040402/ref-ntest1_1_001.img      Filename: /scisoft/pxsoft/data/dna_040402/ref-ntest1_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  214 spots
 Threshold set to    4.2
 sorting  267 spots
 Threshold set to    4.2


 Finding spots on image     1 (Midpoint of phi   0.500 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    318   312   309   306   299   293   293   287   281   277   274   271
 SIGMA     17    17    17    17    17    17    17    16    16    16    16    16
 NREJ      23    22    18    15    15    16    10    10    10     8     3     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    266   261   252   249   246   242   237   234   228   225   223   218
 SIGMA     16    16    15    15    15    15    15    15    15    15    14    14
 NREJ       3     5     8     5     2     1     2     1     2     1     0     1
 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    215   211   208   204   200   199   193   192   188   185   182   180
 SIGMA     14    14    14    14    14    14    13    13    13    13    13    13
 NREJ       0     0     0     0     0     0     1     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    177   175   175   172   169   165   163   161   159   156   154   153
 SIGMA     13    13    13    13    13    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    149   148   145   143   141   140   137   136   134   131   130   128
 SIGMA     12    12    12    11    11    11    11    11    11    11    11    11
 NREJ       0     0     0     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    127   126   124   124   122   121   119   118   117   117   114   113
 SIGMA     11    11    11    11    11    11    10    10    10    10    10    10
 NREJ       0     0     0     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    112   110   109   108   107   105   105   103   103   102   100    98
 SIGMA     10    10    10    10    10    10    10    10    10    10    10     9
 NREJ       0     0     0     0     0     0     0     0     0     0     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     98    97    96    95    93    93    92    91    91    89    88    87
 SIGMA      9     9     9     9     9     9     9     9     9     9     9     9
 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     86    86    85    84    84    83    83    81    82    80    79    78
 SIGMA      9     9     9     9     9     9     9     9     9     8     8     8
 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     78    79    79    77    77    76    75    74    73    73    73    73
 SIGMA      8     8     8     8     8     8     8     8     8     8     8     8
 NREJ       0     0     4    10     7     0     0     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     73    72    71    70    70    70    70    70    69    68    68    67
 SIGMA      8     8     8     8     8     8     8     8     8     8     8     8
 NREJ       0     0     0     0     0     0     0     0     0     0     0     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     66    67    66    66    65    64    65    64    65    64    64    64
 SIGMA      8     8     8     8     8     8     8     8     8     8     8     7
 NREJ       0     0     0     0     0     0     0     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     63    63    63    63    63    63    63    63    63    62    61    61
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     0     0     0     0     7     9     2     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     61    61    62    61    62    62    61    62    63    62    61    61
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     0     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     61    61    60    61    60    60    60    58    59    57    58    58
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     0     0     0     0     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     57    58    57    57    56    57    57    55    56    55    55    55
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     0     0     0     0     0     0     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     54    53    54    54    53    53    53    52    52    51    50    50
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     0     0     0     0     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     50    50    51    50    51    49    48    47    46    46    47    46
 SIGMA      7     7     7     7     7     7     6     6     6     6     6     6
 NREJ       0     0     5     7     0     1     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     46    46    45    45    45    45    45    44    44    43    42    42
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     0     0     0     1     0     0     0     0     0     0     0
 RADIUS  83.8  84.1  84.5
 BACKG     43    42    21
 SIGMA      6     6     3
 NREJ       0     0     0

 Starting spot search...
 sorting  479 spots

  Median spot size is   8 x   7 pixels

  Total number of spots found: 479
  Number rejected as too small on X:  55
  Number rejected as too small on Y:  43
  Number rejected as too big on X:  15
  Number rejected as too big on Y:  33
  Number too close (SEPARATION keyword):   0
  Number stored as OK: 333



             Number of spots found in each bin
              41  36  30  28  11   2   0   5
               4   4   4   7   7   1   5   5
               5   5   3   9   9   4   5  11
               8   6   2   6   6   4   2   9
               8   2   4  10   7   5   6   7

 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  269 spots

 Based on a median spot size of  9 by  8 pixels in X and Y, the measurement box 
 parameters have been set to  23  21  12   6   6
 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  9 by  8 pixels in X and Y, the spot separation 
 parameters (in X and Y) have been set to  0.89  0.81mm.
 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-ntest1_1.spt, Filename: ref-ntest1_1.spt


   333 spots written for image    1
 A total of   333 spots were written to file

 FORMATTED      OLD     file opened on unit  10

 Logical name: ref-ntest1_1.spt, Filename: ref-ntest1_1.spt


DPS Indexing at Two-theta =    0.00 with  193 reflections (minimum spot separation = 0.65mm. Maximum expected cell edge  267.90, Beam position is   93.63   95.18
Generating direct lattice vectors (This may take some time):
|-----------------|
..................
 Refining  30 direct space vectors:
|----------------------------|
..............................
selected 1
 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    hR   208.63   163.76    58.03    90.2  74.5  90.7   H3,H32 (hexagonal settings of R3 and R32)
  43 964    tI   144.16   139.52   104.22    83.1  66.7  43.3   I4,I41,I422,I4122
  42 903    tI   139.52   104.22   144.16    66.7  43.3  83.1   I4,I41,I422,I4122
  41 901    oI   104.22   139.52   144.16    43.3  66.7  83.1   I222,I212121
  40 896    cI   139.52   104.22   144.16    66.7  43.3  83.1   I23,I213,I432,I4132
  39 872    cF   156.07   154.73   173.51   116.3  78.8 136.1   F23,F432,F4132
  38 790    tI   144.16   173.51    58.03    70.7  89.3 110.1   I4,I41,I422,I4122
  37 696    hR   104.82   139.52   173.98   126.4  72.0 109.3   H3,H32 (hexagonal settings of R3 and R32)
  36 692    hR   104.82   140.56   154.73   121.6  80.2  97.7   H3,H32 (hexagonal settings of R3 and R32)
  35 673    oI    58.03   144.16   173.51    69.9  70.7  90.7   I222,I212121
  34 635    cP    58.03    86.93   127.45    97.8  90.6  90.4   P23,P213,P432,P4232,P4332,P4132
  33 584    hP    86.93   127.45    58.03    90.6  90.4  97.8   P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
                                                                P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
  32 492    hR    58.03   104.82   384.14    89.8  98.0 124.0   H3,H32 (hexagonal settings of R3 and R32)
  31 460    oF   104.82   104.22   263.64   106.3  92.7  67.5   F222
  30 451    tP    86.93   127.45    58.03    90.6  90.4  97.8   P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
  29 410    oF    58.03   183.63   260.87    78.8 102.3 108.8   F222
  28 398    mI    58.03   263.64    86.93    78.7  89.6 102.0   C2
  27 397    hP    58.03    86.93   127.45    97.8  90.6  90.4   P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
                                                                P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
  26 386    mC   163.76   144.16    58.03    89.3  90.2 111.6   C2
  25 385    oC   144.16   163.76    58.03    90.2  90.7  68.4   C222,C2221
  24 384    mC   104.22   104.82   127.45    96.2  96.8  67.5   C2
  23 382    mC   144.16   163.76    58.03    90.2  90.7  68.4   C2
  22 341    oI    58.03    86.93   263.64   101.3 102.0  90.4   I222,I212121
  21 341    tI    58.03    86.93   263.64    78.7  78.0  90.4   I4,I41,I422,I4122
  20 293    mC   183.63    58.03   144.16    90.7 117.4  71.2   C2
  19 281    mC    58.03   183.63   127.45    82.8  90.6  71.2   C2
  18 276    mC    58.03   260.87    86.93    82.3  89.6  77.7   C2
  17 254    tP    58.03    86.93   127.45    97.8  90.6  90.4   P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
  16 253    oC   104.22   104.82   127.45    96.2  96.8  67.5   C222,C2221
  15 248    mC   104.22   104.82   127.45    83.8  96.8 112.5   C2
  14 246    mC   104.22   104.82   127.45    96.2  96.8  67.5   C2
  13 214    oC    58.03   182.94   127.45    82.4  90.6 108.1   C222,C2221
  12 209    oC    58.03   260.87    86.93    82.3  90.4 102.3   C222,C2221
  11 208    mC    86.93   257.86    58.03    89.3  89.6  78.3   C2
  10 203    oC    86.93   257.86    58.03    89.3  90.4 101.7   C222,C2221
   9 200    mC   257.86    86.93    58.03    90.4  90.7  78.3   C2
   8 148    mC   182.94    58.03   127.45    90.6  97.6  71.9   C2
   7 143    mC   260.87    58.03    86.93    90.4  97.7  77.7   C2
   6  71    oP    58.03    86.93   127.45    97.8  90.6  90.4   P222,P2221,P21212,P212121
   5  69    mP    58.03   127.45    86.93    97.8  90.4  90.6   P2,P21
   4  67    mP    58.03    86.93   127.45    97.8  90.6  90.4   P2,P21
   3   5    mP    86.93    58.03   127.45    90.6  97.8  90.4   P2,P21
   2   1    aP    58.03    86.93   127.45    82.2  89.4  90.4   P1
   1   0    aP    58.03    86.93   127.45    97.8  90.6  90.4   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 # 3 with P2     (number   3) symmetry imposed

Initial cell (before refinement) is   86.9275   58.0342  127.4495  90.000  97.829  90.000
Using  190 indexed reflections (out of  193 spots found, {delta(XY) <= 2.5 sigma}),
final sd in spot positions is 0.16mm and in phi 0.26 degrees
Refined cell parameters   86.92   58.07  126.29  90.00  98.03  90.00
Beam coordinates of  93.63  95.18 have been refined to  93.41  95.01
This is a shift of  0.28mm or  0.104 times the minimum spot separation of ca  2.71mm.
  Final cell (after refinement) is    86.9196   58.0652  126.2925  90.000  98.031  90.000

 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   9459.473  9500.791

 ****** 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 ( 0.9330) 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-ntest1_1.gen      Filename: ref-ntest1_1.gen




 Title for MTZ and GENERATE Files (TITLE):
 .
 Crystal identifier (IDENT): ref-ntest1_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=    35

 Beam divergence refinement

 Beam divergence refinement

 Refining DIV  with stepsize  0.01 Degrees
 Divergence      0.000 0.100 0.200 0.300 0.400 0.500 0.600 0.700 0.800 0.900 1.000 1.100 1.200 1.300 1.400 1.500 1.600 1.700 1.800
 Divergence      1.900 2.000
 No gained          87   173   173   147   196   152   174   175   165   168   167     3     5     2     0     3     1     1     2
 No gained           0     2
 Total intensity 86512 94835 96112 96465 96576 99779 99978 99983 99990 99998 99990 99989 99983 99983 99983 99981 99983 99981 99985
 Total intensity 99985 99985
 SD of intensity   126   131   132   132   133   138   138   139   140   140   141   141   141   141   141   141   141   141   141
 SD of intensity   141   141
 The mosaicity has been estimated as ---> 0.45 <--- for this image only; 
This value can be used cautiously as an initial estimate.
Storing space group from DPS autoindexing: P2         number   3



 *********** 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-ntest1_1_###.img
 ===> directory /scisoft/pxsoft/data/dna_040402
 ===> detector adsc
 ===> beam 93.585000 92.245000
 ===> 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_040402/ref-ntest1_1_001.img      Filename: /scisoft/pxsoft/data/dna_040402/ref-ntest1_1_001.img



 Crystal to detector distance of  249.95mm taken from image header

 Wavelength of 0.93300A taken from image header

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

 Input beam coordinates   93.58mm   92.24mm will be used


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

 image FILENAME: /scisoft/pxsoft/data/dna_040402/ref-ntest1_1_001.img

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

 Logical Name: /scisoft/pxsoft/data/dna_040402/ref-ntest1_1_001.img      Filename: /scisoft/pxsoft/data/dna_040402/ref-ntest1_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  30 spots
 Threshold set to    4.4
 sorting  29 spots
 Threshold set to    4.3


 Finding spots on image     1 (Midpoint of phi   0.500 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    382   372   373   357   356   346   334   333   324   316   309   301
 SIGMA     19    19    19    18    18    18    18    18    17    17    17    17
 NREJ      19    21     7    16     7     7     7     2     4     4     2     1
 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    296   289   284   276   269   264   260   253   248   245   239   235
 SIGMA     17    17    16    16    16    16    16    15    15    15    15    15
 NREJ       1     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    228   224   222   216   213   211   206   204   200   196   192   189
 SIGMA     15    14    14    14    14    14    14    14    14    13    13    13
 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    185   184   180   179   176   172   171   168   164   163   160   158
 SIGMA     13    13    13    13    13    13    13    12    12    12    12    12
 NREJ       0     0     0     0     0     0     0     0     0     0     0     1
 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   153   150   148   146   144   142   141   139   136   133   132
 SIGMA     12    12    12    12    12    12    11    11    11    11    11    11
 NREJ       0     0     0     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    133   130   127   127   124   123   122   120   119   118   116   115
 SIGMA     11    11    11    11    11    11    11    10    10    10    10    10
 NREJ       0     0     0     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    115   112   112   109   109   108   107   105   105   104   102   100
 SIGMA     10    10    10    10    10    10    10    10    10    10    10    10
 NREJ       0     0     0     0     0     0     0     0     0     0     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    101    99    97    96    95    95    93    92    92    89    90    89
 SIGMA     10     9     9     9     9     9     9     9     9     9     9     9
 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     87    88    86    85    84    84    82    83    81    81    80    79
 SIGMA      9     9     9     9     9     9     9     9     9     9     8     8
 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     79    78    77    77    77    76    75    75    74    74    73    73
 SIGMA      8     8     8     8     8     8     8     8     8     8     8     8
 NREJ       0     0     0     0     0     0     0     0     0     0     1     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     73    73    74    72    72    72    71    70    69    68    68    68
 SIGMA      8     8     8     8     8     8     8     8     8     8     8     8
 NREJ       0     0     5    11     9     0     0     0     0     0     0     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     67    67    66    66    66    65    65    65    65    64    65    63
 SIGMA      8     8     8     8     8     8     8     8     8     8     8     7
 NREJ       0     0     0     0     0     0     0     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     63    64    64    63    63    63    63    64    63    62    61    62
 SIGMA      7     8     8     7     7     7     7     7     7     7     7     7
 NREJ       0     0     0     0     0     1     7     7     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     61    61    61    61    61    62    61    62    62    61    60    60
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     0     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     61    61    61    61    60    59    59    59    59    58    58    58
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     0     0     0     0     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     59    58    57    57    56    57    57    56    56    56    57    56
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     0     0     0     0     0     0     0     0     6    11
 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     55    55    54    53    54    53    52    52    52    52    51    50
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       8     0     0     0     0     0     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     51    51    50    48    48    49    48    47    47    47    47    46
 SIGMA      7     7     7     6     6     6     6     6     6     6     6     6
 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     46    46    46    45    45    45    45    44    43    43    43    42
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     0     1     4     1     0     0     1     0     0     0     0
 RADIUS  83.8  84.1  84.5
 BACKG     43    42    21
 SIGMA      6     6     3
 NREJ       0     0     0

 Starting spot search...
 sorting  236 spots

  Median spot size is   7 x   7 pixels

  Total number of spots found: 236
  Number rejected as too small on X:  27
  Number rejected as too small on Y:   8
  Number rejected as too big on X:   2
  Number rejected as too big on Y:   0
  Number too close (SEPARATION keyword):   0
  Number stored as OK: 199



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

 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  31 spots

 Based on a median spot size of  7 by  7 pixels in X and Y, the measurement box 
 parameters have been set to  21  21  12   6   6
 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  7 by  7 pixels in X and Y, the spot separation 
 parameters (in X and Y) have been set to  0.73  0.73mm.
 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-ntest1_1.spt, Filename: ref-ntest1_1.spt


   199 spots written for image    1
 A total of   199 spots were written to file

 FORMATTED      OLD     file opened on unit  10

 Logical name: ref-ntest1_1.spt, Filename: ref-ntest1_1.spt


DPS Indexing at Two-theta =    0.00 with  189 reflections (minimum spot separation = 0.57mm. Maximum expected cell edge  267.90, Beam position is   93.58   92.24
Generating direct lattice vectors (This may take some time):
|-----------------|
..................
 Refining  30 direct space vectors:
|----------------------------|
..............................
selected 24
 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    hR   143.64    89.18    54.58    90.2  68.2 100.4   H3,H32 (hexagonal settings of R3 and R32)
  43 791    cF   104.20   103.19   104.42   112.0 100.0 116.5   F23,F432,F4132
  42 776    cI    86.06    79.44    88.17    62.1  54.6  65.1   I23,I213,I432,I4132
  41 754    tI    88.17   104.42    54.58    58.6  89.4  96.7   I4,I41,I422,I4122
  40 719    mI    54.58   154.83    58.05    68.7  90.3  70.0   C2
  39 705    hR    54.58    79.93   215.13    91.2 104.1 133.4   H3,H32 (hexagonal settings of R3 and R32)
  38 668    oF    54.58   128.60   144.29    80.3 111.7 115.5   F222
  37 587    tI    88.17    86.06    79.44    65.1  62.1  54.6   I4,I41,I422,I4122
  36 587    tI    86.06    79.44    88.17    62.1  54.6  65.1   I4,I41,I422,I4122
  35 586    oI    79.44    86.06    88.17    54.6  62.1  65.1   I222,I212121
  34 536    oI    54.58    89.18   103.19    83.1  58.7  90.2   I222,I212121
  33 501    oF    79.44    79.93   154.83    91.7 120.0  86.5   F222
  32 500    mC    79.93    79.44    86.06    65.1 116.0  86.5   C2
  31 475    tI    54.58    58.05   154.83    68.7  70.0  90.3   I4,I41,I422,I4122
  30 475    oI    54.58    58.05   154.83   111.3 110.0  90.3   I222,I212121
  29 450    mC   128.00    54.58    89.18    90.2 126.8  65.1   C2
  28 340    hP    58.05    67.03    54.58    90.5  90.3  90.7   P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
                                                                P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
  27 260    hP    54.58    58.05    67.03    90.7  90.5  90.3   P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
                                                                P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
  26 259    mC    58.05   145.48    54.58    89.4  89.7  67.1   C2
  25 255    oC    58.05   145.48    54.58    89.4  90.3 112.9   C222,C2221
  24 252    mC   145.48    58.05    54.58    90.3  90.6  67.1   C2
  23 236    mC    54.58   128.60    67.03    89.6  90.5  64.5   C2
  22 232    mC    54.58   144.29    58.05    89.3  89.7  68.3   C2
  21 231    oC    54.58   128.00    67.03    89.2  90.5 114.9   C222,C2221
  20 227    mC   128.00    54.58    67.03    90.5  90.8  65.1   C2
  19 227    oC    54.58   144.29    58.05    89.3  90.3 111.7   C222,C2221
  18 224    mC   144.29    54.58    58.05    90.3  90.7  68.3   C2
  17 123    hR    79.93    86.06   104.69   100.1  87.2 116.0   H3,H32 (hexagonal settings of R3 and R32)
  16 123    cP    54.58    58.05    67.03    90.7  90.5  90.3   P23,P213,P432,P4232,P4332,P4132
  15 118    hR    79.93    86.82   103.19    99.6  87.4 115.5   H3,H32 (hexagonal settings of R3 and R32)
  14  93    tP    58.05    67.03    54.58    90.5  90.3  90.7   P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
  13  90    oC    88.17    89.18    54.58    90.2  90.6  81.8   C222,C2221
  12  90    mC    88.17    89.18    54.58    89.8  90.6  98.2   C2
  11  87    mC    88.17    89.18    54.58    90.2  90.6  81.8   C2
  10  37    tP    54.58    58.05    67.03    90.7  90.5  90.3   P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
   9  36    oC    79.44    79.93    67.03    90.1  90.8  86.5   C222,C2221
   8  32    mC    79.44    79.93    67.03    89.9  90.8  93.5   C2
   7  31    mC    79.44    79.93    67.03    90.1  90.8  86.5   C2
   6   7    oP    54.58    58.05    67.03    90.7  90.5  90.3   P222,P2221,P21212,P212121
   5   6    mP    54.58    67.03    58.05    90.7  90.3  90.5   P2,P21
   4   5    mP    54.58    58.05    67.03    90.7  90.5  90.3   P2,P21
   3   4    mP    58.05    54.58    67.03    90.5  90.7  90.3   P2,P21
   2   1    aP    54.58    58.05    67.03    89.3  89.5  90.3   P1
   1   0    aP    54.58    58.05    67.03    90.7  90.5  90.3   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 # 6 with P222   (number  16) symmetry imposed

Initial cell (before refinement) is   54.5823   58.0540   67.0293  90.000  90.000  90.000
Using  181 indexed reflections (out of  189 spots found, {delta(XY) <= 2.5 sigma}),
final sd in spot positions is 0.09mm and in phi 0.24 degrees
Refined cell parameters   54.77   58.06   67.29  90.00  90.00  90.00
Beam coordinates of  93.58  92.24 have been refined to  93.60  91.98
This is a shift of  0.26mm or  0.076 times the minimum spot separation of ca  3.47mm.
  Final cell (after refinement) is    54.7749   58.0600   67.2939  90.000  90.000  90.000

 FORMATTED      UNKNOWN file opened on unit  12

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


Updating the stored central beam position from   9358.500  9224.500 to   9440.455  9198.185

 ****** 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 ( 0.9330) 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-ntest1_1.gen      Filename: ref-ntest1_1.gen




 Title for MTZ and GENERATE Files (TITLE):
 .
 Crystal identifier (IDENT): ref-ntest1_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=    26

 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    27    28    37    28    32    27    26    24    22    26    32    28    28    27    28    30    35    33
 No gained          25    33
 Total intensity 98729 99431 99737 99800 99838 99861 99884 99904 99922 99942 99953 99958 99967 99977 99987 99987 99991 99993 99994
 Total intensity 99994 99998
 SD of intensity   178   178   178   178   178   178   179   179   179   179   179   179   179   179   179   179   179   179   179
 SD of intensity   179   179
 The mosaicity has been estimated as ---> 0.20 <--- for this image only; 
This value can be used cautiously as an initial estimate.
Storing space group from DPS autoindexing: P222       number  16



 *********** 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-ntest1_1_###.img
 ===> directory /scisoft/pxsoft/data/dna_040402
 ===> detector adsc
 ===> beam 93.585000 92.245000
 ===> 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_040402/ref-ntest1_1_002.img      Filename: /scisoft/pxsoft/data/dna_040402/ref-ntest1_1_002.img



 Crystal to detector distance of  249.95mm taken from image header

 Wavelength of 0.93300A taken from image header

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

 Input beam coordinates   93.58mm   92.24mm will be used


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

 image FILENAME: /scisoft/pxsoft/data/dna_040402/ref-ntest1_1_002.img

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

 Logical Name: /scisoft/pxsoft/data/dna_040402/ref-ntest1_1_002.img      Filename: /scisoft/pxsoft/data/dna_040402/ref-ntest1_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  30 spots
 Threshold set to    4.1
 sorting  33 spots
 Threshold set to    4.1


 Finding spots on image     2 (Midpoint of phi  90.500 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     29    30    30    30    30    30    30    29    29    29    29    29
 SIGMA      5     5     5     5     5     5     5     5     5     5     5     5
 NREJ       0     1     0     0     0     0     0     1     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     29    29    29    29    29    28    29    29    29    29    29    29
 SIGMA      5     5     5     5     5     5     5     5     5     5     5     5
 NREJ       0     0     0     0     0     0     0     0     0     0     0     1
 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     29    28    29    29    29    29    28    29    29    29    29    28
 SIGMA      5     5     5     5     5     5     5     5     5     5     5     5
 NREJ       1     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     28    28    29    29    28    28    28    29    28    28    28    28
 SIGMA      5     5     5     5     5     5     5     5     5     5     5     5
 NREJ       0     0     1     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     28    28    28    28    28    28    28    28    28    28    27    28
 SIGMA      5     5     5     5     5     5     5     5     5     5     5     5
 NREJ       0     0     0     1     0     0     0     0     1     1     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     28    28    28    28    27    28    28    28    28    28    27    27
 SIGMA      5     5     5     5     5     5     5     5     5     5     5     5
 NREJ       0     0     0     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     27    27    28    28    28    27    27    28    28    28    27    28
 SIGMA      5     5     5     5     5     5     5     5     5     5     5     5
 NREJ       1     1     1     0     0     1     2     0     0     0     0     1
 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     27    28    28    27    28    28    28    27    27    28    28    29
 SIGMA      5     5     5     5     5     5     5     5     5     5     5     5
 NREJ       1     2     1     0     0     0     0     0     0     1     8    13
 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     28    28    27    27    27    27    27    28    27    27    27    27
 SIGMA      5     5     5     5     5     5     5     5     5     5     5     5
 NREJ      13     4     1     0     0     0     0     0     1     1     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     27    27    27    27    27    27    27    27    28    27    27    27
 SIGMA      5     5     5     5     5     5     5     5     5     5     5     5
 NREJ       0     1     0     0     0     0     1     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     26    27    27    27    27    27    27    27    27    27    27    27
 SIGMA      5     5     5     5     5     5     5     5     5     5     5     5
 NREJ       0     0     0     0     0     0     0     0     1     0     0     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     27    27    27    27    27    27    27    27    28    28    28    28
 SIGMA      5     5     5     5     5     5     5     5     5     5     5     5
 NREJ       0     0     0     0     0     0     0     0     0     0     0     1
 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     28    28    28    29    28    29    29    29    29    29    28    29
 SIGMA      5     5     5     5     5     5     5     5     5     5     5     5
 NREJ       0     0     0     0     1     0     0     0     0     0     1     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     30    30    30    31    31    31    31    31    31    31    32    32
 SIGMA      5     5     5     5     5     5     5     5     5     5     5     5
 NREJ       0     0     0     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     32    32    33    33    33    32    32    32    32    32    32    32
 SIGMA      5     5     5     5     5     5     5     5     5     5     5     5
 NREJ       0     0     0     0     0     0     0     0     0     0     0     1
 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     32    32    31    32    32    32    31    31    31    31    31    30
 SIGMA      5     5     5     5     5     5     5     5     5     5     5     5
 NREJ       0     0     0     0     0     0     0     0     0     0     1     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     31    30    31    31    31    30    30    31    31    30    29    30
 SIGMA      5     5     5     5     5     5     5     5     5     5     5     5
 NREJ       0     0     0     0     3    10    12     5     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     29    30    29    28    28    28    28    28    28    28    27    27
 SIGMA      5     5     5     5     5     5     5     5     5     5     5     5
 NREJ       0     0     0     1     1     0     0     0     0     0     0     1
 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     27    27    27    27    27    27    27    26    27    26    26    26
 SIGMA      5     5     5     5     5     5     5     5     5     5     5     5
 NREJ       0     0     0     2     0     0     0     1     0     0     0     0
 RADIUS  83.8  84.1  84.5
 BACKG     27    26    13
 SIGMA      5     5     2
 NREJ       0     0     0

 Starting spot search...
 sorting  218 spots

  Median spot size is   8 x   7 pixels

  Total number of spots found: 218
  Number rejected as too small on X:  13
  Number rejected as too small on Y:   7
  Number rejected as too big on X:   3
  Number rejected as too big on Y:   2
  Number too close (SEPARATION keyword):   0
  Number stored as OK: 193



             Number of spots found in each bin
               1   2   2   5   1   1   2   7
              10   1   4   6   9   0   4   0
               6   3   8   6   7   6   0  11
               7   5   1   8   7   2   7   8
               5   3   2   9   5   7   0  15

 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  33 spots

 Based on a median spot size of  7 by  6 pixels in X and Y, the measurement box 
 parameters have been set to  21  19  11   6   6
 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  7 by  6 pixels in X and Y, the spot separation 
 parameters (in X and Y) have been set to  0.73  0.65mm.
 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-ntest1_1.spt, Filename: ref-ntest1_1.spt


   193 spots written for image    2
 A total of   193 spots were written to file

 FORMATTED      OLD     file opened on unit  10

 Logical name: ref-ntest1_1.spt, Filename: ref-ntest1_1.spt


DPS Indexing at Two-theta =    0.00 with  192 reflections (minimum spot separation = 0.49mm. Maximum expected cell edge  267.90, Beam position is   93.58   92.24
Generating direct lattice vectors (This may take some time):
|-----------------|
..................
 Refining  30 direct space vectors:
|----------------------------|
..............................
selected 23
 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    hR   140.24    88.96    54.89    89.3  67.7  98.8   H3,H32 (hexagonal settings of R3 and R32)
  43 775    cF   102.06   102.85   103.93   113.8  98.6 115.2   F23,F432,F4132
  42 768    cI    86.85    78.11    86.51    63.2  54.5  65.0   I23,I213,I432,I4132
  41 745    tI    86.51   103.93    54.89    58.9  90.5  98.7   I4,I41,I422,I4122
  40 675    hR    54.89    78.11   214.87    89.6 104.9 133.7   H3,H32 (hexagonal settings of R3 and R32)
  39 672    mI    54.89   154.10    56.48    70.4  91.0  69.3   C2
  38 645    oF    54.89   124.78   144.92    79.4 112.1 115.1   F222
  37 573    tI    86.51    86.85    78.11    65.0  63.2  54.5   I4,I41,I422,I4122
  36 568    tI    86.85    78.11    86.51    63.2  54.5  65.0   I4,I41,I422,I4122
  35 564    oI    78.11    86.85    86.51    54.5  63.2  65.0   I222,I212121
  34 549    oI    54.89    86.51   103.93    81.3  58.9  89.5   I222,I212121
  33 472    oF    78.11    79.42   154.10    89.7 119.4  88.4   F222
  32 463    mC    79.42    78.11    86.85    65.0 117.5  88.4   C2
  31 461    tI    54.89    56.48   154.48    69.7  69.0  89.0   I4,I41,I422,I4122
  30 461    oI    54.89    56.48   154.48   110.3 111.0  89.0   I222,I212121
  29 449    mC   124.78    54.89    86.51    89.5 124.6  64.9   C2
  28 332    hP    56.48    67.14    54.89    89.8  91.0  91.6   P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
                                                                P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
  27 245    hP    54.89    56.48    67.14    91.6  89.8  91.0   P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
                                                                P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
  26 243    oC    54.89   144.92    56.48    88.9  89.0 112.1   C222,C2221
  25 240    mC    54.89   144.92    56.48    88.9  91.0  67.9   C2
  24 237    mC    54.89   124.78    67.14    88.6  90.2  64.9   C2
  23 235    mC   144.92    54.89    56.48    89.0  91.1  67.9   C2
  22 232    oC    56.48   144.20    54.89    89.8  91.0 111.4   C222,C2221
  21 231    oC    54.89   124.78    67.14    88.6  89.8 115.1   C222,C2221
  20 231    mC   144.20    56.48    54.89    91.0  90.2  68.6   C2
  19 228    mC    56.48   144.20    54.89    90.2  91.0  68.6   C2
  18 223    mC   124.78    54.89    67.14    89.8  91.4  64.9   C2
  17 128    hR    79.42    86.60   102.06    99.4  89.6 115.4   H3,H32 (hexagonal settings of R3 and R32)
  16 127    cP    54.89    56.48    67.14    91.6  89.8  91.0   P23,P213,P432,P4232,P4332,P4132
  15 125    hR    78.11    86.60   105.13    99.8  88.1 116.9   H3,H32 (hexagonal settings of R3 and R32)
  14 114    tP    56.48    67.14    54.89    89.8  91.0  91.6   P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
  13 106    oC    86.51    88.96    54.89    89.3  90.5  80.1   C222,C2221
  12 106    mC    86.51    88.96    54.89    89.3  90.5  80.1   C2
  11 103    mC    88.96    86.51    54.89    90.5  90.7  99.9   C2
  10  27    tP    54.89    56.48    67.14    91.6  89.8  91.0   P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
   9  23    oC    78.11    79.42    67.14    91.3  91.1  88.4   C222,C2221
   8  23    mC    78.11    79.42    67.14    91.3  91.1  88.4   C2
   7  21    mC    79.42    78.11    67.14    88.9  91.3  91.6   C2
   6  14    oP    54.89    56.48    67.14    91.6  89.8  91.0   P222,P2221,P21212,P212121
   5  13    mP    54.89    56.48    67.14    91.6  89.8  91.0   P2,P21
   4  10    mP    54.89    67.14    56.48    91.6  91.0  89.8   P2,P21
   3   6    mP    56.48    54.89    67.14    89.8  91.6  91.0   P2,P21
   2   1    aP    54.89    56.48    67.14    91.6  89.8  91.0   P1
   1   0    aP    54.89    56.48    67.14    88.4  89.8  89.0   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 P4     (number  75) symmetry imposed

Initial cell (before refinement) is   55.6889   55.6889   67.1423  90.000  90.000  90.000
Using  181 indexed reflections (out of  192 spots found, {delta(XY) <= 2.5 sigma}),
final sd in spot positions is 0.10mm and in phi 0.48 degrees
Refined cell parameters   54.84   54.84   67.29  90.00  90.00  90.00
Beam coordinates of  93.58  92.24 have been refined to  93.61  92.05
This is a shift of  0.20mm or  0.057 times the minimum spot separation of ca  3.47mm.
  Final cell (after refinement) is    54.8368   54.8368   67.2860  90.000  90.000  90.000

 FORMATTED      UNKNOWN file opened on unit  12

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


Updating the stored central beam position from   9358.500  9224.500 to   9439.480  9204.795

 ****** 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 ( 0.9330) 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-ntest1_1.gen      Filename: ref-ntest1_1.gen




 Title for MTZ and GENERATE Files (TITLE):
 .
 Crystal identifier (IDENT): ref-ntest1_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=    17

 Beam divergence refinement

 Beam divergence refinement

 Refining DIV  with stepsize  0.01 Degrees
 Divergence      0.000 0.100 0.200 0.300 0.400 0.500 0.600 0.700 0.800 0.900 1.000 1.100 1.200 1.300 1.400 1.500 1.600 1.700 1.800
 Divergence      1.900 2.000
 No gained          35    61    70    52    49    57    59    49    38    40    57     1     0     2     0     1     1     0     1
 No gained           0     0
 Total intensity 50645 60776 65227 69833 75081 80829 88001 92189 95846 97459 99997 99998 99998 99998 99998 99998 99997 99997 99993
 Total intensity 99993 99993
 SD of intensity   116   135   139   142   148   151   162   164   167   167   169   169   169   169   169   169   169   169   169
 SD of intensity   169   169
 The mosaicity has been estimated as ---> 0.74 <--- for this image only; 
This value can be used cautiously as an initial estimate.
Storing space group from DPS autoindexing: P4         number  75



 *********** 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-ntest1_1_###.img
 ===> directory /scisoft/pxsoft/data/dna_040402
 ===> detector adsc
 ===> beam 93.585000 92.245000
 ===> 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_040402/ref-ntest1_1_001.img      Filename: /scisoft/pxsoft/data/dna_040402/ref-ntest1_1_001.img



 Crystal to detector distance of  249.95mm taken from image header

 Wavelength of 0.93300A taken from image header

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

 Input beam coordinates   93.58mm   92.24mm will be used


 Autoindexing using  2 images
 Image numbers:     1    2
 image FILENAME: /scisoft/pxsoft/data/dna_040402/ref-ntest1_1_001.img

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

 Logical Name: /scisoft/pxsoft/data/dna_040402/ref-ntest1_1_001.img      Filename: /scisoft/pxsoft/data/dna_040402/ref-ntest1_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  30 spots
 Threshold set to    4.4
 sorting  29 spots
 Threshold set to    4.3


 Finding spots on image     1 (Midpoint of phi   0.500 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    382   372   373   357   356   346   334   333   324   316   309   301
 SIGMA     19    19    19    18    18    18    18    18    17    17    17    17
 NREJ      19    21     7    16     7     7     7     2     4     4     2     1
 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    296   289   284   276   269   264   260   253   248   245   239   235
 SIGMA     17    17    16    16    16    16    16    15    15    15    15    15
 NREJ       1     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    228   224   222   216   213   211   206   204   200   196   192   189
 SIGMA     15    14    14    14    14    14    14    14    14    13    13    13
 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    185   184   180   179   176   172   171   168   164   163   160   158
 SIGMA     13    13    13    13    13    13    13    12    12    12    12    12
 NREJ       0     0     0     0     0     0     0     0     0     0     0     1
 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   153   150   148   146   144   142   141   139   136   133   132
 SIGMA     12    12    12    12    12    12    11    11    11    11    11    11
 NREJ       0     0     0     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    133   130   127   127   124   123   122   120   119   118   116   115
 SIGMA     11    11    11    11    11    11    11    10    10    10    10    10
 NREJ       0     0     0     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    115   112   112   109   109   108   107   105   105   104   102   100
 SIGMA     10    10    10    10    10    10    10    10    10    10    10    10
 NREJ       0     0     0     0     0     0     0     0     0     0     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    101    99    97    96    95    95    93    92    92    89    90    89
 SIGMA     10     9     9     9     9     9     9     9     9     9     9     9
 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     87    88    86    85    84    84    82    83    81    81    80    79
 SIGMA      9     9     9     9     9     9     9     9     9     9     8     8
 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     79    78    77    77    77    76    75    75    74    74    73    73
 SIGMA      8     8     8     8     8     8     8     8     8     8     8     8
 NREJ       0     0     0     0     0     0     0     0     0     0     1     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     73    73    74    72    72    72    71    70    69    68    68    68
 SIGMA      8     8     8     8     8     8     8     8     8     8     8     8
 NREJ       0     0     5    11     9     0     0     0     0     0     0     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     67    67    66    66    66    65    65    65    65    64    65    63
 SIGMA      8     8     8     8     8     8     8     8     8     8     8     7
 NREJ       0     0     0     0     0     0     0     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     63    64    64    63    63    63    63    64    63    62    61    62
 SIGMA      7     8     8     7     7     7     7     7     7     7     7     7
 NREJ       0     0     0     0     0     1     7     7     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     61    61    61    61    61    62    61    62    62    61    60    60
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     0     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     61    61    61    61    60    59    59    59    59    58    58    58
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     0     0     0     0     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     59    58    57    57    56    57    57    56    56    56    57    56
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     0     0     0     0     0     0     0     0     6    11
 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     55    55    54    53    54    53    52    52    52    52    51    50
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       8     0     0     0     0     0     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     51    51    50    48    48    49    48    47    47    47    47    46
 SIGMA      7     7     7     6     6     6     6     6     6     6     6     6
 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     46    46    46    45    45    45    45    44    43    43    43    42
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     0     1     4     1     0     0     1     0     0     0     0
 RADIUS  83.8  84.1  84.5
 BACKG     43    42    21
 SIGMA      6     6     3
 NREJ       0     0     0

 Starting spot search...
 sorting  236 spots

  Median spot size is   7 x   7 pixels

  Total number of spots found: 236
  Number rejected as too small on X:  27
  Number rejected as too small on Y:   8
  Number rejected as too big on X:   2
  Number rejected as too big on Y:   0
  Number too close (SEPARATION keyword):   0
  Number stored as OK: 199



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

 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  31 spots

 Based on a median spot size of  7 by  7 pixels in X and Y, the measurement box 
 parameters have been set to  21  21  12   6   6
 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  7 by  7 pixels in X and Y, the spot separation 
 parameters (in X and Y) have been set to  0.73  0.73mm.
 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_040402/ref-ntest1_1_002.img

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

 Logical Name: /scisoft/pxsoft/data/dna_040402/ref-ntest1_1_002.img      Filename: /scisoft/pxsoft/data/dna_040402/ref-ntest1_1_002.img




 Finding spots on image     2 (Midpoint of phi  90.500 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     29    30    30    30    30    30    30    29    29    29    29    29
 SIGMA      5     5     5     5     5     5     5     5     5     5     5     5
 NREJ       0     1     0     0     0     0     0     1     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     29    29    29    29    29    28    29    29    29    29    29    29
 SIGMA      5     5     5     5     5     5     5     5     5     5     5     5
 NREJ       0     0     0     0     0     0     0     0     0     0     0     1
 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     29    28    29    29    29    29    28    29    29    29    29    28
 SIGMA      5     5     5     5     5     5     5     5     5     5     5     5
 NREJ       1     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     28    28    29    29    28    28    28    29    28    28    28    28
 SIGMA      5     5     5     5     5     5     5     5     5     5     5     5
 NREJ       0     0     1     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     28    28    28    28    28    28    28    28    28    28    27    28
 SIGMA      5     5     5     5     5     5     5     5     5     5     5     5
 NREJ       0     0     0     1     0     0     0     0     1     1     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     28    28    28    28    27    28    28    28    28    28    27    27
 SIGMA      5     5     5     5     5     5     5     5     5     5     5     5
 NREJ       0     0     0     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     27    27    28    28    28    27    27    28    28    28    27    28
 SIGMA      5     5     5     5     5     5     5     5     5     5     5     5
 NREJ       1     1     1     0     0     1     2     0     0     0     0     1
 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     27    28    28    27    28    28    28    27    27    28    28    29
 SIGMA      5     5     5     5     5     5     5     5     5     5     5     5
 NREJ       1     2     1     0     0     0     0     0     0     1     8    13
 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     28    28    27    27    27    27    27    28    27    27    27    27
 SIGMA      5     5     5     5     5     5     5     5     5     5     5     5
 NREJ      13     4     1     0     0     0     0     0     1     1     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     27    27    27    27    27    27    27    27    28    27    27    27
 SIGMA      5     5     5     5     5     5     5     5     5     5     5     5
 NREJ       0     1     0     0     0     0     1     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     26    27    27    27    27    27    27    27    27    27    27    27
 SIGMA      5     5     5     5     5     5     5     5     5     5     5     5
 NREJ       0     0     0     0     0     0     0     0     1     0     0     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     27    27    27    27    27    27    27    27    28    28    28    28
 SIGMA      5     5     5     5     5     5     5     5     5     5     5     5
 NREJ       0     0     0     0     0     0     0     0     0     0     0     1
 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     28    28    28    29    28    29    29    29    29    29    28    29
 SIGMA      5     5     5     5     5     5     5     5     5     5     5     5
 NREJ       0     0     0     0     1     0     0     0     0     0     1     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     30    30    30    31    31    31    31    31    31    31    32    32
 SIGMA      5     5     5     5     5     5     5     5     5     5     5     5
 NREJ       0     0     0     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     32    32    33    33    33    32    32    32    32    32    32    32
 SIGMA      5     5     5     5     5     5     5     5     5     5     5     5
 NREJ       0     0     0     0     0     0     0     0     0     0     0     1
 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     32    32    31    32    32    32    31    31    31    31    31    30
 SIGMA      5     5     5     5     5     5     5     5     5     5     5     5
 NREJ       0     0     0     0     0     0     0     0     0     0     1     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     31    30    31    31    31    30    30    31    31    30    29    30
 SIGMA      5     5     5     5     5     5     5     5     5     5     5     5
 NREJ       0     0     0     0     3    10    12     5     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     29    30    29    28    28    28    28    28    28    28    27    27
 SIGMA      5     5     5     5     5     5     5     5     5     5     5     5
 NREJ       0     0     0     1     1     0     0     0     0     0     0     1
 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     27    27    27    27    27    27    27    26    27    26    26    26
 SIGMA      5     5     5     5     5     5     5     5     5     5     5     5
 NREJ       0     0     0     2     0     0     0     1     0     0     0     0
 RADIUS  83.8  84.1  84.5
 BACKG     27    26    13
 SIGMA      5     5     2
 NREJ       0     0     0

 Starting spot search...
 sorting  218 spots

  Median spot size is   8 x   7 pixels

  Total number of spots found: 218
  Number rejected as too small on X:  14
  Number rejected as too small on Y:   7
  Number rejected as too big on X:   3
  Number rejected as too big on Y:   1
  Number too close (SEPARATION keyword):   4
  Number stored as OK: 193



             Number of spots found in each bin
               1   2   2   5   1   1   2   8
              10   1   4   6   9   0   4   0
               6   3   8   6   7   6   0  11
               7   5   0   8   7   2   7   8
               5   3   2   9   5   7   0  15

 FORMATTED      UNKNOWN file opened on unit  10

 Logical name: ref-ntest1_1.spt, Filename: ref-ntest1_1.spt


   199 spots written for image    1
   193 spots written for image    2
 A total of   392 spots were written to file

 FORMATTED      OLD     file opened on unit  10

 Logical name: ref-ntest1_1.spt, Filename: ref-ntest1_1.spt


DPS Indexing at Two-theta =    0.00 with  382 reflections (minimum spot separation = 0.57mm. Maximum expected cell edge  267.90, Beam position is   93.58   92.24
Generating direct lattice vectors (This may take some time):
|-----------------|
..................
 Refining  30 direct space vectors:
|----------------------------|
..............................
selected 1
 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    hR   144.79    88.64    54.79    90.0  67.9 100.0   H3,H32 (hexagonal settings of R3 and R32)
  43 777    cI    86.69    79.72    88.64    61.6  54.2  64.3   I23,I213,I432,I4132
  42 776    cF   104.19   104.23   104.23   112.4  99.8 116.6   F23,F432,F4132
  41 748    tI    88.64   104.23    54.79    58.4  90.0  97.1   I4,I41,I422,I4122
  40 719    mI    54.79   156.34    58.02    68.1  89.9  69.4   C2
  39 692    hR    54.79    79.72   216.47    91.2 104.6 133.3   H3,H32 (hexagonal settings of R3 and R32)
  38 664    oF    54.79   128.22   144.92    80.7 112.1 115.2   F222
  37 582    oI    79.88    86.69    88.79    54.0  61.5  64.2   I222,I212121
  36 582    tI    86.69    79.88    88.79    61.5  54.0  64.2   I4,I41,I422,I4122
  35 582    tI    88.79    86.69    79.88    64.2  61.5  54.0   I4,I41,I422,I4122
  34 528    oI    54.79    88.64   104.23    82.9  58.4  90.0   I222,I212121
  33 498    oF    79.88    79.72   156.34    91.7 120.8  86.7   F222
  32 498    mC    79.72    79.88    86.69    64.2 115.7  86.7   C2
  31 471    tI    54.79    58.02   156.07    68.2  69.5  89.9   I4,I41,I422,I4122
  30 471    oI    54.79    58.02   156.07   111.8 110.5  89.9   I222,I212121
  29 443    mC   128.22    54.79    88.64    90.0 126.2  64.8   C2
  28 334    hP    58.02    67.12    54.79    89.9  90.1  90.1   P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
                                                                P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
  27 250    hP    54.79    58.02    67.12    90.1  89.9  90.1   P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
                                                                P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
  26 250    oC    58.02   146.15    54.79    90.0  90.1 113.3   C222,C2221
  25 249    mC    58.02   146.15    54.79    90.0  90.1  66.7   C2
  24 249    mC   146.15    58.02    54.79    90.1  90.0  66.7   C2
  23 223    mC   144.92    54.79    58.02    89.9  90.0  67.9   C2
  22 223    oC    54.79   128.22    67.12    89.9  89.9 115.2   C222,C2221
  21 223    oC    54.79   144.92    58.02    90.0  89.9 112.1   C222,C2221
  20 222    mC   128.22    54.79    67.12    89.9  90.1  64.8   C2
  19 222    mC    54.79   144.92    58.02    90.0  90.1  67.9   C2
  18 222    mC    54.79   128.22    67.12    89.9  90.1  64.8   C2
  17 113    cP    54.79    58.02    67.12    90.1  89.9  90.1   P23,P213,P432,P4232,P4332,P4132
  16 112    hR    79.72    86.59   104.43    99.6  87.5 115.7   H3,H32 (hexagonal settings of R3 and R32)
  15 112    hR    79.88    86.59   104.19    99.6  87.6 115.7   H3,H32 (hexagonal settings of R3 and R32)
  14  86    tP    58.02    67.12    54.79    89.9  90.1  90.1   P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
  13  85    mC    88.79    88.64    54.79    90.0  90.1  98.3   C2
  12  85    oC    88.64    88.79    54.79    89.9  90.0  81.7   C222,C2221
  11  85    mC    88.79    88.64    54.79    90.0  90.1  81.7   C2
  10  29    tP    54.79    58.02    67.12    90.1  89.9  90.1   P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
   9  28    oC    79.72    79.88    67.12    90.1  90.0  86.7   C222,C2221
   8  28    mC    79.88    79.72    67.12    90.0  90.1  86.7   C2
   7  27    mC    79.88    79.72    67.12    90.0  90.1  93.3   C2
   6   2    oP    54.79    58.02    67.12    90.1  89.9  90.1   P222,P2221,P21212,P212121
   5   1    mP    54.79    58.02    67.12    90.1  89.9  90.1   P2,P21
   4   1    mP    54.79    67.12    58.02    90.1  90.1  89.9   P2,P21
   3   1    mP    58.02    54.79    67.12    89.9  90.1  90.1   P2,P21
   2   0    aP    54.79    58.02    67.12    89.9  89.9  89.9   P1
   1   0    aP    54.79    58.02    67.12    90.1  89.9  90.1   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 # 6 with P222   (number  16) symmetry imposed

Initial cell (before refinement) is   54.7895   58.0195   67.1157  90.000  90.000  90.000
Using  375 indexed reflections (out of  382 spots found, {delta(XY) <= 2.5 sigma}),
final sd in spot positions is 0.10mm and in phi 0.29 degrees
Refined cell parameters   54.79   58.07   67.20  90.00  90.00  90.00
Beam coordinates of  93.58  92.24 have been refined to  93.59  91.96
This is a shift of  0.29mm or  0.083 times the minimum spot separation of ca  3.47mm.
  Final cell (after refinement) is    54.7869   58.0682   67.2004  90.000  90.000  90.000

 FORMATTED      UNKNOWN file opened on unit  12

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


Updating the stored central beam position from   9358.500  9224.500 to   9441.932  9195.560

 ****** 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 ( 0.9330) 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-ntest1_1.gen      Filename: ref-ntest1_1.gen




 Title for MTZ and GENERATE Files (TITLE):
 .
 Crystal identifier (IDENT): ref-ntest1_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=    19

 Beam divergence refinement

 Beam divergence refinement

 Refining DIV  with stepsize  0.01 Degrees
 Divergence      0.000 0.100 0.200 0.300 0.400 0.500 0.600 0.700 0.800 0.900 1.000 1.100 1.200 1.300 1.400 1.500 1.600 1.700 1.800
 Divergence      1.900 2.000
 No gained          25    53    46    51    69    56    66    57    46    65    54     1     0     2     0     0     0     0     0
 No gained           1     0
 Total intensity 74557 80652 83769 88345 94098 96848 99914 99942 99950 99977 99998 99998 99998 99996 99996 99996 99996 99996 99996
 Total intensity 99995 99995
 SD of intensity   122   125   128   132   138   140   145   145   145   145   146   146   146   146   146   146   146   146   146
 SD of intensity   146   146
 The mosaicity has been estimated as ---> 0.50 <--- for this image only; 
This value can be used cautiously as an initial estimate.
Storing space group from DPS autoindexing: P222       number  16
Storing space group from DPS autoindexing: P222       number  16



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