Index results for ntest2_1

Symmetry and refined cell parameters

Image Symmetry a b c alpha beta gamma
1 F23 180.970 180.970 180.970 90.000 90.000 90.000
2 F23 180.931 180.931 180.931 90.000 90.000 90.000
1+2 F23 180.952 180.952 180.952 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
1 957 9 0.009 0.080 0.025 -0.235
2 1124 23 0.020 0.080 0.015 -0.245
1+2 2106 48 0.023 0.100 0.015 -0.275

Image 1: /scisoft/pxsoft/data/dna_040402/ref-ntest2_1_001.img

Image 2: /scisoft/pxsoft/data/dna_040402/ref-ntest2_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-ntest2_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-ntest2_1_001.img      Filename: /scisoft/pxsoft/data/dna_040402/ref-ntest2_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-ntest2_1_001.img

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

 Logical Name: /scisoft/pxsoft/data/dna_040402/ref-ntest2_1_001.img      Filename: /scisoft/pxsoft/data/dna_040402/ref-ntest2_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  116 spots
 Threshold set to    4.5
 sorting  118 spots
 Threshold set to    4.5


 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    357   349   345   338   331   322   317   310   303   295   290   284
 SIGMA     18    18    18    18    18    17    17    17    17    17    17    16
 NREJ      19    16    10    10     8     9     3     2     2     4     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    276   273   265   259   252   248   244   240   235   229   225   220
 SIGMA     16    16    16    16    15    15    15    15    15    15    14    14
 NREJ       1     0     1     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    217   214   209   206   202   198   194   191   189   186   182   180
 SIGMA     14    14    14    14    14    14    13    13    13    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    177   176   173   169   167   165   165   162   157   156   152   151
 SIGMA     13    13    13    13    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    149   146   142   141   141   140   136   134   133   132   130   127
 SIGMA     12    12    11    11    11    11    11    11    11    11    11    11
 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    127   125   123   123   122   121   122   120   116   115   113   112
 SIGMA     11    11    11    11    11    10    11    10    10    10    10    10
 NREJ       0     0     0     0     0     1     6     4     4     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    110   109   108   107   106   104   104   101   100    99    97    98
 SIGMA     10    10    10    10    10    10    10    10    10     9     9     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    96    95    95    93    92    93    92    90    88    88    87
 SIGMA      9     9     9     9     9     9     9     9     9     9     9     9
 NREJ       1     0     0     0     0     0     2     6     7     2     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     88    86    86    85    84    84    83    82    82    81    81    80
 SIGMA      9     9     9     9     9     9     9     9     9     9     9     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    79    79    78    77    78    79    80    79    76    75    75
 SIGMA      8     8     8     8     8     8     8     8     8     8     8     8
 NREJ       1     0     0     0     0     0     5     8     8     5     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     75    74    75    75    74    74    73    72    73    72    72    71
 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     72    71    70    69    68    69    69    70    69    68    67    67
 SIGMA      8     8     8     8     8     8     8     8     8     8     8     8
 NREJ       0     2     0     0     0     0     0     2     4     2     1     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     68    67    68    67    68    66    67    66    67    68    67    68
 SIGMA      8     8     8     8     8     8     8     8     8     8     8     8
 NREJ       0     0     4     2     2     0     0     0     0     0     7     7
 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     67    68    66    66    66    65    66    65    66    65    67    66
 SIGMA      8     8     8     8     8     8     8     8     8     8     8     8
 NREJ       5     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     66    65    65    66    66    66    66    65    64    65    65    65
 SIGMA      8     8     8     8     8     8     8     8     8     8     8     8
 NREJ       0     0     0     0     2     2     0     0     0     0     0     2
 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     65    65    63    63    63    63    63    63    61    62    62    62
 SIGMA      8     8     7     7     7     7     7     7     7     7     7     7
 NREJ       0     1     0     0     1     0     3     0     0     0     0     2
 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     61    61    60    59    59    58    58    59    60    58    57    57
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       4     4     2     0     0     0     0     2     1     3     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     56    56    55    55    55    54    54    54    54    53    53    53
 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  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     53    52    51    50    50    49    50    50    50    50    49    49
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     6
 NREJ       0     0     1     1     0     0     0     1     0     3     4     3
 RADIUS  83.8  84.1  84.5
 BACKG     49    48    24
 SIGMA      7     6     3
 NREJ       0     0     0

 Starting spot search...
 sorting  957 spots

  Median spot size is   4 x   4 pixels

  Total number of spots found: 957
  Number rejected as too small on X:   0
  Number rejected as too small on Y:   0
  Number rejected as too big on X:   7
  Number rejected as too big on Y:   2
  Number too close (SEPARATION keyword):   0
  Number stored as OK: 948



             Number of spots found in each bin
              21  14   7  22  24   8   9  17
              36  19  13  29  34  17  19  33
              38  27  21  39  42  19  20  37
              35  20  20  31  38  16  20  36
              21  21  14  35  21  20  14  21

 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  118 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-ntest2_1.spt, Filename: ref-ntest2_1.spt


   948 spots written for image    1
 A total of   948 spots were written to file

 FORMATTED      OLD     file opened on unit  10

 Logical name: ref-ntest2_1.spt, Filename: ref-ntest2_1.spt


DPS Indexing at Two-theta =    0.00 with  815 reflections (minimum spot separation = 0.33mm. Maximum expected cell edge  297.43, Beam position is   93.58   92.24
Generating direct lattice vectors (This may take some time):
|-----------------|
..................
 Refining  30 direct space vectors:
|----------------------------|
..............................
selected 7
 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   128.65   180.74   127.97    89.9  90.1  89.8   I23,I213,I432,I4132
  43 509    cP   127.74   128.08   128.16    90.3 119.6 120.0   P23,P213,P432,P4232,P4332,P4132
  42 508    tP   127.74   128.08   128.16    90.3 119.6 120.0   P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
  41 506    oP   127.74   128.08   128.16    90.3 119.6 120.0   P222,P2221,P21212,P212121
  40 506    tP   128.08   128.16   127.74   119.6 120.0  90.3   P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
  39 502    hR   221.71   181.64   127.74    89.8 106.7 114.0   H3,H32 (hexagonal settings of R3 and R32)
  38 502    tI   180.74   128.65   127.97    90.1  90.1  90.2   I4,I41,I422,I4122
  37 499    oF   127.97   221.52   222.19    70.9  90.0  90.2   F222
  36 257    hP   128.25   128.16   127.74   119.6  90.2 120.1   P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
                                                                P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
  35 257    hR   221.52   181.28   128.16    90.4 106.4 114.1   H3,H32 (hexagonal settings of R3 and R32)
  34 257    hP   127.74   128.08   128.16    90.3 119.6 120.0   P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
                                                                P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
  33 256    oC   128.25   221.70   127.74    55.0  90.2  89.9   C222,C2221
  32 256    oC   127.97   221.52   128.16    73.6 119.9  89.8   C222,C2221
  31 255    oC   127.74   221.91   128.16    73.1 119.6  89.9   C222,C2221
  30 255    oC   127.97   222.19   127.74   106.5 119.9  90.0   C222,C2221
  29 254    mP   127.74   128.16   128.08    90.3 120.0 119.6   P2,P21
  28 254    mP   128.25   127.74   128.16   119.6 120.1  90.2   P2,P21
  27 254    oC   127.74   221.91   128.16    73.1 119.6  89.9   C222,C2221
  26 253    mP   127.74   128.16   128.08    90.3 120.0 119.6   P2,P21
  25 252    mC   127.97   221.52   128.16    73.6 119.9  89.8   C2
  24 251    mC   127.97   222.19   127.74    73.5 119.9  90.0   C2
  23 249    mC   127.97   222.19   127.74    73.5 119.9  90.0   C2
  22   9    tI   127.74   128.25   181.64    89.8  90.2  90.2   I4,I41,I422,I4122
  21   9    tI   128.65   127.97   180.74    90.1  89.8  89.9   I4,I41,I422,I4122
  20   9    cF   180.74   181.28   181.64    90.3  90.0  90.2   F23,F432,F4132
  19   8    oI   127.74   128.25   181.64    90.2  90.2  89.8   I222,I212121
  18   8    hR   127.74   128.08   314.92    89.7  90.2 120.0   H3,H32 (hexagonal settings of R3 and R32)
  17   8    oF   180.74   181.28   181.64    90.3  90.0  89.8   F222
  16   7    tI   128.65   127.97   180.74    89.9  89.8  90.1   I4,I41,I422,I4122
  15   7    hR   128.08   128.65   312.97    90.2  89.8 120.1   H3,H32 (hexagonal settings of R3 and R32)
  14   6    mC   180.74   181.64   127.74    89.8 134.8  90.0   C2
  13   6    mI   127.74   181.64   128.25    89.8  90.2  90.2   C2
  12   6    oI   127.74   128.25   181.64    89.8  89.8  89.8   I222,I212121
  11   6    mC   221.70   128.25   127.74    90.2 125.0  90.1   C2
  10   5    mC   221.91   127.74   128.25    89.8 125.1  89.9   C2
   9   5    mC   221.91   127.74   128.25    90.2 125.1  90.1   C2
   8   5    oI   127.97   128.65   180.74    89.8  89.9  90.1   I222,I212121
   7   4    mC   180.74   181.64   127.74    89.8 134.8  90.0   C2
   6   4    mC   221.52   127.97   128.65    90.1 125.3  89.8   C2
   5   4    mC   221.91   127.74   128.25    90.2 125.1  90.1   C2
   4   4    mC   221.31   128.08   128.16    89.7 125.0  90.1   C2
   3   3    mC   221.70   128.25   127.74    90.2 125.0  90.1   C2
   2   1    aP   127.74   128.08   128.16    90.3 119.6 120.0   P1
   1   0    aP   127.74   127.97   128.16    60.1  60.4  60.1   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 #20 with F23    (number 196) symmetry imposed

Initial cell (before refinement) is  181.2189  181.2189  181.2189  90.000  90.000  90.000
Using  782 indexed reflections (out of  815 spots found, {delta(XY) <= 2.5 sigma}),
final sd in spot positions is 0.08mm and in phi 0.22 degrees
Refined cell parameters  180.97  180.97  180.97  90.00  90.00  90.00
Beam coordinates of  93.58  92.24 have been refined to  93.61  92.01
This is a shift of  0.24mm or  0.187 times the minimum spot separation of ca  1.29mm.
  Final cell (after refinement) is   180.9697  180.9697  180.9697  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   9439.999  9200.513

 ****** 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-ntest2_1.gen      Filename: ref-ntest2_1.gen




 Title for MTZ and GENERATE Files (TITLE):
 .
 Crystal identifier (IDENT): ref-ntest2_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=    72

 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   193   180   199   218   211   221   205   187   204   160   180   199   186   197   204   201   219   216
 No gained         212   170
 Total intensity 91745 96654 98252 98889 99116 99298 99397 99566 99524 99701 99751 99795 99838 99858 99895 99940 99945 99970 99987
 Total intensity 99997 99997
 SD of intensity   319   331   334   334   334   334   334   334   336   336   336   336   336   336   336   336   339   339   339
 SD of intensity   339   339
 The mosaicity has been estimated as ---> 0.17 <--- for this image only; 
This value can be used cautiously as an initial estimate.
Storing space group from DPS autoindexing: F23        number 196



 *********** 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-ntest2_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-ntest2_1_002.img      Filename: /scisoft/pxsoft/data/dna_040402/ref-ntest2_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-ntest2_1_002.img

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

 Logical Name: /scisoft/pxsoft/data/dna_040402/ref-ntest2_1_002.img      Filename: /scisoft/pxsoft/data/dna_040402/ref-ntest2_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  130 spots
 Threshold set to    4.7
 sorting  130 spots
 Threshold set to    4.7


 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    354   349   342   339   329   321   314   306   301   290   286   281
 SIGMA     18    18    18    18    18    17    17    17    17    17    16    16
 NREJ      19    13    13     4     7     3     6     3     1     6     3     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    275   269   263   256   253   247   240   235   231   227   224   219
 SIGMA     16    16    16    16    15    15    15    15    15    15    14    14
 NREJ       0     0     0     2     0     0     1     0     0     0     1     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    213   208   206   203   202   198   194   189   188   184   181   178
 SIGMA     14    14    14    14    14    14    13    13    13    13    13    13
 NREJ       2     0     0     0     3     7     3     0     0     0     2     8
 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    175   173   170   168   164   162   160   158   154   152   150   149
 SIGMA     13    13    13    12    12    12    12    12    12    12    12    12
 NREJ      10     4     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    146   145   143   141   140   136   134   133   130   130   128   127
 SIGMA     12    12    11    11    11    11    11    11    11    11    11    11
 NREJ       0     0     0     0     2     0     0     0     0     0     0     3
 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    124   122   121   120   119   117   116   115   114   114   111   111
 SIGMA     11    11    11    10    10    10    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    108   107   107   105   104   103   101   100    99    98    98    97
 SIGMA     10    10    10    10    10    10    10    10     9     9     9     9
 NREJ       0     0     0     2     2     0     0     0     0     0     0     3
 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     95    94    95    91    91    91    91    89    88    86    87    87
 SIGMA      9     9     9     9     9     9     9     9     9     9     9     9
 NREJ       0     0     0     0     0     2     1     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     85    84    83    83    83    82    81    80    80    80    80    80
 SIGMA      9     9     9     9     9     9     9     8     8     8     8     8
 NREJ       0     0     0     2     4     0     0     0     0     0     4     7
 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    77    76    76    75    75    74    74    74    74    73    73
 SIGMA      8     8     8     8     8     8     8     8     8     8     8     8
 NREJ       1     0     0     0     0     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     72    72    73    73    74    72    71    70    70    70    70    69
 SIGMA      8     8     8     8     8     8     8     8     8     8     8     8
 NREJ       0     0     0     4     8     5     0     0     0     0     0     3
 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     69    69    68    68    67    68    66    66    67    68    66    66
 SIGMA      8     8     8     8     8     8     8     8     8     8     8     8
 NREJ       2     0     0     0     0     0     0     0     0     1     5     2
 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     66    66    66    65    66    67    66    66    65    64    65    65
 SIGMA      8     8     8     8     8     8     8     8     8     8     8     8
 NREJ       0     0     0     0     0     5     2     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     65    65    65    64    65    66    64    65    65    63    64    64
 SIGMA      8     8     8     7     8     8     8     8     8     7     8     7
 NREJ       0     0     0     0     0     1     0     0     0     0     0     1
 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     63    63    63    62    62    62    61    62    62    61    63    63
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       1     0     0     0     0     0     0     0     0     0     0     4
 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     61    60    60    61    61    60    61    60    59    58    58    59
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       2     0     0     0     0     3     6     2     0     0     2     2
 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     58    57    56    56    56    56    56    56    54    55    54    54
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     0     0     0     0     5     3     1     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     53    53    52    51    52    52    52    50    50    50    50    49
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     0     0     0     2     2     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     51    49    49    48    48    49    47    48    48    47    47    47
 SIGMA      7     7     7     6     6     6     6     6     6     6     6     6
 NREJ       0     1     0     0     0     0     2     1     0     0     0     0
 RADIUS  83.8  84.1  84.5
 BACKG     48    47    24
 SIGMA      6     6     3
 NREJ       1     6     1

 Starting spot search...
 sorting  1124 spots

  Median spot size is   4 x   4 pixels

  Total number of spots found:1124
  Number rejected as too small on X:   0
  Number rejected as too small on Y:   0
  Number rejected as too big on X:  16
  Number rejected as too big on Y:   7
  Number too close (SEPARATION keyword):   0
  Number stored as OK:1101



             Number of spots found in each bin
              26  12  10  17  21  11  13  19
              37  23  17  40  33  21  19  32
              44  50  18  40  41  29  22  45
              40  41  25  44  36  19  19  43
              33  14   9  34  28  26  14  36

 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  130 spots

 Based on a median spot size of  5 by  4 pixels in X and Y, the measurement box 
 parameters have been set to  17  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  5 by  4 pixels in X and Y, the spot separation 
 parameters (in X and Y) have been set to  0.57  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-ntest2_1.spt, Filename: ref-ntest2_1.spt


  1101 spots written for image    2
 A total of  1101 spots were written to file

 FORMATTED      OLD     file opened on unit  10

 Logical name: ref-ntest2_1.spt, Filename: ref-ntest2_1.spt


DPS Indexing at Two-theta =    0.00 with  948 reflections (minimum spot separation = 0.33mm. 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 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   180.31   129.29   127.64    89.8  90.2  89.7   I23,I213,I432,I4132
  43 514    cP   127.42   128.07   128.26   119.4  90.3 120.1   P23,P213,P432,P4232,P4332,P4132
  42 510    tP   127.42   127.64   128.26   119.9  89.7 119.7   P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
  41 509    tP   128.07   128.26   127.42    90.3 120.1 119.4   P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
  40 507    oP   127.42   128.07   128.26   119.4  90.3 120.1   P222,P2221,P21212,P212121
  39 504    hR   220.48   181.29   128.07    89.7 106.5 113.6   H3,H32 (hexagonal settings of R3 and R32)
  38 494    tI   129.29   180.31   127.64    89.8  89.8  90.3   I4,I41,I422,I4122
  37 488    oF   127.64   221.33   222.41    71.3  90.0  90.3   F222
  36 264    hP   128.07   127.42   128.26    90.3 119.4 120.1   P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
                                                                P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
  35 260    hR   221.33   181.29   128.17    90.8 106.0 114.2   H3,H32 (hexagonal settings of R3 and R32)
  34 260    oC   128.07   220.57   128.26    73.1 119.4  90.1   C222,C2221
  33 260    oC   127.64   222.41   127.42   106.2 119.7  90.0   C222,C2221
  32 259    hP   128.26   128.17   127.42   119.2  90.3 120.3   P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
                                                                P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
  31 259    oC   128.07   220.57   128.26    73.1 119.4  90.1   C222,C2221
  30 258    oC   127.64   222.41   127.42    73.8 119.7  90.0   C222,C2221
  29 256    mP   127.42   128.26   128.07   119.4 120.1  90.3   P2,P21
  28 255    mP   127.42   128.26   128.07   119.4 120.1  90.3   P2,P21
  27 255    oC   127.64   222.41   127.42   106.2 119.7  90.0   C222,C2221
  26 254    mP   128.26   127.42   128.17   119.2 120.3  90.3   P2,P21
  25 247    mC   127.64   221.33   128.17    74.0 119.8  89.7   C2
  24 245    mC   127.64   222.41   127.42    73.8 119.7  90.0   C2
  23 244    mC   127.64   222.41   127.42    73.8 119.7  90.0   C2
  22  22    tI   129.29   127.64   180.31    90.2  89.7  89.8   I4,I41,I422,I4122
  21  21    tI   127.42   128.26   182.07    89.4  90.5  90.3   I4,I41,I422,I4122
  20  19    cF   180.31   181.29   182.07    90.7  90.0  90.4   F23,F432,F4132
  19  18    oI   127.42   128.26   182.07    90.6  90.5  89.7   I222,I212121
  18  17    tI   129.29   127.64   180.31    90.2  89.7  89.8   I4,I41,I422,I4122
  17  16    oF   180.31   181.29   182.07    90.7  90.0  89.6   F222
  16  16    mC   180.31   181.29   128.07    89.7 134.7  89.6   C2
  15  15    mC   180.31   181.29   128.07    89.7 134.7  89.6   C2
  14  15    hR   127.42   128.07   316.00    89.4  90.5 120.1   H3,H32 (hexagonal settings of R3 and R32)
  13  13    mC   221.32   128.26   127.42    90.3 124.7  90.3   C2
  12  13    mI   127.42   182.07   128.26    89.4  90.3  90.5   C2
  11  13    hR   128.07   129.29   311.91    90.4  89.7 120.2   H3,H32 (hexagonal settings of R3 and R32)
  10  13    oI   127.64   129.29   180.31    89.7  90.2  89.8   I222,I212121
   9  12    oI   127.64   180.31   129.29    89.7  89.8  90.2   I222,I212121
   8  11    mC   221.70   127.42   128.26    90.3 124.8  90.2   C2
   7  10    mC   221.70   127.42   128.26    90.3 124.8  90.2   C2
   6  10    mC   221.33   127.64   180.31    90.2 144.3  89.7   C2
   5   8    mC   221.33   127.64   129.29    90.2 125.4  89.7   C2
   4   7    mC   221.32   128.26   127.42    90.3 124.7  90.3   C2
   3   7    mC   220.57   128.07   128.17    89.4 124.7  90.1   C2
   2   4    aP   127.42   128.07   128.26   119.4  90.3 120.1   P1
   1   0    aP   127.42   127.64   128.17    60.2  60.8  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 #20 with F23    (number 196) symmetry imposed

Initial cell (before refinement) is  181.2205  181.2205  181.2205  90.000  90.000  90.000
Using  928 indexed reflections (out of  948 spots found, {delta(XY) <= 2.5 sigma}),
final sd in spot positions is 0.08mm and in phi 0.23 degrees
Refined cell parameters  180.93  180.93  180.93  90.00  90.00  90.00
Beam coordinates of  93.58  92.24 have been refined to  93.60  92.00
This is a shift of  0.24mm or  0.189 times the minimum spot separation of ca  1.29mm.
  Final cell (after refinement) is   180.9307  180.9307  180.9307  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   9440.518  9200.215

 ****** 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-ntest2_1.gen      Filename: ref-ntest2_1.gen




 Title for MTZ and GENERATE Files (TITLE):
 .
 Crystal identifier (IDENT): ref-ntest2_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=    65

 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   185   187   198   192   195   163   196   183   179   206   186   170   172   193   164   176   187   188
 No gained         189   178
 Total intensity 94819 97549 98310 98703 99054 99283 99396 99540 99612 99681 99735 99780 99837 99873 99893 99917 99935 99952 99976
 Total intensity 99988 99998
 SD of intensity   182   184   184   185   185   185   185   187   187   187   187   188   188   188   188   188   190   190   190
 SD of intensity   190   192
 The mosaicity has been estimated as ---> 0.27 <--- for this image only; 
This value can be used cautiously as an initial estimate.
Storing space group from DPS autoindexing: F23        number 196



 *********** 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-ntest2_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-ntest2_1_001.img      Filename: /scisoft/pxsoft/data/dna_040402/ref-ntest2_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-ntest2_1_001.img

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

 Logical Name: /scisoft/pxsoft/data/dna_040402/ref-ntest2_1_001.img      Filename: /scisoft/pxsoft/data/dna_040402/ref-ntest2_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  116 spots
 Threshold set to    4.5
 sorting  118 spots
 Threshold set to    4.5


 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    357   349   345   338   331   322   317   310   303   295   290   284
 SIGMA     18    18    18    18    18    17    17    17    17    17    17    16
 NREJ      19    16    10    10     8     9     3     2     2     4     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    276   273   265   259   252   248   244   240   235   229   225   220
 SIGMA     16    16    16    16    15    15    15    15    15    15    14    14
 NREJ       1     0     1     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    217   214   209   206   202   198   194   191   189   186   182   180
 SIGMA     14    14    14    14    14    14    13    13    13    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    177   176   173   169   167   165   165   162   157   156   152   151
 SIGMA     13    13    13    13    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    149   146   142   141   141   140   136   134   133   132   130   127
 SIGMA     12    12    11    11    11    11    11    11    11    11    11    11
 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    127   125   123   123   122   121   122   120   116   115   113   112
 SIGMA     11    11    11    11    11    10    11    10    10    10    10    10
 NREJ       0     0     0     0     0     1     6     4     4     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    110   109   108   107   106   104   104   101   100    99    97    98
 SIGMA     10    10    10    10    10    10    10    10    10     9     9     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    96    95    95    93    92    93    92    90    88    88    87
 SIGMA      9     9     9     9     9     9     9     9     9     9     9     9
 NREJ       1     0     0     0     0     0     2     6     7     2     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     88    86    86    85    84    84    83    82    82    81    81    80
 SIGMA      9     9     9     9     9     9     9     9     9     9     9     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    79    79    78    77    78    79    80    79    76    75    75
 SIGMA      8     8     8     8     8     8     8     8     8     8     8     8
 NREJ       1     0     0     0     0     0     5     8     8     5     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     75    74    75    75    74    74    73    72    73    72    72    71
 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     72    71    70    69    68    69    69    70    69    68    67    67
 SIGMA      8     8     8     8     8     8     8     8     8     8     8     8
 NREJ       0     2     0     0     0     0     0     2     4     2     1     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     68    67    68    67    68    66    67    66    67    68    67    68
 SIGMA      8     8     8     8     8     8     8     8     8     8     8     8
 NREJ       0     0     4     2     2     0     0     0     0     0     7     7
 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     67    68    66    66    66    65    66    65    66    65    67    66
 SIGMA      8     8     8     8     8     8     8     8     8     8     8     8
 NREJ       5     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     66    65    65    66    66    66    66    65    64    65    65    65
 SIGMA      8     8     8     8     8     8     8     8     8     8     8     8
 NREJ       0     0     0     0     2     2     0     0     0     0     0     2
 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     65    65    63    63    63    63    63    63    61    62    62    62
 SIGMA      8     8     7     7     7     7     7     7     7     7     7     7
 NREJ       0     1     0     0     1     0     3     0     0     0     0     2
 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     61    61    60    59    59    58    58    59    60    58    57    57
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       4     4     2     0     0     0     0     2     1     3     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     56    56    55    55    55    54    54    54    54    53    53    53
 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  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     53    52    51    50    50    49    50    50    50    50    49    49
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     6
 NREJ       0     0     1     1     0     0     0     1     0     3     4     3
 RADIUS  83.8  84.1  84.5
 BACKG     49    48    24
 SIGMA      7     6     3
 NREJ       0     0     0

 Starting spot search...
 sorting  957 spots

  Median spot size is   4 x   4 pixels

  Total number of spots found: 957
  Number rejected as too small on X:   0
  Number rejected as too small on Y:   0
  Number rejected as too big on X:   7
  Number rejected as too big on Y:   2
  Number too close (SEPARATION keyword):   0
  Number stored as OK: 948



             Number of spots found in each bin
              21  14   7  22  24   8   9  17
              36  19  13  29  34  17  19  33
              38  27  21  39  42  19  20  37
              35  20  20  31  38  16  20  36
              21  21  14  35  21  20  14  21

 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  118 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_040402/ref-ntest2_1_002.img

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

 Logical Name: /scisoft/pxsoft/data/dna_040402/ref-ntest2_1_002.img      Filename: /scisoft/pxsoft/data/dna_040402/ref-ntest2_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    354   349   342   339   329   321   314   306   301   290   286   281
 SIGMA     18    18    18    18    18    17    17    17    17    17    16    16
 NREJ      19    13    13     4     7     3     6     3     1     6     3     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    275   269   263   256   253   247   240   235   231   227   224   219
 SIGMA     16    16    16    16    15    15    15    15    15    15    14    14
 NREJ       0     0     0     2     0     0     1     0     0     0     1     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    213   208   206   203   202   198   194   189   188   184   181   178
 SIGMA     14    14    14    14    14    14    13    13    13    13    13    13
 NREJ       2     0     0     0     3     7     3     0     0     0     2     8
 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    175   173   170   168   164   162   160   158   154   152   150   149
 SIGMA     13    13    13    12    12    12    12    12    12    12    12    12
 NREJ      10     4     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    146   145   143   141   140   136   134   133   130   130   128   127
 SIGMA     12    12    11    11    11    11    11    11    11    11    11    11
 NREJ       0     0     0     0     2     0     0     0     0     0     0     3
 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    124   122   121   120   119   117   116   115   114   114   111   111
 SIGMA     11    11    11    10    10    10    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    108   107   107   105   104   103   101   100    99    98    98    97
 SIGMA     10    10    10    10    10    10    10    10     9     9     9     9
 NREJ       0     0     0     2     2     0     0     0     0     0     0     3
 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     95    94    95    91    91    91    91    89    88    86    87    87
 SIGMA      9     9     9     9     9     9     9     9     9     9     9     9
 NREJ       0     0     0     0     0     2     1     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     85    84    83    83    83    82    81    80    80    80    80    80
 SIGMA      9     9     9     9     9     9     9     8     8     8     8     8
 NREJ       0     0     0     2     4     0     0     0     0     0     4     7
 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    77    76    76    75    75    74    74    74    74    73    73
 SIGMA      8     8     8     8     8     8     8     8     8     8     8     8
 NREJ       1     0     0     0     0     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     72    72    73    73    74    72    71    70    70    70    70    69
 SIGMA      8     8     8     8     8     8     8     8     8     8     8     8
 NREJ       0     0     0     4     8     5     0     0     0     0     0     3
 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     69    69    68    68    67    68    66    66    67    68    66    66
 SIGMA      8     8     8     8     8     8     8     8     8     8     8     8
 NREJ       2     0     0     0     0     0     0     0     0     1     5     2
 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     66    66    66    65    66    67    66    66    65    64    65    65
 SIGMA      8     8     8     8     8     8     8     8     8     8     8     8
 NREJ       0     0     0     0     0     5     2     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     65    65    65    64    65    66    64    65    65    63    64    64
 SIGMA      8     8     8     7     8     8     8     8     8     7     8     7
 NREJ       0     0     0     0     0     1     0     0     0     0     0     1
 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     63    63    63    62    62    62    61    62    62    61    63    63
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       1     0     0     0     0     0     0     0     0     0     0     4
 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     61    60    60    61    61    60    61    60    59    58    58    59
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       2     0     0     0     0     3     6     2     0     0     2     2
 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     58    57    56    56    56    56    56    56    54    55    54    54
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     0     0     0     0     5     3     1     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     53    53    52    51    52    52    52    50    50    50    50    49
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     0     0     0     2     2     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     51    49    49    48    48    49    47    48    48    47    47    47
 SIGMA      7     7     7     6     6     6     6     6     6     6     6     6
 NREJ       0     1     0     0     0     0     2     1     0     0     0     0
 RADIUS  83.8  84.1  84.5
 BACKG     48    47    24
 SIGMA      6     6     3
 NREJ       1     6     1

 Starting spot search...
 sorting  1149 spots

  Median spot size is   5 x   4 pixels

  Total number of spots found:1149
  Number rejected as too small on X:  16
  Number rejected as too small on Y:   0
  Number rejected as too big on X:   4
  Number rejected as too big on Y:  17
  Number too close (SEPARATION keyword):   2
  Number stored as OK:1110



             Number of spots found in each bin
              25  13  11  18  22  11  13  21
              36  23  17  40  33  22  19  32
              44  48  18  43  42  28  22  44
              41  40  26  45  38  20  19  43
              33  15   9  34  30  22  15  37

 FORMATTED      UNKNOWN file opened on unit  10

 Logical name: ref-ntest2_1.spt, Filename: ref-ntest2_1.spt


   948 spots written for image    1
  1110 spots written for image    2
 A total of  2058 spots were written to file

 FORMATTED      OLD     file opened on unit  10

 Logical name: ref-ntest2_1.spt, Filename: ref-ntest2_1.spt


DPS Indexing at Two-theta =    0.00 with 1775 reflections (minimum spot separation = 0.33mm. Maximum expected cell edge  297.43, Beam position is   93.58   92.24
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   127.83   180.65   128.22    90.0  90.1  90.0   I23,I213,I432,I4132
  43 505    cP   127.78   127.90   127.93   120.0 119.8  90.1   P23,P213,P432,P4232,P4332,P4132
  42 504    tP   127.90   127.93   127.78   119.8  90.1 120.0   P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
  41 504    tP   127.93   127.93   127.78   119.8 120.0  90.2   P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
  40 503    oP   127.78   127.90   127.93   120.0 119.8  90.1   P222,P2221,P21212,P212121
  39 501    hR   221.38   181.18   127.78    89.9 106.7 114.1   H3,H32 (hexagonal settings of R3 and R32)
  38 500    tI   128.22   180.65   127.83    90.0  89.9  90.0   I4,I41,I422,I4122
  37 499    oF   127.83   221.46   221.60    70.7  90.0  90.1   F222
  36 253    oC   127.83   221.60   127.78    73.4 119.9  90.0   C222,C2221
  35 253    oC   127.93   221.44   127.78    73.2 119.8  90.0   C222,C2221
  34 253    hP   127.93   127.90   127.78    90.1 119.8 120.0   P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
                                                                P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
  33 253    oC   127.93   221.44   127.78    73.2 119.8  90.0   C222,C2221
  32 252    hP   127.93   127.90   127.78    90.1 119.8 120.0   P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
                                                                P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
  31 252    mP   127.78   127.93   127.93    90.2 120.0 119.8   P2,P21
  30 252    mP   127.78   127.93   127.93    90.2 120.0 119.8   P2,P21
  29 252    oC   127.93   221.44   127.78    73.2 119.8  90.0   C222,C2221
  28 252    hR   181.18   221.46   127.90    73.3  89.9 114.2   H3,H32 (hexagonal settings of R3 and R32)
  27 252    oC   127.83   221.60   127.78   106.6 119.9  90.0   C222,C2221
  26 251    mP   127.90   127.78   127.93   119.8 120.0  90.1   P2,P21
  25 250    mC   127.83   221.46   127.93    73.4 120.0  89.9   C2
  24 250    mC   127.83   221.60   127.78   106.6 119.9  90.0   C2
  23 249    mC   127.83   221.60   127.78   106.6 119.9  90.0   C2
  22   5    cF   180.65   180.93   181.18    90.2  90.0  90.1   F23,F432,F4132
  21   4    tI   127.78   127.90   181.18    89.9  89.9  89.9   I4,I41,I422,I4122
  20   4    tI   127.83   128.22   180.65    90.0  90.0  90.1   I4,I41,I422,I4122
  19   4    tI   127.83   128.22   180.65    90.0  90.0  89.9   I4,I41,I422,I4122
  18   4    hR   127.78   127.93   313.78    89.8  90.1 120.0   H3,H32 (hexagonal settings of R3 and R32)
  17   4    oF   180.65   181.18   180.93    90.2  90.1  90.0   F222
  16   4    oI   127.78   127.90   181.18    90.1  90.1  89.9   I222,I212121
  15   4    hR   127.93   128.22   312.95    90.1  89.9 120.1   H3,H32 (hexagonal settings of R3 and R32)
  14   3    mC   180.65   181.18   127.78    89.9 134.9  90.0   C2
  13   3    mC   221.55   127.78   127.90    89.9 125.1  90.0   C2
  12   3    oI   127.83   180.65   128.22    90.0  89.9  90.0   I222,I212121
  11   3    mC   221.55   127.78   127.90    89.9 125.1  90.0   C2
  10   2    mI   127.78   181.18   127.90    90.1  90.1  89.9   C2
   9   2    mC   221.48   127.90   127.78    90.1 125.1  90.0   C2
   8   2    oI   180.65   128.22   127.83    89.9  90.0  90.0   I222,I212121
   7   2    mC   180.93   180.65   127.83    90.0 134.9  90.1   C2
   6   2    mC   221.48   127.90   127.78    90.1 125.1  90.0   C2
   5   2    mC   221.46   127.83   180.65    90.0 144.6  89.9   C2
   4   2    mC   180.93   180.65   128.22    90.0 135.0  89.9   C2
   3   2    mC   180.65   181.18   127.78    90.1 134.9  90.0   C2
   2   1    aP   127.78   127.90   127.93   120.0 119.8  90.1   P1
   1   0    aP   127.78   127.83   127.90    60.0  89.9  60.1   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 #22 with F23    (number 196) symmetry imposed

Initial cell (before refinement) is  180.9202  180.9202  180.9202  90.000  90.000  90.000
Using 1689 indexed reflections (out of 1775 spots found, {delta(XY) <= 2.5 sigma}),
final sd in spot positions is 0.10mm and in phi 0.27 degrees
Refined cell parameters  180.95  180.95  180.95  90.00  90.00  90.00
Beam coordinates of  93.58  92.24 have been refined to  93.60  91.97
This is a shift of  0.27mm or  0.212 times the minimum spot separation of ca  1.29mm.
  Final cell (after refinement) is   180.9525  180.9525  180.9525  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   9440.746  9197.264

 ****** 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-ntest2_1.gen      Filename: ref-ntest2_1.gen




 Title for MTZ and GENERATE Files (TITLE):
 .
 Crystal identifier (IDENT): ref-ntest2_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=    72

 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         179   398   420   386   396   368   378   379   360   365   350    50    39    43    37    40    53    33    40
 No gained          50    25
 Total intensity 59689 67680 76955 83601 93942 98447 99746 99894 99943 99981 99998 99955 99908 99849 99783 99751 99695 99652 99349
 Total intensity 99130 99064
 SD of intensity   245   265   292   303   345   350   352   352   354   354   354   354   354   354   354   354   354   354   354
 SD of intensity   354   354
 The mosaicity has been estimated as ---> 0.42 <--- for this image only; 
This value can be used cautiously as an initial estimate.
Storing space group from DPS autoindexing: F23        number 196
Storing space group from DPS autoindexing: F23        number 196



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