Data Processing Module Log - Back to the index result page



 ************ Version 7.0.0 (beta test)  for Image plate and CCD data 14th June 2006  ***********
 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
 ===> directory /scisoft/users/svensson/tmp/dataBenchmark/AV01-3342167Aa_1
 ===> template ref-AV01-3342167Aa_1_###.img
 ===> BEST ON
 ===> prerefine on
  ****** Keyword NOT RECOGNISED ***** 
 ===> autoindex dps refine image 1 thresh 20.000000
Using DPS code for background indexing
Pre-refining solutions better than penalty of 200 prior to choosing a DPS solution
 ===> autoindex dps refine image 2 thresh 20.000000
Using DPS code for background indexing
Pre-refining solutions better than penalty of 200 prior to choosing a DPS solution
 ===> mosaic estimate
 ===> go

 From information in the image file, the detector has been 
 recognized as: ADSC
 If this is incorrect you must supply a DETECTOR keyword


 Crystal to detector distance of  287.49mm taken from image header

 Wavelength of 0.97950A taken from image header

 Pixel size of 0.1026mm taken from image header.

 Start and end phi values for image     0 from image header are     0.00 and    1.00 degrees.

 Oscillation axis set as PHI from image header

 Main beam position has been calculated as  156.93mm  158.88mm from parameters
 in the image header. You should check these values carefully as they may
 be in error!


 Autoindexing using  2 images
 Image numbers:     1    2
 image FILENAME: /scisoft/users/svensson/tmp/dataBenchmark/AV01-3342167Aa_1/ref-AV01-3342167Aa_1_001.img

 Determining average spot size for spots in centre of image.
 ==========================================================
 Determining best threshold for spot finding.
 Default parameters may be reset with SPOTS keyword.
 Minimum radius  15.8mm, maximum radius 63.07mm, minimum number of spots 10
 Threshold set to    5.0
 Threshold set to    5.0

 Based on a median spot size of  4 by  3 pixels in X and Y, the measurement box 
 parameters have been set to  15  13   8   5   4
 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  3 pixels in X and Y, the spot separation 
 parameters (in X and Y) have been set to  0.61  0.51mm.
 Closest possible spot separation is  0.00mm.
 Determining best threshold for spot finding.
 Default parameters may be reset with SPOTS keyword.
 Minimum radius  15.8mm, maximum radius 63.07mm, minimum number of spots 10
 Threshold set to    5.0
 Threshold set to    5.0


 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 0.0mm from the image centre in Y to avoid any
 backstop shadow
 ** WARNING **
 Fewer than 17 pixels with values greater than    0 (keyword NULLPIX) at a radius of 51.81mm
 ** WARNING **
 Fewer than 17 pixels with values greater than    0 (keyword NULLPIX) at a radius of 51.91mm
 ** WARNING **
 Fewer than 17 pixels with values greater than    0 (keyword NULLPIX) at a radius of 52.01mm
 ** WARNING **
 Fewer than 17 pixels with values greater than    0 (keyword NULLPIX) at a radius of 52.11mm
 Radial Background calculation complete
 RADIUS  15.7  16.1  16.5  16.9  17.3  17.7  18.2  18.6  19.0  19.4  19.8  20.2
 BACKG   6714  6520  6319  6127  5982  5841  5657  5504  5382  5259  5139  5028
 SIGMA     40    40    39    39    38    38    37    37    36    36    35    35
 NREJ      17    18    18    27    18    14    24    30    19    22    12    15
 RADIUS  20.6  21.0  21.4  21.9  22.3  22.7  23.1  23.5  23.9  24.3  24.7  25.1
 BACKG   4892  4771  4666  4567  4470  4377  4271  4186  4100  4029  3943  3858
 SIGMA     34    34    34    33    33    33    32    32    32    31    31    31
 NREJ      17    22    20    14    17    16    24    18    14     8    10    15
 RADIUS  25.5  26.0  26.4  26.8  27.2  27.6  28.0  28.4  28.8  29.2  29.6  30.1
 BACKG   3771  3695  3632  3564  3510  3422  3365  3308  3253  3183  3129  3087
 SIGMA     30    30    30    29    29    29    29    28    28    28    27    27
 NREJ      27    22    14     9     6    19    18    18    13    11    14     8
 RADIUS  30.5  30.9  31.3  31.7  32.1  32.5  32.9  33.3  33.8  34.2  34.6  35.0
 BACKG   3014  2970  2920  2868  2838  2784  2741  2670  2639  2603  2562  2523
 SIGMA     27    27    27    26    26    26    26    25    25    25    25    25
 NREJ      19    18    16    14     7     8    14    17    14    10    11    19
 RADIUS  35.4  35.8  36.2  36.6  37.0  37.4  37.9  38.3  38.7  39.1  39.5  39.9
 BACKG   2482  2436  2401  2367  2335  2299  2263  2232  2191  2155  2138  2107
 SIGMA     24    24    24    24    24    23    23    23    23    23    23    22
 NREJ      12    17    17    13    11    11     8     8    11    20    13    17
 RADIUS  40.3  40.7  41.1  41.5  42.0  42.4  42.8  43.2  43.6  44.0  44.4  44.8
 BACKG   2076  2042  2017  1990  1956  1914  1890  1876  1857  1819  1801  1774
 SIGMA     22    22    22    22    22    21    21    21    21    21    21    21
 NREJ      10     8     9     8    10    17    20     9     8    18    12    14
 RADIUS  45.2  45.7  46.1  46.5  46.9  47.3  47.7  48.1  48.5  48.9  49.3  49.8
 BACKG   1738  1723  1693  1681  1661  1644  1611  1593  1575  1554  1536  1516
 SIGMA     20    20    20    20    20    20    20    19    19    19    19    19
 NREJ      23    14    22    10    11    10    13    12    15    11    10    13
 RADIUS  50.2  50.6  51.0  51.4  51.8  52.2  52.6  53.0  53.4  53.9  54.3  54.7
 BACKG   1510  1489  1462  1435  1435  1387  1390  1384  1365  1354  1325  1311
 SIGMA     19    19    19    18    18    18    18    18    18    18    18    18
 NREJ      14    15    16    13    51    15    13    12    10     7    12    10
 RADIUS  55.1  55.5  55.9  56.3  56.7  57.1  57.6  58.0  58.4  58.8  59.2  59.6
 BACKG   1303  1293  1274  1258  1249  1230  1218  1206  1199  1175  1157  1162
 SIGMA     18    17    17    17    17    17    17    17    17    17    17    17
 NREJ      13    10    10    14     8    13    17    17    13    15    22    15
 RADIUS  60.0  60.4  60.8  61.2  61.7  62.1  62.5  62.9  63.3  63.7  64.1  64.5
 BACKG   1157  1140  1137  1126  1112  1102  1094  1074  1063  1052  1043  1044
 SIGMA     17    16    16    16    16    16    16    16    16    16    16    16
 NREJ      14    21    17    14    10    12     9    13    16    12    20    16
 RADIUS  64.9  65.3  65.8  66.2  66.6  67.0  67.4  67.8  68.2  68.6  69.0  69.5
 BACKG   1034  1020  1024  1015  1008  1001  1001   993   988   975   967   952
 SIGMA     16    15    15    15    15    15    15    15    15    15    15    15
 NREJ      17    21    10    11     9    16    10     9     7    12    18    14
 RADIUS  69.9  70.3  70.7  71.1  71.5  71.9  72.3  72.7  73.1  73.6  74.0  74.4
 BACKG    956   947   937   938   926   934   919   909   911   903   900   905
 SIGMA     15    15    15    15    15    15    15    15    15    15    15    15
 NREJ      12    11     8     9    16     9    19    16    12    17    17    11
 RADIUS  74.8  75.2  75.6  76.0  76.4  76.8  77.2  77.7  78.1  78.5  78.9  79.3
 BACKG    903   899   885   886   878   878   878   870   868   857   852   840
 SIGMA     15    14    14    14    14    14    14    14    14    14    14    14
 NREJ      13    11    24    14    22    19    23    22    17    12    12    15
 RADIUS  79.7  80.1  80.5  80.9  81.4  81.8  82.2  82.6  83.0  83.4  83.8  84.2
 BACKG    842   828   825   824   819   813   798   799   784   779   770   765
 SIGMA     14    14    14    14    14    14    14    14    14    13    13    13
 NREJ      14    16    13     5    10    12    16    12    19    15    17    15
 RADIUS  84.6  85.0  85.5  85.9  86.3  86.7  87.1  87.5  87.9  88.3  88.7  89.1
 BACKG    763   753   742   737   736   725   719   709   697   698   681   681
 SIGMA     13    13    13    13    13    13    13    13    13    13    13    13
 NREJ      15    10    22    14    13    15     9    12    16     9    20     9
 RADIUS  89.6  90.0  90.4  90.8  91.2  91.6  92.0  92.4  92.8  93.3  93.7  94.1
 BACKG    672   661   657   652   653   645   636   625   613   613   607   597
 SIGMA     12    12    12    12    12    12    12    12    12    12    12    12
 NREJ      15    21    17    14     6     7     9    15    15    11     8    15
 RADIUS  94.5  94.9  95.3  95.7  96.1  96.5  96.9  97.4  97.8  98.2  98.6  99.0
 BACKG    592   584   584   580   568   571   559   560   554   541   540   540
 SIGMA     12    12    12    12    11    11    11    11    11    11    11    11
 NREJ      13    21    13    11    17     8    18    10    11    18    17    15
 RADIUS  99.4  99.8 100.2 100.6 101.0 101.5 101.9 102.3 102.7 103.1 103.5 103.9
 BACKG    535   528   519   513   510   513   500   486   492   485   480   477
 SIGMA     11    11    11    11    11    11    11    11    11    11    10    10
 NREJ      10     8    13    14    18    11    18    22    13    18    18    10
 RADIUS 104.3 104.7 105.2 105.6 106.0 106.4 106.8 107.2 107.6 108.0 108.4 108.8
 BACKG    473   470   467   465   460   452   446   443   444   444   436   430
 SIGMA     10    10    10    10    10    10    10    10    10    10    10    10
 NREJ      16    19    18    13    10    12    21    16    10    13    14    17
 RADIUS 109.3 109.7 110.1 110.5 110.9 111.3 111.7 112.1 112.5 112.9 113.4 113.8
 BACKG    431   428   418   417   415   414   413   413   406   405   406   403
 SIGMA     10    10    10    10    10    10    10    10    10    10    10    10
 NREJ      11    10    14    10    12    11     9    11    15    12     7     9
 RADIUS 114.2 114.6 115.0 115.4 115.8 116.2 116.6 117.1 117.5 117.9 118.3 118.7
 BACKG    395   395   396   389   386   384   376   377   378   373   374   377
 SIGMA      9     9     9     9     9     9     9     9     9     9     9     9
 NREJ      18     9    12    14    15    12    25    17    10    13    15     8
 RADIUS 119.1 119.5 119.9 120.3 120.7 121.2 121.6 122.0 122.4 122.8 123.2 123.6
 BACKG    368   369   364   358   359   359   353   351   355   356   348   350
 SIGMA      9     9     9     9     9     9     9     9     9     9     9     9
 NREJ      19     9    15    13     7    10    10    12     7    13    15    14
 RADIUS 124.0 124.4 124.8 125.3 125.7 126.1 126.5 126.9 127.3 127.7 128.1 128.5
 BACKG    348   344   342   339   338   339   333   336   335   337   331   328
 SIGMA      9     9     9     9     9     9     9     9     9     9     9     9
 NREJ      10    13    15    11    17    14    20    13     9    10    12    15
 RADIUS 129.0 129.4 129.8 130.2 130.6 131.0 131.4 131.8 132.2 132.6 133.1 133.5
 BACKG    330   328   324   325   328   322   322   319   318   317   316   314
 SIGMA      9     9     9     9     9     8     8     8     8     8     8     8
 NREJ      10    18    16    12    10    15     8    10    13    13    13    11
 RADIUS 133.9 134.3 134.7 135.1 135.5 135.9 136.3 136.7 137.2 137.6 138.0 138.4
 BACKG    315   311   310   311   305   303   305   308   311   302   299   300
 SIGMA      8     8     8     8     8     8     8     8     8     8     8     8
 NREJ       8    11     8     9    17    11    11    11     7    14    20    12
 RADIUS 138.8 139.2 139.6 140.0 140.4 140.9 141.3 141.7
 BACKG    300   302   299   298   298   299   295    73
 SIGMA      8     8     8     8     8     8     8     2
 NREJ      14    11    10     7     9     7    12     3

 Starting spot search...
 Number of spots excluded from possible ice rings:     521

  Median spot size is   7 x   6 pixels, mode size is   6 by   5

  Total number of spots found:2297
  Number rejected as too small on X: 234
  Number rejected as too small on Y:  48
  Number rejected as too big on X:  47
  Number rejected as too big on Y:   8
  Number too close (SEPARATION keyword): 135
  (currently SEPARATION   0.61  0.51)
  Number stored as OK: 805
  highest resolution is     2.16 Angstrom
  99% have resolution less than     2.21 Angstrom



             Number of spots found in each bin
              68  12  18  34  33  19  19  52
             108  21  16  32  25  11  25 109
             256   4   3  11   4   2   9 236
             293   0   0   0   0   0   5 198
             152   0   0   0   0   0   2 109
 image FILENAME: /scisoft/users/svensson/tmp/dataBenchmark/AV01-3342167Aa_1/ref-AV01-3342167Aa_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 0.0mm from the image centre in Y to avoid any
 backstop shadow
 ** WARNING **
 Fewer than 17 pixels with values greater than    0 (keyword NULLPIX) at a radius of 51.81mm
 ** WARNING **
 Fewer than 17 pixels with values greater than    0 (keyword NULLPIX) at a radius of 51.91mm
 ** WARNING **
 Fewer than 17 pixels with values greater than    0 (keyword NULLPIX) at a radius of 52.01mm
 ** WARNING **
 Fewer than 17 pixels with values greater than    0 (keyword NULLPIX) at a radius of 52.11mm
 Radial Background calculation complete
 RADIUS  15.7  16.1  16.5  16.9  17.3  17.7  18.2  18.6  19.0  19.4  19.8  20.2
 BACKG   6750  6555  6336  6167  6023  5855  5716  5580  5428  5303  5186  5043
 SIGMA     41    40    39    39    38    38    37    37    36    36    36    35
 NREJ      17    22    30    28    24    23    14    17    20    13    14    20
 RADIUS  20.6  21.0  21.4  21.9  22.3  22.7  23.1  23.5  23.9  24.3  24.7  25.1
 BACKG   4930  4823  4696  4613  4516  4420  4317  4186  4136  4050  3956  3889
 SIGMA     35    34    34    33    33    33    32    32    32    31    31    31
 NREJ      19    12    17    10     8     8    15    20    18    13    17    19
 RADIUS  25.5  26.0  26.4  26.8  27.2  27.6  28.0  28.4  28.8  29.2  29.6  30.1
 BACKG   3809  3717  3664  3581  3526  3462  3388  3328  3256  3199  3165  3110
 SIGMA     30    30    30    29    29    29    29    28    28    28    28    27
 NREJ      19    26    11    14    10    13    19    15    22    21     8    10
 RADIUS  30.5  30.9  31.3  31.7  32.1  32.5  32.9  33.3  33.8  34.2  34.6  35.0
 BACKG   3046  2995  2935  2907  2858  2802  2745  2702  2663  2618  2585  2542
 SIGMA     27    27    27    26    26    26    26    25    25    25    25    25
 NREJ      15    15    18     9    10    12     9    18    15    12     9    10
 RADIUS  35.4  35.8  36.2  36.6  37.0  37.4  37.9  38.3  38.7  39.1  39.5  39.9
 BACKG   2516  2473  2414  2380  2358  2316  2283  2248  2220  2188  2157  2131
 SIGMA     25    24    24    24    24    24    23    23    23    23    23    23
 NREJ      13    13    26    22    17    17    13    15    13    16    22    15
 RADIUS  40.3  40.7  41.1  41.5  42.0  42.4  42.8  43.2  43.6  44.0  44.4  44.8
 BACKG   2088  2062  2028  2008  1976  1941  1920  1893  1871  1848  1830  1804
 SIGMA     22    22    22    22    22    22    21    21    21    21    21    21
 NREJ      15     8    13    14    13    12    12    10    13    13    12    17
 RADIUS  45.2  45.7  46.1  46.5  46.9  47.3  47.7  48.1  48.5  48.9  49.3  49.8
 BACKG   1770  1734  1731  1702  1678  1661  1650  1622  1593  1571  1555  1531
 SIGMA     21    20    20    20    20    20    20    20    19    19    19    19
 NREJ      10    16    11    12    15    11     6    11    14    12    15    16
 RADIUS  50.2  50.6  51.0  51.4  51.8  52.2  52.6  53.0  53.4  53.9  54.3  54.7
 BACKG   1518  1507  1488  1454  1443  1432  1414  1417  1393  1379  1360  1353
 SIGMA     19    19    19    19    18    18    18    18    18    18    18    18
 NREJ      18    13    18    19    51    21    19     9    19    19    20    10
 RADIUS  55.1  55.5  55.9  56.3  56.7  57.1  57.6  58.0  58.4  58.8  59.2  59.6
 BACKG   1340  1328  1304  1289  1281  1255  1253  1241  1221  1208  1204  1192
 SIGMA     18    18    18    17    17    17    17    17    17    17    17    17
 NREJ       7     7    10    14    16    20    14    12    16    19    11    11
 RADIUS  60.0  60.4  60.8  61.2  61.7  62.1  62.5  62.9  63.3  63.7  64.1  64.5
 BACKG   1178  1175  1172  1162  1157  1145  1143  1140  1135  1136  1135  1129
 SIGMA     17    17    17    17    17    16    16    16    16    16    16    16
 NREJ      12    13    10    10    16    13     4    10    11     8    14    21
 RADIUS  64.9  65.3  65.8  66.2  66.6  67.0  67.4  67.8  68.2  68.6  69.0  69.5
 BACKG   1121  1125  1124  1117  1103  1083  1069  1061  1063  1042  1026  1018
 SIGMA     16    16    16    16    16    16    16    16    16    16    16    15
 NREJ      19    17    16    10     7    12    10    14    16    21    21    15
 RADIUS  69.9  70.3  70.7  71.1  71.5  71.9  72.3  72.7  73.1  73.6  74.0  74.4
 BACKG   1010  1006  1002   993   996   980   977   972   970   974   973   973
 SIGMA     15    15    15    15    15    15    15    15    15    15    15    15
 NREJ      17    20    14    19    10    18    19    12    14    14     7     9
 RADIUS  74.8  75.2  75.6  76.0  76.4  76.8  77.2  77.7  78.1  78.5  78.9  79.3
 BACKG    967   973   969   982   974   976   972   977   973   963   960   949
 SIGMA     15    15    15    15    15    15    15    15    15    15    15    15
 NREJ       9    11    14    12    17    13    13    10    10    14    16    13
 RADIUS  79.7  80.1  80.5  80.9  81.4  81.8  82.2  82.6  83.0  83.4  83.8  84.2
 BACKG    933   931   924   915   898   891   873   867   851   844   834   823
 SIGMA     15    15    15    15    14    14    14    14    14    14    14    14
 NREJ      19    13    14    12    18    15    20     9    16    14    12    13
 RADIUS  84.6  85.0  85.5  85.9  86.3  86.7  87.1  87.5  87.9  88.3  88.7  89.1
 BACKG    815   807   797   785   774   766   761   747   746   736   731   722
 SIGMA     14    14    14    14    13    13    13    13    13    13    13    13
 NREJ      12    13    13    15    18    18    12    17    12    10     7     7
 RADIUS  89.6  90.0  90.4  90.8  91.2  91.6  92.0  92.4  92.8  93.3  93.7  94.1
 BACKG    702   701   696   690   679   669   654   652   645   641   633   630
 SIGMA     13    13    13    13    13    12    12    12    12    12    12    12
 NREJ      16    12    11     6    11    10    20    11    20    22    15    14
 RADIUS  94.5  94.9  95.3  95.7  96.1  96.5  96.9  97.4  97.8  98.2  98.6  99.0
 BACKG    617   618   612   606   597   589   582   584   582   575   568   563
 SIGMA     12    12    12    12    12    12    12    12    12    11    11    11
 NREJ      22    14    11    10    19    18    17     8    10    10    10    12
 RADIUS  99.4  99.8 100.2 100.6 101.0 101.5 101.9 102.3 102.7 103.1 103.5 103.9
 BACKG    552   546   545   541   528   531   525   515   515   512   511   504
 SIGMA     11    11    11    11    11    11    11    11    11    11    11    11
 NREJ      15    12    10    11    20    10    10    18    22    17    12    15
 RADIUS 104.3 104.7 105.2 105.6 106.0 106.4 106.8 107.2 107.6 108.0 108.4 108.8
 BACKG    494   491   487   482   477   470   469   467   470   462   454   451
 SIGMA     11    11    11    10    10    10    10    10    10    10    10    10
 NREJ      14    12    15    13     8    13    11    13     8    10    18    16
 RADIUS 109.3 109.7 110.1 110.5 110.9 111.3 111.7 112.1 112.5 112.9 113.4 113.8
 BACKG    454   446   445   445   440   437   436   429   427   424   417   420
 SIGMA     10    10    10    10    10    10    10    10    10    10    10    10
 NREJ       9    13    12    12    12    14    10    15    22    13    20    14
 RADIUS 114.2 114.6 115.0 115.4 115.8 116.2 116.6 117.1 117.5 117.9 118.3 118.7
 BACKG    418   414   409   407   403   401   402   397   395   389   389   390
 SIGMA     10    10    10    10    10    10    10     9     9     9     9     9
 NREJ       8     9    18    12    14    16     8     8    11    16    11     9
 RADIUS 119.1 119.5 119.9 120.3 120.7 121.2 121.6 122.0 122.4 122.8 123.2 123.6
 BACKG    388   383   382   380   379   378   372   368   370   368   365   366
 SIGMA      9     9     9     9     9     9     9     9     9     9     9     9
 NREJ      13    12    10     9     8    11    10    17    11    13    15     8
 RADIUS 124.0 124.4 124.8 125.3 125.7 126.1 126.5 126.9 127.3 127.7 128.1 128.5
 BACKG    367   362   359   358   358   359   352   351   349   351   357   350
 SIGMA      9     9     9     9     9     9     9     9     9     9     9     9
 NREJ       7     9    17    15    14    11    17    18    18    15     9    11
 RADIUS 129.0 129.4 129.8 130.2 130.6 131.0 131.4 131.8 132.2 132.6 133.1 133.5
 BACKG    349   341   345   344   343   345   340   338   341   341   339   335
 SIGMA      9     9     9     9     9     9     9     9     9     9     9     9
 NREJ      11    19    14    18    18    13    19    18    12    15    12    17
 RADIUS 133.9 134.3 134.7 135.1 135.5 135.9 136.3 136.7 137.2 137.6 138.0 138.4
 BACKG    331   330   330   330   332   326   329   326   324   323   324   321
 SIGMA      9     9     9     9     9     9     9     9     9     8     9     8
 NREJ      15    15    12    11     8    19    11     9    14    14    10    14
 RADIUS 138.8 139.2 139.6 140.0 140.4 140.9 141.3 141.7
 BACKG    320   320   319   316   318   311   313    79
 SIGMA      8     8     8     8     8     8     8     2
 NREJ      11    13    10    15    12    18    14     1

 Starting spot search...
 Number of spots excluded from possible ice rings:     236

  Median spot size is   8 x   6 pixels, mode size is   6 by   5

  Total number of spots found:1920
  Number rejected as too small on X: 119
  Number rejected as too small on Y:  31
  Number rejected as too big on X:  28
  Number rejected as too big on Y:   9
  Number too close (SEPARATION keyword): 143
  (currently SEPARATION   0.61  0.51)
  Number stored as OK: 696
  highest resolution is     2.16 Angstrom
  99% have resolution less than     2.31 Angstrom



             Number of spots found in each bin
              37   8  19  36  32  10   8  51
             135   2  18  31  17   8   4  76
             257   0   8   7   1   0   2 217
             269   0   4   0   0   0   0 169
             132   0   0   0   0   0   0  78

FORMATTED      UNKNOWN file opened on unit  10

Logical name: ref-AV01-3342167Aa_1.spt, Filename: ref-AV01-3342167Aa_1.spt


   805 spots written for image    1
   696 spots written for image    2
 A total of  1501 spots were written to file

FORMATTED      OLD     file opened on unit  10

Logical name: ref-AV01-3342167Aa_1.spt, Filename: ref-AV01-3342167Aa_1.spt


DPS Indexing using  583 reflections with I >=  20 I/sigma(I)
DPS Indexing at Two-theta =    0.00 with  583 reflections (minimum spot separation = 0.62mm. Maximum expected cell edge  293.51, Beam position is  156.93  158.88
Generating direct lattice vectors (This may take some time):
|-----------------|
..................
 Refining  30 direct space vectors:
|----------------------------|
..............................
selected 9

CELL(start) =   78.671  78.736 105.662  90.02  90.09  72.42

CELL(finis) =   78.600  78.647 105.627  89.97  89.99  72.51
Using  532 out of  583 reflections
 List of possible Laue groups, sorted on penalty index.
 The lower the PENALTY, the better
 No PENALTY SDCELL FRACN LATT      a        b        c     alpha  beta gamma  Possible spacegroups

  44  999      unrefined  hR   186.09   131.73    78.60    79.7  80.3  88.5   H3,H32 (hexagonal settings of R3 and R32)
 IN CONRHO, BAD ACOS ARG (TARRAY5)   -1.3427
                               140.71    78.65   105.63    90.0  90.0 121.4   R3,R32 (primitive rhombohedral cell)
  43  969      unrefined  cF   140.71   165.00   140.75   118.7  82.7 118.7   F23,F432,F4132
  42  968      unrefined  tI   131.66   140.75    78.60    67.0 100.3 111.6   I4,I41,I422,I4122
  41  878      unrefined  cI   131.67    92.99   131.66    69.3  57.6  69.4   I23,I213,I432,I4132
  40  758      unrefined  tI   131.67    92.99   131.66    69.3  57.6  69.4   I4,I41,I422,I4122
  39  725      unrefined  hR    78.60    92.99   341.26    90.0 107.4 126.2   H3,H32 (hexagonal settings of R3 and R32)
                               105.63   131.65   131.66    41.4  50.0  49.9   R3,R32 (primitive rhombohedral cell)
  38  725      unrefined  oF    78.60   153.26   225.39    85.9 110.4 101.8   F222
  37  696      unrefined  tI    78.60    78.65   230.79    76.2  76.2 107.5   I4,I41,I422,I4122
  36  696      unrefined  oI    78.60    78.65   230.79   103.8 103.8 107.5   I222,I212121
  35  667      unrefined  oI    92.99   131.67   131.66    57.6  69.3  69.4   I222,I212121
  34  667      unrefined  tI   131.66   131.67    92.99    69.4  69.3  57.6   I4,I41,I422,I4122
  33  666      unrefined  oI    78.60   131.66   140.75    68.4  67.0  79.7   I222,I212121
  32  637      unrefined  hP    78.65   105.63    78.60    90.0 107.5  90.0   P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
                                                                              P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
  31  635      unrefined  mI    92.99   230.79    78.60   103.8 126.2  66.3   C2 (transformed from I2)
  30  424      unrefined  oF    92.99   126.80   230.79    90.0 113.7  90.0   F222
  29  424      unrefined  mC   126.80    92.99   131.67    69.4 118.8  90.0   C2
  28  423      unrefined  mC   153.26    78.60   131.66    79.7 121.4  78.2   C2
  27  394      unrefined  oC    78.65   225.38    78.60    84.0 107.5 110.4   C222,C2221
  26  394      unrefined  mC   225.39    78.60    78.65   107.5  96.0  69.6   C2
  25  394      unrefined  oC    78.60   225.39    78.65    84.0 107.5 110.4   C222,C2221
  24  393      unrefined  mC    78.60   225.39    78.65    96.0 107.5  69.6   C2
  23  393      unrefined  mC    78.60   225.39    78.65    96.0 107.5  69.6   C2
  22  393      unrefined  mC   225.38    78.65    78.60   107.5  96.0  69.6   C2
  21  335      unrefined  cP    78.60    78.65   105.63    90.0  90.0 107.5   P23,P213,P432,P4232,P4332,P4132
  20  335      unrefined  hR   126.80   131.65   140.71   111.6  90.0 118.8   H3,H32 (hexagonal settings of R3 and R32)
                                78.65    78.60   105.63    90.0  90.0 102.9   R3,R32 (primitive rhombohedral cell)
  19  335      unrefined  mC   131.66   131.73    78.60    79.7 100.3  73.3   C2
  18  335      unrefined  tP    78.65   105.63    78.60    90.0 107.5  90.0   P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212,P4322,P43212
  17  335      unrefined  hR    92.99   131.65   165.07    98.3  90.0 110.7   H3,H32 (hexagonal settings of R3 and R32)
                                78.65    78.60   105.63    90.0  90.0  77.1   R3,R32 (primitive rhombohedral cell)
  16  335      unrefined  oC   131.66   131.73    78.60    79.7 100.3  73.3   C222,C2221
  15  334      unrefined  mC   131.73   131.66    78.60   100.3 100.3 106.7   C2
  14  121     0.723 0.98  mC    78.60   153.26   105.63    90.0  90.0  78.2   C2
  13  121     0.721 0.98  oC    78.60   153.26   105.63    90.0  90.0 101.8   C222,C2221
  12  121     0.551 0.99  mC   153.26    78.60   105.63    90.0  90.0  78.2   C2
  11  121     1.137 0.99  hP    78.60    78.65   105.63    90.0  90.0 107.5   P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
                                                                              P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
  10   92     0.969 0.98  tP    78.60    78.65   105.63    90.0  90.0 107.5   P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212,P4322,P43212
   9   91     0.977 0.98  mP    78.60    78.65   105.63    90.0  90.0 107.5   P2,P21
   8   91     0.958 0.99  mP    78.65    78.60   105.63    90.0  90.0 107.5   P2,P21
   7   91     0.974 0.98  oP    78.60    78.65   105.63    90.0  90.0 107.5   P222,P2221,P21212,P212121
   6    1     0.114 0.93  mC    92.99   126.80   105.63    90.0  90.0  90.0   C2
   5    1     0.113 0.93  oC    92.99   126.80   105.63    90.0  90.0  90.0   C222,C2221
   4    1     0.112 0.93  mC   126.80    92.99   105.63    90.0  90.0  90.0   C2
   3    0     0.103 0.92  aP    78.60    78.65   105.63    90.0  90.0  72.5   P1
   2    0     0.106 0.92  mP    78.60   105.63    78.65    90.0 107.5  90.0   P2,P21
   1    0     0.103 0.92  aP    78.60    78.65   105.63    90.0  90.0 107.5   P1
 No PENALTY SDCELL FRACN LATT      a        b        c     alpha  beta gamma  Possible spacegroups


 Suggested Solution:  5  C222
            penalty:  1
               cell:  92.992  126.804  105.627  90.03  90.02  89.96
   regularized cell:  92.992  126.804  105.627  90.00  90.00  90.00
           Symmetry: oC (C Centred Orthorhombic)

 Spacegroup information obtained from library file: 
 Logical Name: SYMINFO   Filename: /opt/pxsoft/ccp4-6.0/lib/data/syminfo.lib


 Spacegroup information obtained from library file: 
 Logical Name: SYMINFO   Filename: /opt/pxsoft/ccp4-6.0/lib/data/syminfo.lib

 Mosflm has chosen solution  5 from the list automatically. You may want to
 re-run the autoindexing and choose a solution yourself.

 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 # 5 with C2221 (number   20) symmetry imposed

Initial cell (before refinement) is   92.9923  126.8040  105.6273  90.000  90.000  90.000
Using  542 indexed reflections (out of  583 spots used in indexing, {delta(XY) <= 2.5 sigma}),
final sd in spot positions is 0.11mm and in phi 0.42 degrees
Refined cell parameters   93.00  126.76  105.63  90.00  90.00  90.00
Beam coordinates of 156.93 158.88 have been refined to 156.92 158.80
This is a shift of  0.07mm or  0.033 times the minimum spot separation of ca  2.22mm.
  Final cell (after refinement) is    92.9987  126.7649  105.6320  90.000  90.000  90.000

FORMATTED      UNKNOWN file opened on unit  12

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


 image FILENAME: /scisoft/users/svensson/tmp/dataBenchmark/AV01-3342167Aa_1/ref-AV01-3342167Aa_1_002.img

 **** 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 ( 0.9795) 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.



 Title for MTZ and GENERATE Files (TITLE):
 .
 Crystal identifier (IDENT): ref-AV01-3342167Aa_1

 Warning: No PROTEIN NAME given by KeyWord PNAME
 It has been set to "Unspecified"

 Warning: No CRYSTAL NAME given by KeyWord XNAME
 It has been set to "ref-AV01-3342167Aa_1"


 Warning: No DATASET NAME given by KeyWord DNAME
 It has been set to "Unspecified"

  PSIX changed by  0.00 Degrees and CCOMEGA set to 0.000

  MAX. No. of Active Reflections=    55

 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           0   338   387   356   360   391   369   379   388   375   383     7     0     6    10     6     4     5     2
 No gained           6     2
 Total intensity 60127 69378 76225 82573 87402 90771 94942 96441 97509 98822 99991 99999 99999 99977 99946 99547 99533 99490 99490
 Total intensity 99482 99461
 SD of intensity   662   675   691   705   721   723   729   729   729   730   730   730   730   730   730   730   730   730   730
 SD of intensity   730   730
 The mosaicity has been estimated as ---> 0.60 <--- for this image only; 
This value can be used cautiously as an initial estimate.
Storing space group from DPS autoindexing: C2221      number  20
Storing space group from DPS autoindexing: C2221      number  20
 ===> BEST OFF
 ===> xgui on
 New gui stuff switched on
 ===> image 1
 ===> go

 Start and end phi values for image     1 from image header are     0.00 and    1.00 degrees.

 Oscillation axis set as PHI from image header

***** WARNING *****
***** WARNING *****
***** WARNING *****
***** WARNING *****
 Input beam coordinates  156.92mm  158.80mm DO NOT agree with 
 those calculated from the image header ( 156.93mm  158.88mm)

Warning - resetting the iseg value to zero because gui_switch = .true.
 image FILENAME: /scisoft/users/svensson/tmp/dataBenchmark/AV01-3342167Aa_1/ref-AV01-3342167Aa_1_001.img
 NeoCtrl => ===> predict_spots
 Predicted
 414 fulls
 4652 partials
 42 wides
 10 overlaps
 NeoCtrl => ===> create_image binary true filename ref-AV01-3342167Aa_1_001.jpg
Output filename set to ref-AV01-3342167Aa_1_001.jpg                                                    
 Beam centre =   156.923599  158.803085
 Calling write_jpeg with arg list:
 trc =  0 0
 blc =  3072 3072
 factor =  1
 write_jpeg -1 3072 3072 0 0
 1 0 0 3072 3072 1 0 0
1 Rotating image by 0 degrees
Done rotating
write_jpeg took:  0.915
Returning from CREATE_IMAGE after  2.173 seconds
 NeoCtrl => ===> create_image prediction on binary true filename ref-AV01-3342167Aa_1_001_pred.jpg
Output filename set to ref-AV01-3342167Aa_1_001_pred.jpg                                               
 Beam centre =   156.923599  158.803085
 writing binary jpeg
  writing predictions
writing a nice binary JPEG with predictions
box sizes are 7 6
zoom is 1
invert_y = 0, invert = 0, invert_x = 0
3 Rotating image by 0 degrees
Done rotating
Returning from CREATE_IMAGE after  2.290 seconds
 NeoCtrl => ===> create_image zoom -4 binary true filename ref-AV01-3342167Aa_1_001_small.jpg
Output filename set to ref-AV01-3342167Aa_1_001_small.jpg                                              
 Beam centre =   156.923599  158.803085
 Calling write_jpeg with arg list:
 trc =  0 0
 blc =  3072 3072
 factor =  -4
 write_jpeg -1 3072 3072 0 0
 -4 0 0 3072 3072 1 0 0
1 Rotating image by 0 degrees
Done rotating
write_jpeg took:  0.055
Returning from CREATE_IMAGE after  0.288 seconds
 NeoCtrl => ===> create_image zoom -4 prediction on binary true filename ref-AV01-3342167Aa_1_001_pred_small.jpg
Output filename set to ref-AV01-3342167Aa_1_001_pred_small.jpg                                         
 Beam centre =   156.923599  158.803085
 writing binary jpeg
  writing predictions
writing a nice binary JPEG with predictions
box sizes are 1 1
zoom is -4
invert_y = 0, invert = 0, invert_x = 0
3 Rotating image by 0 degrees
Done rotating
Returning from CREATE_IMAGE after  0.311 seconds
 NeoCtrl => ===> return
 New gui stuff switched off
 ===> xgui off
 New gui stuff switched off
 ===> xgui on
 New gui stuff switched on
 ===> image 2
 ===> go

 Start and end phi values for image     2 from image header are    90.00 and   91.00 degrees.

 Oscillation axis set as PHI from image header

***** WARNING *****
***** WARNING *****
***** WARNING *****
***** WARNING *****
 Input beam coordinates  156.92mm  158.80mm DO NOT agree with 
 those calculated from the image header ( 156.93mm  158.88mm)

Warning - resetting the iseg value to zero because gui_switch = .true.
 image FILENAME: /scisoft/users/svensson/tmp/dataBenchmark/AV01-3342167Aa_1/ref-AV01-3342167Aa_1_002.img
 NeoCtrl => ===> predict_spots
 Predicted
 434 fulls
 4617 partials
 32 wides
 16 overlaps
 NeoCtrl => ===> create_image binary true filename ref-AV01-3342167Aa_1_002.jpg
Output filename set to ref-AV01-3342167Aa_1_002.jpg                                                    binary                                                                          true                                                                            filename                                                                        ref-AV01-3342167Aa_1_001_pred_small.jpg                                         
 Beam centre =   156.923599  158.803085
 Calling write_jpeg with arg list:
 trc =  0 0
 blc =  3072 3072
 factor =  1
 write_jpeg -1 3072 3072 0 0
 1 0 0 3072 3072 1 0 0
1 Rotating image by 0 degrees
Done rotating
write_jpeg took:  0.913
Returning from CREATE_IMAGE after  2.171 seconds
 NeoCtrl => ===> create_image prediction on binary true filename ref-AV01-3342167Aa_1_002_pred.jpg
Output filename set to ref-AV01-3342167Aa_1_002_pred.jpg                                               filename                                                                        ref-AV01-3342167Aa_1_001_pred_small.jpg                                         
 Beam centre =   156.923599  158.803085
 writing binary jpeg
  writing predictions
writing a nice binary JPEG with predictions
box sizes are 7 6
zoom is 1
invert_y = 0, invert = 0, invert_x = 0
3 Rotating image by 0 degrees
Done rotating
Returning from CREATE_IMAGE after  2.293 seconds
 NeoCtrl => ===> create_image zoom -4 binary true filename ref-AV01-3342167Aa_1_002_small.jpg
Output filename set to ref-AV01-3342167Aa_1_002_small.jpg                                              filename                                                                        ref-AV01-3342167Aa_1_001_pred_small.jpg                                         
 Beam centre =   156.923599  158.803085
 Calling write_jpeg with arg list:
 trc =  0 0
 blc =  3072 3072
 factor =  -4
 write_jpeg -1 3072 3072 0 0
 -4 0 0 3072 3072 1 0 0
1 Rotating image by 0 degrees
Done rotating
write_jpeg took:  0.055
Returning from CREATE_IMAGE after  0.286 seconds
 NeoCtrl => ===> create_image zoom -4 prediction on binary true filename ref-AV01-3342167Aa_1_002_pred_small.jpg
Output filename set to ref-AV01-3342167Aa_1_002_pred_small.jpg                                         
 Beam centre =   156.923599  158.803085
 writing binary jpeg
  writing predictions
writing a nice binary JPEG with predictions
box sizes are 1 1
zoom is -4
invert_y = 0, invert = 0, invert_x = 0
3 Rotating image by 0 degrees
Done rotating
Returning from CREATE_IMAGE after  0.313 seconds
 NeoCtrl => ===> return
 New gui stuff switched off
 ===> xgui off
 New gui stuff switched off



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

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