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/srpol-HA00AG3240_1
 ===> template ref-srpol-HA00AG3240_1_###.img
 ===> BEST ON
 ===> prerefine on
  ****** Keyword NOT RECOGNISED ***** 
 ===> autoindex dps refine image 1 thresh 10.000000
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 10.000000
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  278.71mm taken from image header

 Wavelength of 1.00500A 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    0.50 degrees.

 Oscillation axis set as PHI from image header

 Main beam position has been calculated as  156.94mm  158.85mm 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/srpol-HA00AG3240_1/ref-srpol-HA00AG3240_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  3 by  3 pixels in X and Y, the measurement box 
 parameters have been set to  13  13   8   4   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  3 by  3 pixels in X and Y, the spot separation 
 parameters (in X and Y) have been set to  0.51  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   0.250 degrees)
 Calculating radial background..... 
 The background is radial along the X (slow) direction
 The average of  51 pixels, excluding outliers, is used
 The scan is offset by 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     46    46    45    44    44    45    45    44    42    45    45    45
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ       0     1     9    12     7     3     1    13    16     4     5     3
 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     45    43    43    45    45    44    45    44    43    44    46    44
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ       5    13    12     5     3     6     4    12    16     6     1     6
 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     44    43    44    45    45    46    45    45    45    45    45    44
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ       9    14     8     4     3     2     6    15     6     3     4     7
 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     46    44    44    45    45    45    44    44    44    45    45    44
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ       3    12     9     5     6     4     9    11    15     6     6    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     45    44    43    45    45    45    45    44    44    44    43    45
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ       4    11    14     9     4     4     1     7    15    15    17    11
 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     45    46    46    44    44    44    45    44    44    45    45    45
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ       6     3     7    11    10    11     7    11     7     6     5     5
 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     43    44    44    45    45    46    45    46    46    44    46    45
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ      15     9    14     8     5     2     2     2     3    16     7     6
 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     45    45    44    43    37    42    42    44    45    45    45    45
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ       9     7     9    20    51    25    29    16     9     9     8     6
 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     45    45    45    45    45    44    44    46    43    44    43    46
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ       7     5     4     3     8    14    15     4    21    23    27    10
 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     45    46    46    47    48    48    49    48    48    48    49    47
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ      11    10    11     2     2     6     3     3    11     9     5    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     48    49    50    50    51    50    50    50    50    49    49    49
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ      12     7     7     6     3     2     5     4     4    12    13    12
 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     49    51    51    51    51    51    52    51    50    52    53    52
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ      15     5     7     5     3     8    11    10    17    12     9    14
 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     53    55    54    54    55    53    55    54    56    56    56    56
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ       8     6     7    11    10    18     9    11     9    10    11    10
 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     55    55    56    56    57    56    54    53    54    55    54    55
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ      16    11     9     7     4    12    10    16    15     5     9     9
 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     55    54    54    54    54    55    53    52    52    52    54    52
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ      10     8     9    11     8     5    11    13    14     9     5     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     52    52    50    51    51    52    51    51    50    51    50    50
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ      12    10    16     4     8     7     8     6     9     3     6     9
 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     50    50    48    49    48    49    49    48    49    48    48    45
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ       7     7     8     4     6     7     6     5     7     4     4    13
 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     47    47    46    47    45    46    46    46    45    44    45    47
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ       8     4    15     6    17     8     6     4    11    16    10     5
 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     45    46    46    46    46    45    45    45    45    46    46    45
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ      13     7     4     4     4     8    10     8     5     4     4     3
 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     45    46    44    45    44    45    44    45    44    44    46    45
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ       6     4    11     7     4     2    13     7    13     8     1     7
 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     45    44    45    44    44    44    44    44    45    44    43    45
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ       5     5     7     9    10     5    12     5     3    11    13     5
 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     45    44    43    44    43    45    45    45    45    44    44    44
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ       3     5    10    10     9     3     2     5     8     9     8     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     45    44    44    44    44    45    44    44    44    45    45    45
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ       6     7     6    14    10     6     7     7     8     6     7     5
 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     44    44    45    44    44    44    44    45    45    44    44    44
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ      10     8     2     8     6    13    12    10     7     7     9     8
 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     46    46    45    44    45    45    45    45    45    46    44    45
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ       3     3     3     8     3     6     5     6     4     3     7     6
 RADIUS 138.8 139.2 139.6 140.0 140.4 140.9 141.3 141.7
 BACKG     44    46    46    45    45    45    45    11
 SIGMA      3     3     3     3     3     3     3     2
 NREJ      12     6     3     7     7     6     6     1

 Starting spot search...
 Number of spots excluded from possible ice rings:      91

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

  Total number of spots found: 594
  Number rejected as too small on X:  67
  Number rejected as too small on Y:   4
  Number rejected as too big on X:  34
  Number rejected as too big on Y:  10
  Number too close (SEPARATION keyword):  33
  (currently SEPARATION   0.51  0.51)
  Number stored as OK: 374
  highest resolution is     2.16 Angstrom
  99% have resolution less than     3.48 Angstrom



             Number of spots found in each bin
               9   8   8  14  22  15  13  22
              33  25  33  28  35  43  33  70
               0   0   0   0   0   1   0   0
               0   0   0   0   0   0   0   0
               0   0   0   0   0   0   0   0
 image FILENAME: /scisoft/users/svensson/tmp/srpol-HA00AG3240_1/ref-srpol-HA00AG3240_1_002.img


 Finding spots on image     2 (Midpoint of phi  89.750 degrees)
 Calculating radial background..... 
 The background is radial along the X (slow) direction
 The average of  51 pixels, excluding outliers, is used
 The scan is offset by 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     44    44    44    42    43    44    43    44    43    43    44    44
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ       2     4     8    13     5     5     9     7    11    11     5     5
 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     43    43    42    43    43    44    43    42    43    43    45    44
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ       8    10    16     7     6     4     6    11    12     7     7     7
 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     43    42    43    44    44    43    43    43    45    43    43    43
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ      10    16     7     2     4     7    12    15    10    20    10     7
 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     44    42    43    43    43    44    43    43    44    43    44    44
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ      13    13     8     5     3     6     8     9    11    11     3     2
 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     43    43    42    42    43    43    43    43    43    42    42    43
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ       6    10    15    13     7     9     5    10    12    11    15    11
 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     43    43    43    43    42    43    42    44    44    44    44    43
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ       7     4     7     7    14    13    14     8     5     4     4    10
 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     44    41    43    43    43    43    44    43    43    43    43    43
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ       7    21     9    12     6     7     3     7     6    13    13     9
 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     44    42    43    40    34    41    43    42    41    43    42    43
 SIGMA      3     3     3     3     2     3     3     3     3     3     3     3
 NREJ       9    13     9    22    51    18    14    15    16     9     8     7
 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     43    42    42    43    43    42    43    42    42    42    41    42
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ       9     9    11    11    10     9     7    11    16    18    22    18
 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     41    42    43    42    44    44    44    44    43    44    44    43
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ      17    16    10    16     6     7    14    11    10    10    10    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     43    44    44    44    46    44    45    45    45    45    44    44
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ      16    11     6     9     5    12     4    10     8    15    19    19
 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     45    46    45    46    48    47    47    44    46    46    47    48
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ      16     6    11     4     0     5     4    16     9    14     4     4
 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     48    49    48    48    48    47    49    48    49    49    49    48
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ       2     2     6     8    10    13     9     8     3     4     6    10
 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     49    48    49    49    49    50    50    48    49    50    48    49
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ       9     6     5     2     3     5     7     9    10     5    10     5
 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     49    49    49    49    48    48    48    48    48    49    48    48
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ       8     7    10     6     6     5    10     7     7     5     5     4
 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     47    47    47    47    47    47    47    46    46    46    45    46
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ      10    13     9     8     4     5     5    17     2     4     8    10
 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     45    44    43    46    44    44    45    43    45    43    44    44
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ      12    17    17    10    11    16     8    15     4    16    14    11
 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     44    44    44    43    43    44    42    44    43    42    42    43
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ      11     6     6     9    13     8    16     6    11    13    15     9
 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     43    43    42    43    43    43    43    42    43    43    43    43
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ      12     6    13    11     5     6    13    12    11     7     8    11
 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     42    43    41    42    42    42    43    42    42    42    43    41
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ       8     6    12     7     8     7     8     4     9    11     5    10
 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     42    42    42    43    42    42    42    42    42    41    42    41
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ       9     6    10     5     7     9    10     7     5    11     8    16
 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     42    41    41    41    42    42    41    41    42    41    42    41
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ       7    12    13    12     6     8    12    10     6     9     9     9
 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     41    42    42    42    41    42    42    42    41    42    41    42
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ      13     9     8    10    14     8     9    11    10    10     8    12
 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     42    42    42    41    41    42    41    42    42    42    42    41
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ      11    10     7     9     9    12    12     5     6    11     8    15
 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     43    41    42    42    42    41    42    42    42    42    42    43
 SIGMA      3     3     3     3     3     3     3     3     3     3     3     3
 NREJ       5     9     8     9    10     9     8     8     8     8     7     5
 RADIUS 138.8 139.2 139.6 140.0 140.4 140.9 141.3 141.7
 BACKG     41    42    41    42    42    42    41    10
 SIGMA      3     3     3     3     3     3     3     2
 NREJ      12     8    10     8     8    10    12     3

 Starting spot search...
 Number of spots excluded from possible ice rings:      45

  Median spot size is   6 x   5 pixels, mode size is   4 by   3

  Total number of spots found: 281
  Number rejected as too small on X:  11
  Number rejected as too small on Y:  12
  Number rejected as too big on X:  17
  Number rejected as too big on Y:   1
  Number too close (SEPARATION keyword):   8
  (currently SEPARATION   0.51  0.51)
  Number stored as OK: 215
  highest resolution is     2.19 Angstrom
  99% have resolution less than     3.74 Angstrom



             Number of spots found in each bin
               9   4   7   9   4   6   5  10
               5   9   5   7  14  10  10   8
               3   4   3  10  16   7   6  15
               3   2   8   3   6   4   2   5
               0   0   0   0   0   1   1   0

FORMATTED      UNKNOWN file opened on unit  10

Logical name: ref-srpol-HA00AG3240_1.spt, Filename: ref-srpol-HA00AG3240_1.spt


   374 spots written for image    1
   215 spots written for image    2
 A total of   589 spots were written to file

FORMATTED      OLD     file opened on unit  10

Logical name: ref-srpol-HA00AG3240_1.spt, Filename: ref-srpol-HA00AG3240_1.spt


DPS Indexing using  101 reflections with I >=  10 I/sigma(I)
DPS Indexing at Two-theta =    0.00 with  101 reflections (minimum spot separation = 0.51mm. Maximum expected cell edge  277.33, Beam position is  156.94  158.85
Generating direct lattice vectors (This may take some time):
|-----------------|
..................
 Refining  30 direct space vectors:
|----------------------------|
..............................
selected 3

CELL(start) =  170.625 199.192 200.316 117.20 100.45  79.23

CELL(finis) =  171.063 200.199 200.372 117.17 100.36  79.63
Using   89 out of  101 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  cI   269.93   238.76   200.37    75.3  73.2  88.8   I23,I213,I432,I4132
  43  830      unrefined  tI   208.80   348.51   171.06    73.5  90.0  90.1   I4,I41,I422,I4122
  42  829      unrefined  oF   171.06   406.09   406.44    61.9 104.1 104.1   F222
  41  643      unrefined  hR   348.51   356.94   171.06    84.2  73.5 114.9   H3,H32 (hexagonal settings of R3 and R32)
                               238.76   200.37   208.80   121.5 121.3 106.9   R3,R32 (primitive rhombohedral cell)
  40  572      unrefined  hR   285.79   238.92   269.92    88.9 100.2  99.2   H3,H32 (hexagonal settings of R3 and R32)
                               200.20   171.06   200.37    79.6 122.3 100.4   R3,R32 (primitive rhombohedral cell)
  39  565      unrefined  tI   200.37   269.93   238.76    88.8  75.3  73.2   I4,I41,I422,I4122
  38  564      unrefined  hP   171.06   200.20   208.80   121.4  90.0 100.4   P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
                                                                              P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
  37  555      unrefined  cF   269.92   269.93   348.51   100.4 100.3 101.3   F23,F432,F4132
  36  554      unrefined  hR   171.06   238.76   544.17    78.6 100.5 124.4   H3,H32 (hexagonal settings of R3 and R32)
                               200.37   238.92   208.80    64.0  64.0  47.1   R3,R32 (primitive rhombohedral cell)
  35  527      unrefined  oF   238.76   285.79   379.93    72.5  98.5  80.9   F222
  34  505      unrefined  tI   171.06   200.20   379.93    82.7  69.2  79.6   I4,I41,I422,I4122
  33  505      unrefined  mC   171.06   406.44   200.20    68.0 100.4  75.9   C2
  32  505      unrefined  mC   171.06   406.09   200.37    68.0 100.4  75.9   C2
  31  487      unrefined  cP   171.06   200.20   208.80   121.4  90.0 100.4   P23,P213,P432,P4232,P4332,P4132
  30  449      unrefined  tP   171.06   200.20   208.80   121.4  90.0 100.4   P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212,P4322,P43212
  29  449      unrefined  oC   171.06   406.09   208.80    59.1  90.0 104.1   C222,C2221
  28  449      unrefined  oC   171.06   406.09   208.80    59.1  90.0 104.1   C222,C2221
  27  398      unrefined  tI   269.92   238.92   200.20    75.3  73.2  88.9   I4,I41,I422,I4122
  26  384      unrefined  oC   238.76   285.79   208.80   111.4 115.9  80.9   C222,C2221
  25  375      unrefined  hR   238.76   238.92   413.27   103.5  76.5 128.2   H3,H32 (hexagonal settings of R3 and R32)
                               200.20   171.06   200.37    79.6  57.7  79.6   R3,R32 (primitive rhombohedral cell)
  24  372      unrefined  tP   200.20   208.80   171.06    90.0 100.4 121.4   P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212,P4322,P43212
  23  361      unrefined  oI   171.06   208.80   348.51    89.9  73.5  90.0   I222,I212121
  22  360      unrefined  mC   406.09   171.06   208.80    90.0 120.9  75.9   C2
  21  334      unrefined  oP   171.06   200.20   208.80   121.4  90.0 100.4   P222,P2221,P21212,P212121
  20  333      unrefined  oI   238.92   269.92   200.20    73.2  75.3  88.9   I222,I212121
  19  310      unrefined  mC   285.79   238.76   200.37   104.7 115.3  80.9   C2
  18  295      unrefined  mC   285.79   238.76   269.93    88.8 137.9  80.9   C2
  17  269      unrefined  mP   171.06   208.80   200.20   121.4 100.4  90.0   P2,P21
  16  268      unrefined  mP   171.06   208.80   200.20   121.4 100.4  90.0   P2,P21
  15  245      unrefined  mC   285.79   238.76   200.37    75.3 115.3  99.1   C2
  14  218      unrefined  mC   406.09   171.06   208.80    90.0 120.9  75.9   C2
  13  218      unrefined  oI   171.06   208.80   348.51    90.1 106.5  90.0   I222,I212121
  12  218      unrefined  mI   269.92   348.51   171.06   106.5 129.3  79.7   C2 (transformed from I2)
  11  217      unrefined  mC   406.09   171.06   208.80    90.0 120.9  75.9   C2
  10  141     0.501 0.99  hP   208.80   200.37   171.06   100.4  90.0 121.5   P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
                                                                              P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
   9  140     0.355 0.99  oC   200.20   356.94   171.06    84.2 100.4  87.2   C222,C2221
   8  140     0.326 0.99  mC   200.20   356.94   171.06    84.2 100.4  87.2   C2
   7  104     0.233 0.97  oC   208.80   341.85   171.06    77.8  90.0  89.9   C222,C2221
   6  102     0.326 0.99  mC   200.20   356.94   171.06    84.2 100.4  87.2   C2
   5  102     0.412 0.97  mP   200.20   171.06   208.80    90.0 121.4 100.4   P2,P21
   4   38     0.057 0.89  mC   341.85   208.80   171.06    90.0 102.2  90.1   C2
   3   37     0.059 0.89  aP   171.06   200.20   208.80   121.4  90.0 100.4   P1
   2    1     0.057 0.89  mC   341.85   208.80   171.06    90.0 102.2  90.1   C2
   1    0     0.059 0.89  aP   171.06   200.20   200.37    62.8  79.6  79.6   P1
 No PENALTY SDCELL FRACN LATT      a        b        c     alpha  beta gamma  Possible spacegroups


 Suggested Solution:  2  C2
            penalty:  1
               cell: 341.850  208.795  171.063  90.00 102.17  90.06
   regularized cell: 341.850  208.795  171.063  90.00 102.17  90.00
           Symmetry: mC (C Centred Monoclinic)

 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  2 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 # 2 with C2 (number    5) symmetry imposed

Initial cell (before refinement) is  341.8503  208.7951  171.0627  90.000 102.175  90.000
Using   90 indexed reflections (out of  101 spots used in indexing, {delta(XY) <= 2.5 sigma}),
final sd in spot positions is 0.06mm and in phi 0.17 degrees
Refined cell parameters  342.01  208.71  171.08  90.00 102.14  90.00
Beam coordinates of 156.94 158.85 have been refined to 156.88 158.75
This is a shift of  0.12mm or  0.142 times the minimum spot separation of ca  0.84mm.
  Final cell (after refinement) is   342.0149  208.7128  171.0817  90.000 102.140  90.000

FORMATTED      UNKNOWN file opened on unit  12

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


 image FILENAME: /scisoft/users/svensson/tmp/srpol-HA00AG3240_1/ref-srpol-HA00AG3240_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 ( 1.0050) 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-srpol-HA00AG3240_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-srpol-HA00AG3240_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=   100

 Beam divergence refinement
Too many reflections generated; temporarily reducing resolution to   1.816
 (it will revert to   1.513 after mosaicity estimation)
  PSIX changed by  0.00 Degrees and CCOMEGA set to 0.000

  MAX. No. of Active Reflections=   100

 Beam divergence refinement
Too many reflections generated; temporarily reducing resolution to   2.179
 (it will revert to   1.513 after mosaicity estimation)
  PSIX changed by  0.00 Degrees and CCOMEGA set to 0.000

  MAX. No. of Active Reflections=   100

 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        1001  1593  1598  1506  1492  1526  1390  1422  1445  1414  1308   523   509   442   407   368   375   353   310
 No gained         307   267
 Total intensity 59810 69692 75495 79887 83076 87206 90343 93009 95885 97819 99963 99231 97715 96931 95780 94107 93271 91964 90500
 Total intensity 88879 87154
 SD of intensity   993  1098  1202  1307  1359  1464  1516  1568  1673  1725  1778  1725  1725  1725  1673  1673  1673  1621  1621
 SD of intensity  1621  1568
 The mosaicity has been estimated as ---> 0.77 <--- for this image only; 
This value can be used cautiously as an initial estimate.
Storing space group from DPS autoindexing: C2         number   5
Storing space group from DPS autoindexing: C2         number   5
 ===> 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    0.50 degrees.

 Oscillation axis set as PHI from image header

***** WARNING *****
***** WARNING *****
***** WARNING *****
***** WARNING *****
 Input beam coordinates  156.88mm  158.75mm DO NOT agree with 
 those calculated from the image header ( 156.94mm  158.85mm)

Warning - resetting the iseg value to zero because gui_switch = .true.
 image FILENAME: /scisoft/users/svensson/tmp/srpol-HA00AG3240_1/ref-srpol-HA00AG3240_1_001.img
 NeoCtrl => ===> predict_spots
 Predicted
 0 fulls
 28698 partials
 2195 wides
 12168 overlaps
 NeoCtrl => ===> create_image binary true filename ref-srpol-HA00AG3240_1_001.jpg
Output filename set to ref-srpol-HA00AG3240_1_001.jpg                                                  
 Beam centre =   156.878571  158.746552
 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:  1.121
Returning from CREATE_IMAGE after  2.427 seconds
 NeoCtrl => ===> create_image prediction on binary true filename ref-srpol-HA00AG3240_1_001_pred.jpg
Output filename set to ref-srpol-HA00AG3240_1_001_pred.jpg                                             
 Beam centre =   156.878571  158.746552
 writing binary jpeg
  writing predictions
writing a nice binary JPEG with predictions
box sizes are 6 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  2.907 seconds
 NeoCtrl => ===> create_image zoom -4 binary true filename ref-srpol-HA00AG3240_1_001_small.jpg
Output filename set to ref-srpol-HA00AG3240_1_001_small.jpg                                            
 Beam centre =   156.878571  158.746552
 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:  0.059
Returning from CREATE_IMAGE after  0.292 seconds
 NeoCtrl => ===> create_image zoom -4 prediction on binary true filename ref-srpol-HA00AG3240_1_001_pred_small.jpg
Output filename set to ref-srpol-HA00AG3240_1_001_pred_small.jpg                                       
 Beam centre =   156.878571  158.746552
 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  0.442 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    89.50 and   90.00 degrees.

 Oscillation axis set as PHI from image header

***** WARNING *****
***** WARNING *****
***** WARNING *****
***** WARNING *****
 Input beam coordinates  156.88mm  158.75mm DO NOT agree with 
 those calculated from the image header ( 156.94mm  158.85mm)

Warning - resetting the iseg value to zero because gui_switch = .true.
 image FILENAME: /scisoft/users/svensson/tmp/srpol-HA00AG3240_1/ref-srpol-HA00AG3240_1_002.img
 NeoCtrl => ===> predict_spots
 Predicted
 0 fulls
 32981 partials
 2091 wides
 8181 overlaps
 NeoCtrl => ===> create_image binary true filename ref-srpol-HA00AG3240_1_002.jpg
Output filename set to ref-srpol-HA00AG3240_1_002.jpg                                                  binary                                                                          true                                                                            filename                                                                        ref-srpol-HA00AG3240_1_001_pred_small.jpg                                       
 Beam centre =   156.878571  158.746552
 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:  1.119
Returning from CREATE_IMAGE after  2.393 seconds
 NeoCtrl => ===> create_image prediction on binary true filename ref-srpol-HA00AG3240_1_002_pred.jpg
Output filename set to ref-srpol-HA00AG3240_1_002_pred.jpg                                             filename                                                                        ref-srpol-HA00AG3240_1_001_pred_small.jpg                                       
 Beam centre =   156.878571  158.746552
 writing binary jpeg
  writing predictions
writing a nice binary JPEG with predictions
box sizes are 6 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  2.923 seconds
 NeoCtrl => ===> create_image zoom -4 binary true filename ref-srpol-HA00AG3240_1_002_small.jpg
Output filename set to ref-srpol-HA00AG3240_1_002_small.jpg                                            filename                                                                        ref-srpol-HA00AG3240_1_001_pred_small.jpg                                       
 Beam centre =   156.878571  158.746552
 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:  0.060
Returning from CREATE_IMAGE after  0.294 seconds
 NeoCtrl => ===> create_image zoom -4 prediction on binary true filename ref-srpol-HA00AG3240_1_002_pred_small.jpg
Output filename set to ref-srpol-HA00AG3240_1_002_pred_small.jpg                                       
 Beam centre =   156.878571  158.746552
 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  0.396 seconds
 NeoCtrl => ===> return
 New gui stuff switched off
 ===> xgui off
 New gui stuff switched off



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

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