Index results for ftest_1

Symmetry and refined cell parameters

Image Symmetry a b c alpha beta gamma
1 F23 181.690 181.690 181.690 90.000 90.000 90.000
2 F23 181.587 181.587 181.587 90.000 90.000 90.000
1+2 F23 181.643 181.643 181.643 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 1579 115 0.073 0.080 0.025 -0.255
2 1439 73 0.051 0.080 0.025 -0.245
1+2 3025 187 0.062 0.110 0.015 -0.275

Image 1: /scisoft/pxsoft/data/dna_040402/ref-ftest_1_001.img

Image 2: /scisoft/pxsoft/data/dna_040402/ref-ftest_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-ftest_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-ftest_1_001.img      Filename: /scisoft/pxsoft/data/dna_040402/ref-ftest_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-ftest_1_001.img

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

 Logical Name: /scisoft/pxsoft/data/dna_040402/ref-ftest_1_001.img      Filename: /scisoft/pxsoft/data/dna_040402/ref-ftest_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  218 spots
 Threshold set to    4.2
 sorting  233 spots
 Threshold set to    4.1


 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     84    82    77    76    73    72    69    69    67    65    61    59
 SIGMA      9     9     8     8     8     8     8     8     8     8     7     7
 NREJ      18    11     8     0     3     5     0     0     1     4     1     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     56    56    56    55    54    53    52    51    50    51    50    49
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     0     0     0     0     0     0     0     1     2     1
 RADIUS  17.2  17.5  17.9  18.2  18.5  18.8  19.2  19.5  19.8  20.2  20.5  20.8
 BACKG     50    51    50    50    49    48    47    46    46    46    46    46
 SIGMA      7     7     7     7     7     6     6     6     6     6     6     6
 NREJ       3     8    11     3     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     45    46    46    45    45    44    44    45    45    45    45    44
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     0     0     0     0     0     0     0     2     8     1     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     44    44    43    43    43    43    43    44    44    44    44    44
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     2     1     0     0     0     0     2     5     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     43    44    43    43    43    44    43    43    44    44    44    44
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       3     0     1     0     0     0     0     0     0     0     0     0
 RADIUS  32.9  33.2  33.5  33.9  34.2  34.5  34.8  35.2  35.5  35.8  36.1  36.5
 BACKG     44    45    44    43    43    43    43    44    44    44    44    45
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       5     7     1     0     0     0     0     7     6     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     44    44    43    44    44    44    45    44    44    44    44    44
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       6     1     8     3     0     0     4     4     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     44    45    45    45    45    45    46    46    46    46    45    46
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     0     0     0     0     0     0     3     1     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     46    47    46    46    47    47    47    48    48    49    47    48
 SIGMA      6     6     6     6     6     6     6     6     6     7     6     6
 NREJ       1     0     1     0     0     0     7     7     0     0     1     2
 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     50    50    50    49    49    50    51    50    51    51    51    51
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     4     3     0     0     0     3     0     0     1     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     52    53    52    54    56    55    56    57    55    57    56    56
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       1     4     0     0     2     8     1     3     7     0     0     3
 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     58    58    58    58    59    60    60    62    61    62    65    64
 SIGMA      7     7     7     7     7     7     7     7     7     7     8     8
 NREJ       7     2     0     0     0     6    18    22    21    13     0     3
 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     64    63    64    64    65    66    67    68    68    68    69    71
 SIGMA      8     7     8     8     8     8     8     8     8     8     8     8
 NREJ       3     0     0     0     0     0     6     6     0     0     1     4
 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     73    73    71    71    72    73    72    73    73    72    72    72
 SIGMA      8     8     8     8     8     8     8     8     8     8     8     8
 NREJ       1     8    11     3     0     6    13     9     0     0     0     0
 RADIUS  68.1  68.5  68.8  69.1  69.4  69.8  70.1  70.4  70.7  71.1  71.4  71.7
 BACKG     73    73    73    74    74    72    71    72    70    69    69    69
 SIGMA      8     8     8     8     8     8     8     8     8     8     8     8
 NREJ      12    18    17    10     0     3     7     1     1     1     0     0
 RADIUS  72.1  72.4  72.7  73.0  73.4  73.7  74.0  74.3  74.7  75.0  75.3  75.6
 BACKG     70    68    68    66    67    66    67    68    66    66    66    66
 SIGMA      8     8     8     8     8     8     8     8     8     8     8     8
 NREJ       2     9     3     0     0     2     3     4    12    12     2     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     66    65    64    63    62    61    62    64    63    62    61    60
 SIGMA      8     8     7     7     7     7     7     8     7     7     7     7
 NREJ       2     8     3     0     0     0     0     0     5     5     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     61    60    60    58    59    59    60    59    60    59    59    59
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       1     6     1     0     1     0     0     0     3     5     0     0
 RADIUS  83.8  84.1  84.5
 BACKG     58    59    29
 SIGMA      7     7     3
 NREJ       0     0     0

 Starting spot search...
 sorting  1579 spots

  Median spot size is   6 x   6 pixels

  Total number of spots found:1579
  Number rejected as too small on X:  29
  Number rejected as too small on Y:  31
  Number rejected as too big on X:  15
  Number rejected as too big on Y:   8
  Number too close (SEPARATION keyword):   0
  Number stored as OK:1464



             Number of spots found in each bin
              36  26  26  37  32  17  22  35
              44  27  32  51  56  28  34  51
              49  29  41  68  56  28  45  48
              49  30  39  49  45  26  33  46
              44  26  36  41  31  26  22  35

 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  233 spots

 Based on a median spot size of  6 by  6 pixels in X and Y, the measurement box 
 parameters have been set to  19  19  11   6   6
 The overall size of the box has been fixed.
 To prevent this use keywords PROFILE NOFIXBOX.
 ***** WARNING ***** Lattice type not specified, so assumed primitive

 Based on a median spot size of  6 by  6 pixels in X and Y, the spot separation 
 parameters (in X and Y) have been set to  0.65  0.65mm.
 Closest possible spot separation is  0.00mm.

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

 FORMATTED      UNKNOWN file opened on unit  10

 Logical name: ref-ftest_1.spt, Filename: ref-ftest_1.spt


  1464 spots written for image    1
 A total of  1464 spots were written to file

 FORMATTED      OLD     file opened on unit  10

 Logical name: ref-ftest_1.spt, Filename: ref-ftest_1.spt


DPS Indexing at Two-theta =    0.00 with 1212 reflections (minimum spot separation = 0.49mm. Maximum expected cell edge  267.90, Beam position is   93.58   92.24
Generating direct lattice vectors (This may take some time):
|-----------------|
..................
 Refining  30 direct space vectors:
|----------------------------|
..............................
selected 12
 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   128.42   128.95   181.23    89.7  89.6  89.8   I23,I213,I432,I4132
  43 505    cP   128.03   128.16   128.41    90.1 119.9 119.6   P23,P213,P432,P4232,P4332,P4132
  42 504    tP   128.16   128.41   128.03   119.9 119.6  90.1   P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
  41 503    tI   128.95   181.23   128.42    89.6  90.2  90.3   I4,I41,I422,I4122
  40 503    tP   128.03   128.16   128.41    90.1 119.9 119.6   P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
  39 502    hR   222.88   181.61   128.03    90.2 106.3 114.0   H3,H32 (hexagonal settings of R3 and R32)
  38 502    oF   128.42   221.96   222.88    70.9  90.5  90.2   F222
  37 502    oP   128.03   128.16   128.41    90.1 119.9 119.6   P222,P2221,P21212,P212121
  36 257    hR   181.61   221.96   129.07    73.5  89.9 114.4   H3,H32 (hexagonal settings of R3 and R32)
  35 255    hP   128.03   128.41   128.16    90.1 119.6 119.9   P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
                                                                P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
  34 254    hP   128.03   128.41   128.16    90.1 119.6 119.9   P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
                                                                P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
  33 254    oC   128.42   221.96   128.16    73.5 119.6  89.8   C222,C2221
  32 254    mC   128.03   222.64   128.16    73.4 119.6  90.0   C2
  31 254    oC   128.95   221.36   128.41    73.3 119.8  89.9   C222,C2221
  30 252    mP   128.03   128.16   128.41    90.1 119.9 119.6   P2,P21
  29 252    oC   128.03   222.64   128.16    73.4 119.6  90.0   C222,C2221
  28 252    mC   128.03   222.64   128.16    73.4 119.6  90.0   C2
  27 251    oC   128.03   222.64   128.16    73.4 119.6  90.0   C222,C2221
  26 251    mC   128.03   222.64   128.16    73.4 119.6  90.0   C2
  25 251    mP   128.03   128.16   128.41    90.1 119.9 119.6   P2,P21
  24 250    mP   128.03   128.16   128.41    90.1 119.9 119.6   P2,P21
  23 250    oC   128.03   222.64   128.16    73.4 119.6  90.0   C222,C2221
  22  16    tI   128.03   129.07   181.61    89.9  89.8  89.6   I4,I41,I422,I4122
  21  15    oF   181.61   181.23   182.37    89.5  90.2  89.9   F222
  20  14    tI   128.16   128.41   182.37    89.8  89.5  90.1   I4,I41,I422,I4122
  19  14    oI   128.16   128.41   182.37    89.8  90.5  89.9   I222,I212121
  18  14    cF   182.37   181.23   181.61    90.1  90.2  90.5   F23,F432,F4132
  17  12    hR   128.03   128.95   315.40    90.3  89.8 120.2   H3,H32 (hexagonal settings of R3 and R32)
  16  11    tI   128.42   128.95   181.23    89.7  89.6  89.8   I4,I41,I422,I4122
  15  10    mI   128.16   182.37   128.41    90.2  89.9  89.5   C2
  14   9    oI   128.03   129.07   181.61    90.1  89.8  90.4   I222,I212121
  13   8    mC   181.23   181.61   128.03    90.2 134.6  89.9   C2
  12   8    oI   128.95   128.42   181.23    89.6  89.7  89.8   I222,I212121
  11   7    mC   222.96   128.03   129.07    90.4 125.5  89.6   C2
  10   7    mC   221.99   128.41   128.16    90.1 124.8  89.8   C2
   9   7    mC   221.99   128.41   128.16    90.1 124.8  89.8   C2
   8   7    mC   221.99   128.41   128.16    90.1 124.8  89.8   C2
   7   6    hR   128.95   128.41   313.28    90.2  90.1 119.8   H3,H32 (hexagonal settings of R3 and R32)
   6   6    mC   221.36   128.95   128.42    89.8 125.0  89.9   C2
   5   5    mC   181.23   181.61   128.03    90.2 134.6  89.9   C2
   4   5    mC   221.99   128.41   128.16    89.9 124.8  90.2   C2
   3   3    mC   221.36   128.95   128.42    90.2 125.0  90.1   C2
   2   0    aP   128.03   128.16   128.42    60.4  60.1  60.4   P1
   1   0    aP   128.03   128.16   128.41    90.1 119.9 119.6   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 #18 with F23    (number 196) symmetry imposed

Initial cell (before refinement) is  181.7338  181.7338  181.7338  90.000  90.000  90.000
Using 1154 indexed reflections (out of 1212 spots found, {delta(XY) <= 2.5 sigma}),
final sd in spot positions is 0.08mm and in phi 0.27 degrees
Refined cell parameters  181.69  181.69  181.69  90.00  90.00  90.00
Beam coordinates of  93.58  92.24 have been refined to  93.61  91.99
This is a shift of  0.25mm or  0.196 times the minimum spot separation of ca  1.28mm.
  Final cell (after refinement) is   181.6902  181.6901  181.6902  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   9440.142  9199.460

 ****** 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-ftest_1.gen      Filename: ref-ftest_1.gen




 Title for MTZ and GENERATE Files (TITLE):
 .
 Crystal identifier (IDENT): ref-ftest_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=    51

 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         153   421   393   351   388   358   336   343   353   347   324    78    94    99   107   121   113   128   124
 No gained         135   114
 Total intensity 83518 89923 94167 96080 97472 98336 98966 99364 99633 99825 99998 99930 99856 99745 99583 98957 98617 98225 97749
 Total intensity 97171 96424
 SD of intensity   111   115   117   118   119   121   121   122   123   123   124   124   124   124   123   123   122   122   122
 SD of intensity   122   121
 The mosaicity has been estimated as ---> 0.45 <--- for this image only; 
This value can be used cautiously as an initial estimate.
Storing space group from DPS autoindexing: 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-ftest_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-ftest_1_002.img      Filename: /scisoft/pxsoft/data/dna_040402/ref-ftest_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-ftest_1_002.img

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

 Logical Name: /scisoft/pxsoft/data/dna_040402/ref-ftest_1_002.img      Filename: /scisoft/pxsoft/data/dna_040402/ref-ftest_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  184 spots
 Threshold set to    4.2
 sorting  194 spots
 Threshold set to    4.2


 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     70    68    66    63    61    58    57    57    55    54    52    51
 SIGMA      8     8     8     7     7     7     7     7     7     7     7     7
 NREJ      10     6     1     1     0     1     0     0     0     0     0     0
 RADIUS  13.3  13.6  14.0  14.3  14.6  14.9  15.3  15.6  15.9  16.2  16.6  16.9
 BACKG     50    50    49    49    48    48    48    46    46    45    45    44
 SIGMA      7     7     7     7     6     6     6     6     6     6     6     6
 NREJ       0     0     7     8     4     0     0     0     0     0     0     0
 RADIUS  17.2  17.5  17.9  18.2  18.5  18.8  19.2  19.5  19.8  20.2  20.5  20.8
 BACKG     43    45    44    44    43    44    43    43    43    43    42    42
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     0     3     1     0     1     1     0     0     1     4     4
 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     42    42    43    41    41    41    42    41    41    41    40    40
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     0     6     8     0     0     3     7     1     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     41    41    40    41    41    40    40    40    40    40    40    40
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     0     8     7     1     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     39    39    39    39    40    39    40    39    39    39    39    40
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 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     38    39    39    39    39    39    38    39    39    39    39    39
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       1     0     0     4     1     0     0     0     0     0     1     4
 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     39    39    40    39    40    40    40    40    39    39    39    40
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     0     1     8     5     0     0     0     0     0     0     2
 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     40    39    40    40    40    40    40    40    40    40    40    41
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       1     0     1     6     5     0     0     2     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     41    40    40    41    41    41    41    41    41    42    41    42
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       1     0     0     5     2     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     42    42    43    43    44    44    45    45    46    44    44    45
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     0     0     5     8     2     0     1     1     0     0     0
 RADIUS  52.5  52.8  53.1  53.4  53.8  54.1  54.4  54.8  55.1  55.4  55.7  56.1
 BACKG     45    44    45    45    45    45    46    47    49    48    48    47
 SIGMA      6     6     6     6     6     6     6     6     7     6     6     6
 NREJ       0     0     0     0     0     0     0     0     1     1     0     0
 RADIUS  56.4  56.7  57.0  57.4  57.7  58.0  58.3  58.7  59.0  59.3  59.6  60.0
 BACKG     48    47    48    50    51    51    51    52    51    51    50    50
 SIGMA      6     6     6     7     7     7     7     7     7     7     7     7
 NREJ       0     0     0     0     6    10     5     0     1     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     52    53    53    52    54    55    56    54    54    57    58    57
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     0     0     0     0     0     0     0     2     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     57    56    57    56    56    56    58    58    57    57    56    56
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     0     0     0     0     1     0     0     0     0     0
 RADIUS  68.1  68.5  68.8  69.1  69.4  69.8  70.1  70.4  70.7  71.1  71.4  71.7
 BACKG     55    56    54    55    55    54    54    55    54    53    54    54
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     1     1     0     0     0     0     0     0     1     4
 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     53    53    53    53    52    52    52    52    51    52    52    52
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     0     0     0     0     0     2     3     0     0     1
 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     54    52    52    51    53    51    51    51    51    50    49    48
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     6
 NREJ       2     0     0     0     3     1     0     0     6     3     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     48    48    48    47    49    48    48    47    47    47    46    46
 SIGMA      6     6     6     6     7     6     6     6     6     6     6     6
 NREJ       0     0     0     0     1     7     2     1     0     1     3     0
 RADIUS  83.8  84.1  84.5
 BACKG     46    46    23
 SIGMA      6     6     3
 NREJ       0     0     1

 Starting spot search...
 sorting  1439 spots

  Median spot size is   6 x   6 pixels

  Total number of spots found:1439
  Number rejected as too small on X:  24
  Number rejected as too small on Y:  24
  Number rejected as too big on X:  14
  Number rejected as too big on Y:   1
  Number too close (SEPARATION keyword):   0
  Number stored as OK:1366



             Number of spots found in each bin
              34  22  16  29  26  18  16  30
              39  34  27  39  46  27  33  43
              52  32  33  48  53  37  29  53
              51  33  26  48  50  32  31  51
              45  24  27  28  30  20  25  39

 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  194 spots

 Based on a median spot size of  7 by  6 pixels in X and Y, the measurement box 
 parameters have been set to  21  19  11   6   6
 The overall size of the box has been fixed.
 To prevent this use keywords PROFILE NOFIXBOX.
 ***** WARNING ***** Lattice type not specified, so assumed primitive

 Based on a median spot size of  7 by  6 pixels in X and Y, the spot separation 
 parameters (in X and Y) have been set to  0.73  0.65mm.
 Closest possible spot separation is  0.00mm.

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

 FORMATTED      UNKNOWN file opened on unit  10

 Logical name: ref-ftest_1.spt, Filename: ref-ftest_1.spt


  1366 spots written for image    2
 A total of  1366 spots were written to file

 FORMATTED      OLD     file opened on unit  10

 Logical name: ref-ftest_1.spt, Filename: ref-ftest_1.spt


DPS Indexing at Two-theta =    0.00 with 1108 reflections (minimum spot separation = 0.49mm. Maximum expected cell edge  267.90, Beam position is   93.58   92.24
Generating direct lattice vectors (This may take some time):
|-----------------|
..................
 Refining  30 direct space vectors:
|----------------------------|
..............................
selected 2
 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   130.05   181.20   128.25    89.9  89.9  89.8   I23,I213,I432,I4132
  43 513    cP   128.46   128.57   128.60    90.4 119.2 120.1   P23,P213,P432,P4232,P4332,P4132
  42 512    tP   128.57   128.60   128.46   119.2 120.1  90.4   P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
  41 512    tP   128.57   128.60   128.46   119.2 120.1  90.4   P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
  40 512    oP   128.57   128.46   128.60   119.2  90.4 120.1   P222,P2221,P21212,P212121
  39 502    hR   222.25   182.50   128.46    89.4 106.6 113.9   H3,H32 (hexagonal settings of R3 and R32)
  38 493    tI   130.05   181.20   128.25    89.9  90.1  90.2   I4,I41,I422,I4122
  37 492    oF   128.25   222.76   223.32    71.3  90.2  90.1   F222
  36 258    hP   128.57   128.46   128.60   119.2  90.4 120.1   P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
                                                                P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
  35 258    oC   128.57   222.19   128.60    55.4  90.4  89.9   C222,C2221
  34 258    hP   128.57   128.46   128.60   119.2  90.4 120.1   P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
                                                                P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
  33 258    oC   128.57   222.19   128.60    55.4  90.4  89.9   C222,C2221
  32 257    oC   128.25   222.76   128.60   106.1 119.7  90.1   C222,C2221
  31 257    hR   182.50   222.76   128.93    73.9  89.4 114.5   H3,H32 (hexagonal settings of R3 and R32)
  30 257    oC   128.57   222.19   128.60    55.4  90.4  89.9   C222,C2221
  29 256    mP   128.57   128.60   128.46   119.2 120.1  90.4   P2,P21
  28 256    mP   128.57   128.60   128.46   119.2 120.1  90.4   P2,P21
  27 256    oC   128.25   222.76   128.60   106.1 119.7  90.1   C222,C2221
  26 256    mP   128.57   128.60   128.46   119.2 120.1  90.4   P2,P21
  25 249    mC   128.25   223.32   128.46    74.0 119.9  89.8   C2
  24 247    mC   128.25   222.76   128.60    73.9 119.7  89.9   C2
  23 247    mC   128.25   223.32   128.46    74.0 119.9  89.8   C2
  22  17    tI   128.57   128.60   182.81    89.3  89.6  89.6   I4,I41,I422,I4122
  21  16    cF   182.50   182.81   181.20    90.2  90.0  90.8   F23,F432,F4132
  20  16    oI   128.25   130.05   181.20    90.2  90.1  89.9   I222,I212121
  19  15    tI   128.25   130.05   181.20    89.8  89.9  89.9   I4,I41,I422,I4122
  18  15    hR   128.25   128.57   317.40    90.6  90.2 120.0   H3,H32 (hexagonal settings of R3 and R32)
  17  14    oF   181.20   182.50   182.81    90.8  90.2  90.0   F222
  16  13    tI   130.05   128.25   181.20    89.9  89.8  89.9   I4,I41,I422,I4122
  15  12    mI   128.60   182.81   128.57    90.4  90.4  89.3   C2
  14  11    hR   128.57   130.05   313.68    90.0  89.9 120.2   H3,H32 (hexagonal settings of R3 and R32)
  13   9    mC   182.50   181.20   128.25    90.1 134.6  90.0   C2
  12   9    mC   182.50   181.20   128.25    89.9 134.6  90.0   C2
  11   8    mC   222.19   128.57   128.60    90.4 124.6  90.1   C2
  10   8    mC   222.19   128.57   128.60    90.4 124.6  90.1   C2
   9   8    mC   222.19   128.57   128.60    90.4 124.6  90.1   C2
   8   6    oI   128.25   130.05   181.20    89.8  89.9  89.9   I222,I212121
   7   6    mC   222.76   128.25   181.20    89.9 144.3  90.1   C2
   6   5    mC   182.50   181.20   128.25    90.1 134.6  90.0   C2
   5   5    oI   128.25   181.20   130.05    89.8  89.9  89.9   I222,I212121
   4   4    mC   222.76   128.25   130.05    89.9 125.6  89.9   C2
   3   3    aP   128.57   128.46   128.60   119.2  90.4 120.1   P1
   2   2    mC   221.74   130.05   128.25    90.1 125.2  90.1   C2
   1   0    aP   128.25   128.46   128.60    60.8  60.3  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 #21 with F23    (number 196) symmetry imposed

Initial cell (before refinement) is  182.1671  182.1671  182.1671  90.000  90.000  90.000
Using 1051 indexed reflections (out of 1108 spots found, {delta(XY) <= 2.5 sigma}),
final sd in spot positions is 0.08mm and in phi 0.24 degrees
Refined cell parameters  181.59  181.59  181.59  90.00  90.00  90.00
Beam coordinates of  93.58  92.24 have been refined to  93.61  92.00
This is a shift of  0.25mm or  0.193 times the minimum spot separation of ca  1.28mm.
  Final cell (after refinement) is   181.5874  181.5874  181.5874  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   9440.112  9199.854

 ****** 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-ftest_1.gen      Filename: ref-ftest_1.gen




 Title for MTZ and GENERATE Files (TITLE):
 .
 Crystal identifier (IDENT): ref-ftest_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=    46

 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   160   191   161   173   168   184   178   188   184   169   161   154   172   155   144   176   149   139
 No gained         146   159
 Total intensity 81796 86595 91136 93370 94433 95218 97211 97717 98329 98644 98904 99132 99276 99433 99533 99593 99696 99765 99877
 Total intensity 99936 99998
 SD of intensity    93    96    98    99   101   101   106   107   108   108   109   109   109   110   110   112   112   112   113
 SD of intensity   113   114
 The mosaicity has been estimated as ---> 0.35 <--- 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-ftest_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-ftest_1_001.img      Filename: /scisoft/pxsoft/data/dna_040402/ref-ftest_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-ftest_1_001.img

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

 Logical Name: /scisoft/pxsoft/data/dna_040402/ref-ftest_1_001.img      Filename: /scisoft/pxsoft/data/dna_040402/ref-ftest_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  218 spots
 Threshold set to    4.2
 sorting  233 spots
 Threshold set to    4.1


 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     84    82    77    76    73    72    69    69    67    65    61    59
 SIGMA      9     9     8     8     8     8     8     8     8     8     7     7
 NREJ      18    11     8     0     3     5     0     0     1     4     1     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     56    56    56    55    54    53    52    51    50    51    50    49
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     0     0     0     0     0     0     0     1     2     1
 RADIUS  17.2  17.5  17.9  18.2  18.5  18.8  19.2  19.5  19.8  20.2  20.5  20.8
 BACKG     50    51    50    50    49    48    47    46    46    46    46    46
 SIGMA      7     7     7     7     7     6     6     6     6     6     6     6
 NREJ       3     8    11     3     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     45    46    46    45    45    44    44    45    45    45    45    44
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     0     0     0     0     0     0     0     2     8     1     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     44    44    43    43    43    43    43    44    44    44    44    44
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     2     1     0     0     0     0     2     5     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     43    44    43    43    43    44    43    43    44    44    44    44
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       3     0     1     0     0     0     0     0     0     0     0     0
 RADIUS  32.9  33.2  33.5  33.9  34.2  34.5  34.8  35.2  35.5  35.8  36.1  36.5
 BACKG     44    45    44    43    43    43    43    44    44    44    44    45
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       5     7     1     0     0     0     0     7     6     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     44    44    43    44    44    44    45    44    44    44    44    44
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       6     1     8     3     0     0     4     4     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     44    45    45    45    45    45    46    46    46    46    45    46
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     0     0     0     0     0     0     3     1     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     46    47    46    46    47    47    47    48    48    49    47    48
 SIGMA      6     6     6     6     6     6     6     6     6     7     6     6
 NREJ       1     0     1     0     0     0     7     7     0     0     1     2
 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     50    50    50    49    49    50    51    50    51    51    51    51
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     4     3     0     0     0     3     0     0     1     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     52    53    52    54    56    55    56    57    55    57    56    56
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       1     4     0     0     2     8     1     3     7     0     0     3
 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     58    58    58    58    59    60    60    62    61    62    65    64
 SIGMA      7     7     7     7     7     7     7     7     7     7     8     8
 NREJ       7     2     0     0     0     6    18    22    21    13     0     3
 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     64    63    64    64    65    66    67    68    68    68    69    71
 SIGMA      8     7     8     8     8     8     8     8     8     8     8     8
 NREJ       3     0     0     0     0     0     6     6     0     0     1     4
 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     73    73    71    71    72    73    72    73    73    72    72    72
 SIGMA      8     8     8     8     8     8     8     8     8     8     8     8
 NREJ       1     8    11     3     0     6    13     9     0     0     0     0
 RADIUS  68.1  68.5  68.8  69.1  69.4  69.8  70.1  70.4  70.7  71.1  71.4  71.7
 BACKG     73    73    73    74    74    72    71    72    70    69    69    69
 SIGMA      8     8     8     8     8     8     8     8     8     8     8     8
 NREJ      12    18    17    10     0     3     7     1     1     1     0     0
 RADIUS  72.1  72.4  72.7  73.0  73.4  73.7  74.0  74.3  74.7  75.0  75.3  75.6
 BACKG     70    68    68    66    67    66    67    68    66    66    66    66
 SIGMA      8     8     8     8     8     8     8     8     8     8     8     8
 NREJ       2     9     3     0     0     2     3     4    12    12     2     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     66    65    64    63    62    61    62    64    63    62    61    60
 SIGMA      8     8     7     7     7     7     7     8     7     7     7     7
 NREJ       2     8     3     0     0     0     0     0     5     5     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     61    60    60    58    59    59    60    59    60    59    59    59
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       1     6     1     0     1     0     0     0     3     5     0     0
 RADIUS  83.8  84.1  84.5
 BACKG     58    59    29
 SIGMA      7     7     3
 NREJ       0     0     0

 Starting spot search...
 sorting  1579 spots

  Median spot size is   6 x   6 pixels

  Total number of spots found:1579
  Number rejected as too small on X:  29
  Number rejected as too small on Y:  31
  Number rejected as too big on X:  15
  Number rejected as too big on Y:   8
  Number too close (SEPARATION keyword):   0
  Number stored as OK:1464



             Number of spots found in each bin
              36  26  26  37  32  17  22  35
              44  27  32  51  56  28  34  51
              49  29  41  68  56  28  45  48
              49  30  39  49  45  26  33  46
              44  26  36  41  31  26  22  35

 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  233 spots

 Based on a median spot size of  6 by  6 pixels in X and Y, the measurement box 
 parameters have been set to  19  19  11   6   6
 The overall size of the box has been fixed.
 To prevent this use keywords PROFILE NOFIXBOX.
 ***** WARNING ***** Lattice type not specified, so assumed primitive

 Based on a median spot size of  6 by  6 pixels in X and Y, the spot separation 
 parameters (in X and Y) have been set to  0.65  0.65mm.
 Closest possible spot separation is  0.00mm.

 Because the minimum possible spot separation is less than the estimated spot
 size plus a safety margin of 2 pixels (set by keywords SPOTS SAFE) the
 "CLOSE" option for integration has been set.
 ****************************************************
 ****************************************************
 It is advisable to ensure that all images for this dataset are also
 processed using the "CLOSE" option by explicitly including keywords:
 SEPARATION CLOSE
 ****************************************************
 ****************************************************
 image FILENAME: /scisoft/pxsoft/data/dna_040402/ref-ftest_1_002.img

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

 Logical Name: /scisoft/pxsoft/data/dna_040402/ref-ftest_1_002.img      Filename: /scisoft/pxsoft/data/dna_040402/ref-ftest_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     70    68    66    63    61    58    57    57    55    54    52    51
 SIGMA      8     8     8     7     7     7     7     7     7     7     7     7
 NREJ      10     6     1     1     0     1     0     0     0     0     0     0
 RADIUS  13.3  13.6  14.0  14.3  14.6  14.9  15.3  15.6  15.9  16.2  16.6  16.9
 BACKG     50    50    49    49    48    48    48    46    46    45    45    44
 SIGMA      7     7     7     7     6     6     6     6     6     6     6     6
 NREJ       0     0     7     8     4     0     0     0     0     0     0     0
 RADIUS  17.2  17.5  17.9  18.2  18.5  18.8  19.2  19.5  19.8  20.2  20.5  20.8
 BACKG     43    45    44    44    43    44    43    43    43    43    42    42
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     0     3     1     0     1     1     0     0     1     4     4
 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     42    42    43    41    41    41    42    41    41    41    40    40
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     0     6     8     0     0     3     7     1     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     41    41    40    41    41    40    40    40    40    40    40    40
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     0     8     7     1     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     39    39    39    39    40    39    40    39    39    39    39    40
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 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     38    39    39    39    39    39    38    39    39    39    39    39
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       1     0     0     4     1     0     0     0     0     0     1     4
 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     39    39    40    39    40    40    40    40    39    39    39    40
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     0     1     8     5     0     0     0     0     0     0     2
 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     40    39    40    40    40    40    40    40    40    40    40    41
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       1     0     1     6     5     0     0     2     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     41    40    40    41    41    41    41    41    41    42    41    42
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       1     0     0     5     2     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     42    42    43    43    44    44    45    45    46    44    44    45
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     0     0     5     8     2     0     1     1     0     0     0
 RADIUS  52.5  52.8  53.1  53.4  53.8  54.1  54.4  54.8  55.1  55.4  55.7  56.1
 BACKG     45    44    45    45    45    45    46    47    49    48    48    47
 SIGMA      6     6     6     6     6     6     6     6     7     6     6     6
 NREJ       0     0     0     0     0     0     0     0     1     1     0     0
 RADIUS  56.4  56.7  57.0  57.4  57.7  58.0  58.3  58.7  59.0  59.3  59.6  60.0
 BACKG     48    47    48    50    51    51    51    52    51    51    50    50
 SIGMA      6     6     6     7     7     7     7     7     7     7     7     7
 NREJ       0     0     0     0     6    10     5     0     1     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     52    53    53    52    54    55    56    54    54    57    58    57
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     0     0     0     0     0     0     0     2     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     57    56    57    56    56    56    58    58    57    57    56    56
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     0     0     0     0     1     0     0     0     0     0
 RADIUS  68.1  68.5  68.8  69.1  69.4  69.8  70.1  70.4  70.7  71.1  71.4  71.7
 BACKG     55    56    54    55    55    54    54    55    54    53    54    54
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     1     1     0     0     0     0     0     0     1     4
 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     53    53    53    53    52    52    52    52    51    52    52    52
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     0     0     0     0     0     2     3     0     0     1
 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     54    52    52    51    53    51    51    51    51    50    49    48
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     6
 NREJ       2     0     0     0     3     1     0     0     6     3     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     48    48    48    47    49    48    48    47    47    47    46    46
 SIGMA      6     6     6     6     7     6     6     6     6     6     6     6
 NREJ       0     0     0     0     1     7     2     1     0     1     3     0
 RADIUS  83.8  84.1  84.5
 BACKG     46    46    23
 SIGMA      6     6     3
 NREJ       0     0     1

 Starting spot search...
 sorting  1446 spots

  Median spot size is   6 x   6 pixels

  Total number of spots found:1446
  Number rejected as too small on X:  25
  Number rejected as too small on Y:  21
  Number rejected as too big on X:  14
  Number rejected as too big on Y:   1
  Number too close (SEPARATION keyword):   1
  Number stored as OK:1374



             Number of spots found in each bin
              34  22  16  30  27  18  16  30
              39  34  27  39  47  28  33  43
              53  33  33  48  53  37  29  53
              51  33  26  48  50  32  31  51
              45  24  28  29  30  20  25  40

 FORMATTED      UNKNOWN file opened on unit  10

 Logical name: ref-ftest_1.spt, Filename: ref-ftest_1.spt


  1464 spots written for image    1
  1374 spots written for image    2
 A total of  2838 spots were written to file

 FORMATTED      OLD     file opened on unit  10

 Logical name: ref-ftest_1.spt, Filename: ref-ftest_1.spt


DPS Indexing at Two-theta =    0.00 with 2321 reflections (minimum spot separation = 0.49mm. Maximum expected cell edge  267.90, Beam position is   93.58   92.24
Generating direct lattice vectors (This may take some time):
|-----------------|
..................
 Refining  30 direct space vectors:
|----------------------------|
..............................
selected 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   128.56   181.50   128.57    89.9  89.8  89.9   I23,I213,I432,I4132
  43 503    tI   128.57   181.50   128.56    89.9  90.2  90.1   I4,I41,I422,I4122
  42 502    oF   128.56   222.25   222.59    70.6  90.2  90.0   F222
  41 501    cP   128.34   128.36   128.41   119.9 119.9  90.0   P23,P213,P432,P4232,P4332,P4132
  40 500    hR   222.57   181.54   128.41    90.0 106.6 114.1   H3,H32 (hexagonal settings of R3 and R32)
  39 500    tP   128.34   128.36   128.41   119.9 119.9  90.0   P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
  38 500    oP   128.34   128.36   128.41   119.9 119.9  90.0   P222,P2221,P21212,P212121
  37 500    tP   128.36   128.41   128.34   119.9  90.0 119.9   P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
  36 252    hP   128.36   128.41   128.34   119.9  90.0 119.9   P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
                                                                P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
  35 252    mC   128.57   222.26   128.34   106.7 119.9  90.0   C2
  34 252    mC   128.57   222.26   128.34   106.7 119.9  90.0   C2
  33 252    mC   128.57   222.26   128.34   106.7 119.9  90.0   C2
  32 252    hP   128.34   128.41   128.36   119.9  90.0 119.9   P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
                                                                P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
  31 252    oC   128.34   222.62   128.36    54.9  90.0  90.1   C222,C2221
  30 251    oC   128.57   222.26   128.34   106.7 119.9  90.0   C222,C2221
  29 251    oC   128.36   222.62   128.34    54.9  90.0  90.1   C222,C2221
  28 251    oC   128.34   222.62   128.36    54.9  90.0  90.1   C222,C2221
  27 250    mP   128.34   128.36   128.41   119.9 119.9  90.0   P2,P21
  26 250    mP   128.34   128.36   128.41   119.9 119.9  90.0   P2,P21
  25 250    mP   128.36   128.34   128.41   119.9 119.9  90.0   P2,P21
  24 250    hR   181.54   222.25   128.69    73.3  90.0 114.1   H3,H32 (hexagonal settings of R3 and R32)
  23 250    oC   128.57   222.26   128.34   106.7 119.9  90.0   C222,C2221
  22   8    cF   181.54   181.50   182.09    90.1  90.0  90.0   F23,F432,F4132
  21   6    hR   128.36   128.57   314.93    89.8  90.0 120.0   H3,H32 (hexagonal settings of R3 and R32)
  20   5    hR   128.34   128.69   314.51    89.9  90.1 120.0   H3,H32 (hexagonal settings of R3 and R32)
  19   4    oI   128.41   181.54   128.69    90.0  89.8  90.0   I222,I212121
  18   4    mC   222.51   128.41   181.54    90.0 144.7  89.9   C2
  17   4    tI   128.56   128.57   181.50    89.9  89.9  89.8   I4,I41,I422,I4122
  16   3    mI   128.69   181.54   128.41    90.0  90.2  90.0   C2
  15   3    tI   128.57   128.56   181.50    89.9  89.9  89.8   I4,I41,I422,I4122
  14   3    oI   128.34   128.36   182.09    90.1  90.1  90.0   I222,I212121
  13   3    oI   181.50   128.56   128.57    89.8  89.9  89.9   I222,I212121
  12   3    tI   128.34   128.36   182.09    89.9  89.9  90.0   I4,I41,I422,I4122
  11   2    oF   181.50   181.54   182.09    90.0  90.1  90.0   F222
  10   2    mC   182.09   181.54   128.69    90.0 135.2  90.0   C2
   9   2    mC   222.62   128.34   128.36    90.0 125.1  89.9   C2
   8   1    mC   222.62   128.36   128.34    90.0 125.1  89.9   C2
   7   1    mC   181.50   181.54   128.41    90.0 134.8  90.0   C2
   6   1    mC   222.62   128.34   128.36    90.0 125.1  89.9   C2
   5   1    mC   181.50   181.54   128.41    90.0 134.8  90.0   C2
   4   0    mC   181.50   181.54   128.41    90.0 134.8  90.0   C2
   3   0    mC   181.50   181.54   128.41    90.0 134.8  90.0   C2
   2   0    aP   128.34   128.36   128.41    60.1  60.1  90.0   P1
   1   0    aP   128.34   128.36   128.41   119.9 119.9  90.0   P1
 No PENALTY SDCELL FRACN LATT      a        b        c     alpha  beta gamma  Possible spacegroups

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

Refining solution #22 with F23    (number 196) symmetry imposed

Initial cell (before refinement) is  181.7087  181.7087  181.7087  90.000  90.000  90.000
Using 2191 indexed reflections (out of 2321 spots found, {delta(XY) <= 2.5 sigma}),
final sd in spot positions is 0.11mm and in phi 0.30 degrees
Refined cell parameters  181.64  181.64  181.64  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  0.28mm or  0.215 times the minimum spot separation of ca  1.28mm.
  Final cell (after refinement) is   181.6432  181.6432  181.6432  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   9440.320  9196.946

 ****** 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-ftest_1.gen      Filename: ref-ftest_1.gen




 Title for MTZ and GENERATE Files (TITLE):
 .
 Crystal identifier (IDENT): ref-ftest_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=    51

 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         148   398   331   382   354   324   317   294   322   329   307   116   111   113   107   119   127    96    91
 No gained          86    87
 Total intensity 65118 72576 78272 82694 86397 90074 93383 96338 97853 99814 99999 99704 99347 98876 98495 97920 97240 96691 96093
 Total intensity 95473 94309
 SD of intensity   117   123   137   140   143   145   147   151   152   161   161   161   161   161   159   159   159   159   158
 SD of intensity   158   158
 The mosaicity has been estimated as ---> 0.68 <--- 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