Index results for mystery_1

Symmetry and refined cell parameters

Image Symmetry a b c alpha beta gamma
1 P4 78.112 78.112 37.194 90.000 90.000 90.000
2 P4 78.255 78.255 37.181 90.000 90.000 90.000
1+2 P4 78.168 78.168 37.192 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
1 506 119 0.235 0.150 0.080 -0.085
2 637 211 0.331 0.090 0.100 -0.075
1+2 1143 347 0.304 0.130 0.100 -0.055

Image 1: /scisoft/pxsoft/data/dna_061202/ref-mystery_1_001.img

Image 2: /scisoft/pxsoft/data/dna_061202/ref-mystery_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-mystery_1_###.img
 ===> directory /scisoft/pxsoft/data/dna_061202
 ===> detector adsc
 ===> beam 93.630000 95.185000
 ===> autoindex threshold 10 dps image 1
Using DPS code for background indexing
 ===> mosaic estimate
 ===> go

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

 Logical Name: /scisoft/pxsoft/data/dna_061202/ref-mystery_1_001.img      Filename: /scisoft/pxsoft/data/dna_061202/ref-mystery_1_001.img



 Crystal to detector distance of  249.99mm taken from image header

 Wavelength of 0.93400A taken from image header

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

 Input beam coordinates   93.63mm   95.18mm will be used


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

 image FILENAME: /scisoft/pxsoft/data/dna_061202/ref-mystery_1_001.img

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

 Logical Name: /scisoft/pxsoft/data/dna_061202/ref-mystery_1_001.img      Filename: /scisoft/pxsoft/data/dna_061202/ref-mystery_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  54 spots
 Threshold set to    4.3
 sorting  55 spots
 Threshold set to    4.3


 Finding spots on image     1 (Midpoint of phi   0.500 degrees)
 Calculating radial background..... 
 The background is radial along the X (slow) direction
 The average of  51 pixels, excluding outliers, is used
 The scan is offset by 4.7mm from the image centre in Y to avoid any
 backstop shadow
 Radial Background calculation complete
 RADIUS   9.4   9.7  10.0  10.4  10.7  11.0  11.3  11.7  12.0  12.3  12.6  13.0
 BACKG     38    38    38    38    38    38    38    38    39    39    38    39
 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  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     39    39    39    39    39    39    39    39    39    40    39    39
 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  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     40    39    39    39    39    39    39    39    39    39    40    39
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     0     0     0     0     0     0     0     0     1     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     40    40    40    41    41    42    42    42    41    41    42    42
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     0     0     0     0     3     3     0     0     0     0     0
 RADIUS  25.1  25.4  25.7  26.0  26.4  26.7  27.0  27.3  27.7  28.0  28.3  28.6
 BACKG     42    42    42    43    42    43    43    44    45    46    45    45
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       1     2     7     3     0     0     0     1     5    15    21    22
 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     45    45    46    46    44    45    45    46    45    45    45    46
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ      23    19    11     0     0     0     1    11    18    16    12     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     47    45    46    47    46    46    46    46    47    47    48    48
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     2     0     3     8    10    11     8     0     0     0     0
 RADIUS  36.8  37.1  37.5  37.8  38.1  38.4  38.8  39.1  39.4  39.7  40.1  40.4
 BACKG     48    49    50    50    50    51    51    51    51    52    52    52
 SIGMA      6     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     0     0     0     0     0     0     0     1     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     53    53    54    53    54    55    56    57    57    57    57    58
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     0     0     0     0     0     0     0     0     0     0
 RADIUS  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     59    59    58    60    60    61    62    62    62    63    62    64
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     1     0     0     0     0     0     0     0     0     0
 RADIUS  48.6  48.9  49.2  49.5  49.9  50.2  50.5  50.8  51.2  51.5  51.8  52.1
 BACKG     64    63    63    63    63    63    63    63    64    63    63    64
 SIGMA      8     7     7     7     7     7     7     7     8     7     7     8
 NREJ       0     0     0     0     0     0     0     0     0     0     0     0
 RADIUS  52.5  52.8  53.1  53.4  53.8  54.1  54.4  54.8  55.1  55.4  55.7  56.1
 BACKG     64    62    62    63    64    64    64    63    64    61    60    60
 SIGMA      8     7     7     7     8     8     8     7     8     7     7     7
 NREJ       0     0     0     0     0     0     0     1     0     0     0     1
 RADIUS  56.4  56.7  57.0  57.4  57.7  58.0  58.3  58.7  59.0  59.3  59.6  60.0
 BACKG     61    61    62    62    61    60    59    56    55    55    55    56
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     1     2     2     0     0     0     0     0     0     0
 RADIUS  60.3  60.6  61.0  61.3  61.6  61.9  62.3  62.6  62.9  63.2  63.6  63.9
 BACKG     56    56    56    55    53    51    52    51    51    50    51    51
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       1     0     0     0     0     0     0     0     0     0     0     1
 RADIUS  64.2  64.5  64.9  65.2  65.5  65.9  66.2  66.5  66.8  67.2  67.5  67.8
 BACKG     51    52    56    52    49    50    50    49    49    49    47    48
 SIGMA      7     7     7     7     7     7     7     7     6     7     6     6
 NREJ       0     0     0     0     1     0     0     3     3     2     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     47    48    48    48    47    48    48    48    47    48    47    47
 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  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     48    47    48    48    47    47    48    48    48    48    48    47
 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  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     46    46    46    45    44    44    44    44    44    44    44    43
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       1     0     0     0     0     0     0     0     1     0     0     1
 RADIUS  79.9  80.2  80.5  80.9  81.2  81.5  81.8  82.2  82.5  82.8  83.2  83.5
 BACKG     44    44    45    45    44    46    44    43    42    43    43    42
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     0     3     5     6     5     0     0     0     0     0     1
 RADIUS  83.8  84.1  84.5
 BACKG     43    43    22
 SIGMA      6     6     3
 NREJ       1     8     5

 Starting spot search...
 sorting  506 spots

  Median spot size is  12 x  11 pixels

  Total number of spots found: 506
  Number rejected as too small on X:  79
  Number rejected as too small on Y:  34
  Number rejected as too big on X:   4
  Number rejected as too big on Y:   2
  Number too close (SEPARATION keyword):   0
  Number stored as OK: 387



             Number of spots found in each bin
               5   6   6   2   8   4   4   6
              10   7   5   2  10   4   9   9
              10   9  10   9  13  13  12   9
              14  13  13  16  19  12   9  16
              14  13   8   7  13  11  12  15

 Determining average spot size for spots in centre of image.
 ==========================================================
 Finding spot size around direct beam position
 Default parameters may be reset with SPOTS keyword.
 Minimum radius   9.4mm, maximum radius 37.60mm, minimum number of spots 10
 sorting  55 spots

 Based on a median spot size of 10 by 10 pixels in X and Y, the measurement box 
 parameters have been set to  25  25  14   7   7
 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 10 by 10 pixels in X and Y, the spot separation 
 parameters (in X and Y) have been set to  0.97  0.97mm.
 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-mystery_1.spt, Filename: ref-mystery_1.spt


   387 spots written for image    1
 A total of   387 spots were written to file

 FORMATTED      OLD     file opened on unit  10

 Logical name: ref-mystery_1.spt, Filename: ref-mystery_1.spt


DPS Indexing at Two-theta =    0.00 with  380 reflections (minimum spot separation = 0.82mm. Maximum expected cell edge  284.77, Beam position is   93.63   95.18
Generating direct lattice vectors (This may take some time):
|-----------------|
..................
 Refining  30 direct space vectors:
|----------------------------|
..............................
selected 6
 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    mI    36.85   178.25    78.06    64.3  90.1  78.5   C2
  43 906    tI   110.30    86.31    86.28    79.9  50.6  50.3   I4,I41,I422,I4122
  42 906    tI    86.31    86.28   110.30    50.6  50.3  79.9   I4,I41,I422,I4122
  41 905    oI    86.28    86.31   110.30    50.3  50.6  79.9   I222,I212121
  40 903    oF    86.28    86.36   178.25   107.8 118.5  50.5   F222
  39 902    mC    86.36    86.28    86.31    79.9 100.6  50.5   C2
  38 749    hR   178.02   110.84    36.85    90.2  78.3 108.0   H3,H32 (hexagonal settings of R3 and R32)
  37 654    cF   116.49   116.09   116.66    95.7  95.6 143.1   F23,F432,F4132
  36 651    hR    36.85    86.36   249.67   102.6  98.1 115.3   H3,H32 (hexagonal settings of R3 and R32)
  35 649    cI    86.31    86.28   110.30    50.6  50.3  79.9   I23,I213,I432,I4132
  34 549    tI    36.85    78.06   178.25    64.3  78.5  90.1   I4,I41,I422,I4122
  33 549    oI    36.85    78.06   178.25   115.7 101.5  90.1   I222,I212121
  32 458    hP    36.85    78.06    78.31    90.3  90.4  90.1   P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
                                                                P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
  31 455    hP    78.06    78.31    36.85    90.4  90.1  90.3   P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
                                                                P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
  30 454    mC    78.06   174.65    36.85    89.6  89.9  63.7   C2
  29 452    oC    78.06   174.65    36.85    89.6  90.1 116.3   C222,C2221
  28 451    mC   174.65    78.06    36.85    90.1  90.4  63.7   C2
  27 361    cP    36.85    78.06    78.31    90.3  90.4  90.1   P23,P213,P432,P4232,P4332,P4132
  26 360    hR    86.36    86.31   116.94   118.4  62.0 100.6   H3,H32 (hexagonal settings of R3 and R32)
  25 359    hR    86.36    86.77   116.09   118.1  61.9 100.4   H3,H32 (hexagonal settings of R3 and R32)
  24 358    tP    36.85    78.06    78.31    90.3  90.4  90.1   P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
  23 357    oC    86.28    86.36    78.31    90.1  90.4  50.5   C222,C2221
  22 355    mC    86.28    86.36    78.31    89.9  90.4 129.5   C2
  21 354    mC    86.28    86.36    78.31    90.1  90.4  50.5   C2
  20 296    tI   110.30   116.66    36.85    71.8  89.7  90.1   I4,I41,I422,I4122
  19 293    oF    36.85   160.46   160.64    86.8 102.9 103.3   F222
  18 203    oI    36.85   110.30   116.66    89.9  71.8  90.3   I222,I212121
  17 201    mC   160.46    36.85   110.30    90.3 133.4  76.7   C2
  16 105    mC    36.85   160.46    78.31    89.8  90.4  76.7   C2
  15 104    oC    36.85   160.64    78.06    89.7  90.1 102.9   C222,C2221
  14 103    mC    36.85   160.64    78.06    89.7  89.9  77.1   C2
  13 102    mC   160.64    36.85    78.06    90.1  90.3  77.1   C2
  12 101    oC    36.85   160.64    78.06    89.7  90.1 102.9   C222,C2221
  11  99    mC   160.64    36.85    78.06    90.1  90.3  77.1   C2
  10   7    tP    78.06    78.31    36.85    90.4  90.1  90.3   P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
   9   5    mC   110.84   110.30    36.85    89.7  90.2  90.2   C2
   8   5    oC   110.30   110.84    36.85    90.2  90.3  89.8   C222,C2221
   7   4    mC   110.30   110.84    36.85    90.2  90.3  89.8   C2
   6   4    oP    36.85    78.06    78.31    90.3  90.4  90.1   P222,P2221,P21212,P212121
   5   4    mP    36.85    78.31    78.06    90.3  90.1  90.4   P2,P21
   4   2    mP    78.06    36.85    78.31    90.4  90.3  90.1   P2,P21
   3   2    mP    36.85    78.06    78.31    90.3  90.4  90.1   P2,P21
   2   0    aP    36.85    78.06    78.31    89.7  89.6  90.1   P1
   1   0    aP    36.85    78.06    78.31    90.3  90.4  90.1   P1
 No PENALTY SDCELL FRACN LATT      a        b        c     alpha  beta gamma  Possible spacegroups

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

Refining solution #10 with P4     (number  75) symmetry imposed

Initial cell (before refinement) is   78.1849   78.1849   36.8463  90.000  90.000  90.000
Using  356 indexed reflections (out of  380 spots found, {delta(XY) <= 2.5 sigma}),
final sd in spot positions is 0.15mm and in phi 0.41 degrees
Refined cell parameters   78.11   78.11   37.19  90.00  90.00  90.00
Beam coordinates of  93.63  95.18 have been refined to  93.71  95.10
This is a shift of  0.12mm or  0.039 times the minimum spot separation of ca  2.99mm.
  Final cell (after refinement) is    78.1117   78.1117   37.1941  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   9363.000  9518.500 to   9429.308  9510.460

 ****** 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 ( 0.9340) 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-mystery_1.gen      Filename: ref-mystery_1.gen




 Title for MTZ and GENERATE Files (TITLE):
 .
 Crystal identifier (IDENT): ref-mystery_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=    22

 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          31    51    64    48    59    60    62    58    67    57    57     2     0     3     0     1     1     0     0
 No gained           0     1
 Total intensity 68252 71903 78695 84600 89336 93999 96249 98635 99517 99669 99999 99997 99997 99996 99996 99996 99997 99997 99997
 Total intensity 99997 99937
 SD of intensity    68    68    71    75    76    77    78    80    80    80    80    80    80    80    80    80    80    80    80
 SD of intensity    80    80
 The mosaicity has been estimated as ---> 0.59 <--- for this image only; 
This value can be used cautiously as an initial estimate.
Storing space group from DPS autoindexing: P4         number  75



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


 ************ Version 6.2.3 (beta test 1.6) for Image plate and CCD data 4th November 2002  ***********
 A.G.W. Leslie, MRC Laboratory Of Molecular Biology, HILLS ROAD, CAMBRIDGE CB2 2QH, UK
 E-mail andrew@mrc-lmb.cam.ac.uk
 New auto-indexing using DPS due to Ingo Steller Robert Bolotovsky and Michael Rossmann
 (1998) J. Appl. Cryst. 30, 1036-1040
 Original auto-indexing using REFIX due to Wolfgang Kabsch (Kabsch,W. (1993),
J.Appl.Cryst. 24,795-800.)
 X-windows interface using xdl_view due to John Campbell (Daresbury Laboratory, UK.)
 (Campbell,J.W. (1995) J. Appl. Cryst. 28, 236-242.


 ===> newmat autoindex.mat
 ===> template ref-mystery_1_###.img
 ===> directory /scisoft/pxsoft/data/dna_061202
 ===> detector adsc
 ===> beam 93.630000 95.185000
 ===> 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_061202/ref-mystery_1_002.img      Filename: /scisoft/pxsoft/data/dna_061202/ref-mystery_1_002.img



 Crystal to detector distance of  249.99mm taken from image header

 Wavelength of 0.93400A taken from image header

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

 Input beam coordinates   93.63mm   95.18mm will be used


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

 image FILENAME: /scisoft/pxsoft/data/dna_061202/ref-mystery_1_002.img

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

 Logical Name: /scisoft/pxsoft/data/dna_061202/ref-mystery_1_002.img      Filename: /scisoft/pxsoft/data/dna_061202/ref-mystery_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  48 spots
 Threshold set to    4.2
 sorting  48 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     39    38    38    38    38    38    38    38    38    38    37    38
 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  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     38    38    38    38    38    39    40    39    39    39    39    38
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     0     0     0     0     0     5     9     5     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     38    38    38    39    38    38    38    38    37    38    37    38
 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  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     38    38    38    37    39    39    38    38    38    39    39    38
 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  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     38    38    38    38    37    38    38    38    38    38    38    38
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       1     0     0     0     0     0     0     0     0     0     0     0
 RADIUS  29.0  29.3  29.6  29.9  30.3  30.6  30.9  31.3  31.6  31.9  32.2  32.6
 BACKG     39    39    38    38    38    38    38    39    38    38    39    39
 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     40    40    40    40    41    40    41    41    41    41    41    41
 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  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     42    41    41    42    42    43    42    42    43    42    43    43
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     0     0     0     0     0     0     0     0     1     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    44    44    44    45    44    45    44    45    44    45    47
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     0     0     1     0     0     0     0     0     0     0     0
 RADIUS  44.6  45.0  45.3  45.6  45.9  46.3  46.6  46.9  47.2  47.6  47.9  48.2
 BACKG     46    45    46    47    48    48    48    49    49    49    49    49
 SIGMA      6     6     6     6     6     6     6     6     7     6     7     6
 NREJ       0     0     0     0     0     0     0     0     0     0     0     0
 RADIUS  48.6  48.9  49.2  49.5  49.9  50.2  50.5  50.8  51.2  51.5  51.8  52.1
 BACKG     49    49    49    49    49    49    49    49    50    49    50    49
 SIGMA      7     7     6     7     7     7     7     7     7     6     7     7
 NREJ       0     0     0     0     0     0     0     0     1     0     0     0
 RADIUS  52.5  52.8  53.1  53.4  53.8  54.1  54.4  54.8  55.1  55.4  55.7  56.1
 BACKG     48    49    49    49    49    49    50    51    52    55    53    52
 SIGMA      6     6     7     6     7     7     7     7     7     7     7     7
 NREJ       0     1     0     0     0     0     0     0     0     0     0     0
 RADIUS  56.4  56.7  57.0  57.4  57.7  58.0  58.3  58.7  59.0  59.3  59.6  60.0
 BACKG     50    49    48    49    49    48    50    49    48    49    48    49
 SIGMA      7     7     6     6     7     6     7     7     6     6     6     7
 NREJ       1     0     0     0     0     0     0     0     0     0     0     0
 RADIUS  60.3  60.6  61.0  61.3  61.6  61.9  62.3  62.6  62.9  63.2  63.6  63.9
 BACKG     49    50    54    54    52    51    50    50    51    51    51    51
 SIGMA      6     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     0     0     0     0     0     0     1     0     3    12
 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     52    51    57    53    51    51    52    52    53    53    55    53
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ      14    15    13    11     2     1     0     6    11    14     7     1
 RADIUS  68.1  68.5  68.8  69.1  69.4  69.8  70.1  70.4  70.7  71.1  71.4  71.7
 BACKG     52    51    51    52    52    52    50    49    48    47    47    48
 SIGMA      7     7     7     7     7     7     7     7     6     6     6     6
 NREJ       0     0     2     6     8     9     1     0     0     0     0     0
 RADIUS  72.1  72.4  72.7  73.0  73.4  73.7  74.0  74.3  74.7  75.0  75.3  75.6
 BACKG     46    47    47    47    47    47    47    47    48    48    51    52
 SIGMA      6     6     6     6     6     6     6     6     6     6     7     7
 NREJ       0     0     0     0     0     0     0     0     0     0     0    12
 RADIUS  76.0  76.3  76.6  76.9  77.3  77.6  77.9  78.3  78.6  78.9  79.2  79.6
 BACKG     50    50    50    49    50    48    46    47    47    47    47    47
 SIGMA      7     7     7     7     7     6     6     6     6     6     6     6
 NREJ      22    25    24    20     6     1     0     0     0     9    12     1
 RADIUS  79.9  80.2  80.5  80.9  81.2  81.5  81.8  82.2  82.5  82.8  83.2  83.5
 BACKG     46    47    47    47    47    47    45    46    45    44    44    44
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     0     0     0     2     4     2     0     0     0     0     0
 RADIUS  83.8  84.1  84.5
 BACKG     44    44    21
 SIGMA      6     6     3
 NREJ       0     0     0

 Starting spot search...
 sorting  637 spots

  Median spot size is  11 x  12 pixels

  Total number of spots found: 637
  Number rejected as too small on X: 159
  Number rejected as too small on Y:  20
  Number rejected as too big on X:  23
  Number rejected as too big on Y:   9
  Number too close (SEPARATION keyword):   0
  Number stored as OK: 426



             Number of spots found in each bin
               2   1   5   5   7   3   3   7
               9   7   9  15  10   8   5  15
              15  10   9  15  20   6  14  17
              17   9  14  19  17   5  14  20
              12   4  12  14  15   8   8  21

 Determining average spot size for spots in centre of image.
 ==========================================================
 Finding spot size around direct beam position
 Default parameters may be reset with SPOTS keyword.
 Minimum radius   9.4mm, maximum radius 37.60mm, minimum number of spots 10
 sorting  48 spots

 Based on a median spot size of 12 by 12 pixels in X and Y, the measurement box 
 parameters have been set to  29  29  16   8   8
 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 12 by 12 pixels in X and Y, the spot separation 
 parameters (in X and Y) have been set to  1.14  1.14mm.
 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-mystery_1.spt, Filename: ref-mystery_1.spt


   426 spots written for image    2
 A total of   426 spots were written to file

 FORMATTED      OLD     file opened on unit  10

 Logical name: ref-mystery_1.spt, Filename: ref-mystery_1.spt


DPS Indexing at Two-theta =    0.00 with  411 reflections (minimum spot separation = 0.98mm. Maximum expected cell edge  267.65, Beam position is   93.63   95.18
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    mI    37.09   177.22    78.05    64.0  90.0 101.8   C2
  43 994    tI   109.90    86.43    85.78    79.5  50.6  50.3   I4,I41,I422,I4122
  42 994    tI    86.43    85.78   109.90    50.6  50.3  79.5   I4,I41,I422,I4122
  41 992    oI    86.41    77.56   115.86    48.2  61.9  90.0   I222,I212121
  40 988    oF    85.78    86.16   177.97   107.5 118.7  51.1   F222
  39 888    mC    86.43    86.41    77.56    90.0  90.3  50.8   C2
  38 833    hR   177.22   110.17    37.09    89.8  78.2 107.7   H3,H32 (hexagonal settings of R3 and R32)
  37 723    cF   115.86   116.12   116.10    96.2  95.4 142.7   F23,F432,F4132
  36 721    cI    86.43    85.78   109.90    50.6  50.3  79.5   I23,I213,I432,I4132
  35 717    hR    37.09    85.78   249.32   102.4  98.6 115.3   H3,H32 (hexagonal settings of R3 and R32)
  34 608    tI    37.09    77.56   177.97    64.4  78.1  90.3   I4,I41,I422,I4122
  33 608    oI    37.09    77.56   177.97   115.6 101.9  90.3   I222,I212121
  32 501    hP    77.56    78.05    37.09    90.0  90.3  90.1   P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
                                                                P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
  31 495    mC   174.14    77.56    37.09    90.3  90.1  63.7   C2
  30 495    oC    77.56   174.14    37.09    89.9  90.3 116.3   C222,C2221
  29 494    mC    77.56   174.14    37.09    90.1  90.3  63.7   C2
  28 494    hP    37.09    77.56    78.05    90.1  90.0  90.3   P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
                                                                P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
  27 391    cP    37.09    77.56    78.05    90.1  90.0  90.3   P23,P213,P432,P4232,P4332,P4132
  26 390    hR    85.78    86.41   116.40   118.0  62.2 100.7   H3,H32 (hexagonal settings of R3 and R32)
  25 390    hR    86.16    86.41   115.86   118.1  62.4 100.7   H3,H32 (hexagonal settings of R3 and R32)
  24 385    tP    37.09    77.56    78.05    90.1  90.0  90.3   P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
  23 384    oC    85.78    86.16    78.05    90.1  90.1  51.1   C222,C2221
  22 384    mC    85.78    86.16    78.05    90.1  90.1  51.1   C2
  21 383    mC    86.16    85.78    78.05    89.9  90.1 128.9   C2
  20 339    tI   109.90   116.10    37.09    71.6  90.2  90.4   I4,I41,I422,I4122
  19 332    oF    37.09   159.28   160.44    86.9 103.3 103.1   F222
  18 230    oI    37.09   109.90   116.10    89.6  71.6  89.8   I222,I212121
  17 224    mC   159.28    37.09   109.90    89.8 133.2  76.9   C2
  16 116    oC    37.09   160.47    77.56    89.8  90.3 103.4   C222,C2221
  15 115    mC   160.47    37.09    77.56    90.3  90.2  76.6   C2
  14 114    mC    37.09   160.44    77.56    89.9  90.3  76.7   C2
  13 113    mC    37.09   159.28    78.05    89.9  90.0  76.9   C2
  12 112    oC    37.09   159.28    78.05    89.9  90.0 103.1   C222,C2221
  11 111    mC   159.28    37.09    78.05    90.0  90.1  76.9   C2
  10   9    tP    77.56    78.05    37.09    90.0  90.3  90.1   P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
   9   8    oC   109.90   110.17    37.09    89.8  90.2  89.6   C222,C2221
   8   8    mC   110.17   109.90    37.09    90.2  90.2  90.4   C2
   7   8    mC   109.90   110.17    37.09    89.8  90.2  89.6   C2
   6   3    mP    37.09    77.56    78.05    90.1  90.0  90.3   P2,P21
   5   3    oP    37.09    77.56    78.05    90.1  90.0  90.3   P222,P2221,P21212,P212121
   4   2    mP    77.56    37.09    78.05    90.0  90.1  90.3   P2,P21
   3   1    mP    37.09    78.05    77.56    90.1  90.3  90.0   P2,P21
   2   0    aP    37.09    77.56    78.05    89.9  90.0  89.7   P1
   1   0    aP    37.09    77.56    78.05    90.1  90.0  90.3   P1
 No PENALTY SDCELL FRACN LATT      a        b        c     alpha  beta gamma  Possible spacegroups

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

Refining solution #10 with P4     (number  75) symmetry imposed

Initial cell (before refinement) is   77.8064   77.8064   37.0944  90.000  90.000  90.000
Using  375 indexed reflections (out of  411 spots found, {delta(XY) <= 2.5 sigma}),
final sd in spot positions is 0.09mm and in phi 0.47 degrees
Refined cell parameters   78.26   78.26   37.18  90.00  90.00  90.00
Beam coordinates of  93.63  95.18 have been refined to  93.73  95.11
This is a shift of  0.13mm or  0.042 times the minimum spot separation of ca  2.98mm.
  Final cell (after refinement) is    78.2551   78.2551   37.1815  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   9363.000  9518.500 to   9427.524  9511.073

 ****** 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 ( 0.9340) 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-mystery_1.gen      Filename: ref-mystery_1.gen




 Title for MTZ and GENERATE Files (TITLE):
 .
 Crystal identifier (IDENT): ref-mystery_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=    21

 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          20    58    62    62    68    68    58    65    40    61    51     6    14     7    11    13    10    12    15
 No gained          13    14
 Total intensity 62675 71959 78276 84109 87640 91929 94861 97387 98067 99233 99999 99769 99599 99474 98987 98895 98823 98473 98078
 Total intensity 97871 97215
 SD of intensity    50    53    54    56    57    58    58    59    59    59    59    59    59    59    59    59    59    59    59
 SD of intensity    59    59
 The mosaicity has been estimated as ---> 0.62 <--- for this image only; 
This value can be used cautiously as an initial estimate.
Storing space group from DPS autoindexing: P4         number  75



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


 ************ Version 6.2.3 (beta test 1.6) for Image plate and CCD data 4th November 2002  ***********
 A.G.W. Leslie, MRC Laboratory Of Molecular Biology, HILLS ROAD, CAMBRIDGE CB2 2QH, UK
 E-mail andrew@mrc-lmb.cam.ac.uk
 New auto-indexing using DPS due to Ingo Steller Robert Bolotovsky and Michael Rossmann
 (1998) J. Appl. Cryst. 30, 1036-1040
 Original auto-indexing using REFIX due to Wolfgang Kabsch (Kabsch,W. (1993),
J.Appl.Cryst. 24,795-800.)
 X-windows interface using xdl_view due to John Campbell (Daresbury Laboratory, UK.)
 (Campbell,J.W. (1995) J. Appl. Cryst. 28, 236-242.


 ===> newmat autoindex.mat
 ===> template ref-mystery_1_###.img
 ===> directory /scisoft/pxsoft/data/dna_061202
 ===> detector adsc
 ===> beam 93.630000 95.185000
 ===> 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_061202/ref-mystery_1_001.img      Filename: /scisoft/pxsoft/data/dna_061202/ref-mystery_1_001.img



 Crystal to detector distance of  249.99mm taken from image header

 Wavelength of 0.93400A taken from image header

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

 Input beam coordinates   93.63mm   95.18mm will be used


 Autoindexing using  2 images
 Image numbers:     1    2
 image FILENAME: /scisoft/pxsoft/data/dna_061202/ref-mystery_1_001.img

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

 Logical Name: /scisoft/pxsoft/data/dna_061202/ref-mystery_1_001.img      Filename: /scisoft/pxsoft/data/dna_061202/ref-mystery_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  54 spots
 Threshold set to    4.3
 sorting  55 spots
 Threshold set to    4.3


 Finding spots on image     1 (Midpoint of phi   0.500 degrees)
 Calculating radial background..... 
 The background is radial along the X (slow) direction
 The average of  51 pixels, excluding outliers, is used
 The scan is offset by 4.7mm from the image centre in Y to avoid any
 backstop shadow
 Radial Background calculation complete
 RADIUS   9.4   9.7  10.0  10.4  10.7  11.0  11.3  11.7  12.0  12.3  12.6  13.0
 BACKG     38    38    38    38    38    38    38    38    39    39    38    39
 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  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     39    39    39    39    39    39    39    39    39    40    39    39
 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  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     40    39    39    39    39    39    39    39    39    39    40    39
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     0     0     0     0     0     0     0     0     1     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     40    40    40    41    41    42    42    42    41    41    42    42
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     0     0     0     0     3     3     0     0     0     0     0
 RADIUS  25.1  25.4  25.7  26.0  26.4  26.7  27.0  27.3  27.7  28.0  28.3  28.6
 BACKG     42    42    42    43    42    43    43    44    45    46    45    45
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       1     2     7     3     0     0     0     1     5    15    21    22
 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     45    45    46    46    44    45    45    46    45    45    45    46
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ      23    19    11     0     0     0     1    11    18    16    12     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     47    45    46    47    46    46    46    46    47    47    48    48
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     2     0     3     8    10    11     8     0     0     0     0
 RADIUS  36.8  37.1  37.5  37.8  38.1  38.4  38.8  39.1  39.4  39.7  40.1  40.4
 BACKG     48    49    50    50    50    51    51    51    51    52    52    52
 SIGMA      6     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     0     0     0     0     0     0     0     1     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     53    53    54    53    54    55    56    57    57    57    57    58
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     0     0     0     0     0     0     0     0     0     0
 RADIUS  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     59    59    58    60    60    61    62    62    62    63    62    64
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     1     0     0     0     0     0     0     0     0     0
 RADIUS  48.6  48.9  49.2  49.5  49.9  50.2  50.5  50.8  51.2  51.5  51.8  52.1
 BACKG     64    63    63    63    63    63    63    63    64    63    63    64
 SIGMA      8     7     7     7     7     7     7     7     8     7     7     8
 NREJ       0     0     0     0     0     0     0     0     0     0     0     0
 RADIUS  52.5  52.8  53.1  53.4  53.8  54.1  54.4  54.8  55.1  55.4  55.7  56.1
 BACKG     64    62    62    63    64    64    64    63    64    61    60    60
 SIGMA      8     7     7     7     8     8     8     7     8     7     7     7
 NREJ       0     0     0     0     0     0     0     1     0     0     0     1
 RADIUS  56.4  56.7  57.0  57.4  57.7  58.0  58.3  58.7  59.0  59.3  59.6  60.0
 BACKG     61    61    62    62    61    60    59    56    55    55    55    56
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     1     2     2     0     0     0     0     0     0     0
 RADIUS  60.3  60.6  61.0  61.3  61.6  61.9  62.3  62.6  62.9  63.2  63.6  63.9
 BACKG     56    56    56    55    53    51    52    51    51    50    51    51
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       1     0     0     0     0     0     0     0     0     0     0     1
 RADIUS  64.2  64.5  64.9  65.2  65.5  65.9  66.2  66.5  66.8  67.2  67.5  67.8
 BACKG     51    52    56    52    49    50    50    49    49    49    47    48
 SIGMA      7     7     7     7     7     7     7     7     6     7     6     6
 NREJ       0     0     0     0     1     0     0     3     3     2     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     47    48    48    48    47    48    48    48    47    48    47    47
 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  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     48    47    48    48    47    47    48    48    48    48    48    47
 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  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     46    46    46    45    44    44    44    44    44    44    44    43
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       1     0     0     0     0     0     0     0     1     0     0     1
 RADIUS  79.9  80.2  80.5  80.9  81.2  81.5  81.8  82.2  82.5  82.8  83.2  83.5
 BACKG     44    44    45    45    44    46    44    43    42    43    43    42
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     0     3     5     6     5     0     0     0     0     0     1
 RADIUS  83.8  84.1  84.5
 BACKG     43    43    22
 SIGMA      6     6     3
 NREJ       1     8     5

 Starting spot search...
 sorting  506 spots

  Median spot size is  12 x  11 pixels

  Total number of spots found: 506
  Number rejected as too small on X:  79
  Number rejected as too small on Y:  34
  Number rejected as too big on X:   4
  Number rejected as too big on Y:   2
  Number too close (SEPARATION keyword):   0
  Number stored as OK: 387



             Number of spots found in each bin
               5   6   6   2   8   4   4   6
              10   7   5   2  10   4   9   9
              10   9  10   9  13  13  12   9
              14  13  13  16  19  12   9  16
              14  13   8   7  13  11  12  15

 Determining average spot size for spots in centre of image.
 ==========================================================
 Finding spot size around direct beam position
 Default parameters may be reset with SPOTS keyword.
 Minimum radius   9.4mm, maximum radius 37.60mm, minimum number of spots 10
 sorting  55 spots

 Based on a median spot size of 10 by 10 pixels in X and Y, the measurement box 
 parameters have been set to  25  25  14   7   7
 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 10 by 10 pixels in X and Y, the spot separation 
 parameters (in X and Y) have been set to  0.97  0.97mm.
 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_061202/ref-mystery_1_002.img

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

 Logical Name: /scisoft/pxsoft/data/dna_061202/ref-mystery_1_002.img      Filename: /scisoft/pxsoft/data/dna_061202/ref-mystery_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     39    38    38    38    38    38    38    38    38    38    37    38
 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  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     38    38    38    38    38    39    40    39    39    39    39    38
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     0     0     0     0     0     5     9     5     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     38    38    38    39    38    38    38    38    37    38    37    38
 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  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     38    38    38    37    39    39    38    38    38    39    39    38
 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  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     38    38    38    38    37    38    38    38    38    38    38    38
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       1     0     0     0     0     0     0     0     0     0     0     0
 RADIUS  29.0  29.3  29.6  29.9  30.3  30.6  30.9  31.3  31.6  31.9  32.2  32.6
 BACKG     39    39    38    38    38    38    38    39    38    38    39    39
 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     40    40    40    40    41    40    41    41    41    41    41    41
 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  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     42    41    41    42    42    43    42    42    43    42    43    43
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     0     0     0     0     0     0     0     0     1     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    44    44    44    45    44    45    44    45    44    45    47
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     0     0     1     0     0     0     0     0     0     0     0
 RADIUS  44.6  45.0  45.3  45.6  45.9  46.3  46.6  46.9  47.2  47.6  47.9  48.2
 BACKG     46    45    46    47    48    48    48    49    49    49    49    49
 SIGMA      6     6     6     6     6     6     6     6     7     6     7     6
 NREJ       0     0     0     0     0     0     0     0     0     0     0     0
 RADIUS  48.6  48.9  49.2  49.5  49.9  50.2  50.5  50.8  51.2  51.5  51.8  52.1
 BACKG     49    49    49    49    49    49    49    49    50    49    50    49
 SIGMA      7     7     6     7     7     7     7     7     7     6     7     7
 NREJ       0     0     0     0     0     0     0     0     1     0     0     0
 RADIUS  52.5  52.8  53.1  53.4  53.8  54.1  54.4  54.8  55.1  55.4  55.7  56.1
 BACKG     48    49    49    49    49    49    50    51    52    55    53    52
 SIGMA      6     6     7     6     7     7     7     7     7     7     7     7
 NREJ       0     1     0     0     0     0     0     0     0     0     0     0
 RADIUS  56.4  56.7  57.0  57.4  57.7  58.0  58.3  58.7  59.0  59.3  59.6  60.0
 BACKG     50    49    48    49    49    48    50    49    48    49    48    49
 SIGMA      7     7     6     6     7     6     7     7     6     6     6     7
 NREJ       1     0     0     0     0     0     0     0     0     0     0     0
 RADIUS  60.3  60.6  61.0  61.3  61.6  61.9  62.3  62.6  62.9  63.2  63.6  63.9
 BACKG     49    50    54    54    52    51    50    50    51    51    51    51
 SIGMA      6     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     0     0     0     0     0     0     1     0     3    12
 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     52    51    57    53    51    51    52    52    53    53    55    53
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ      14    15    13    11     2     1     0     6    11    14     7     1
 RADIUS  68.1  68.5  68.8  69.1  69.4  69.8  70.1  70.4  70.7  71.1  71.4  71.7
 BACKG     52    51    51    52    52    52    50    49    48    47    47    48
 SIGMA      7     7     7     7     7     7     7     7     6     6     6     6
 NREJ       0     0     2     6     8     9     1     0     0     0     0     0
 RADIUS  72.1  72.4  72.7  73.0  73.4  73.7  74.0  74.3  74.7  75.0  75.3  75.6
 BACKG     46    47    47    47    47    47    47    47    48    48    51    52
 SIGMA      6     6     6     6     6     6     6     6     6     6     7     7
 NREJ       0     0     0     0     0     0     0     0     0     0     0    12
 RADIUS  76.0  76.3  76.6  76.9  77.3  77.6  77.9  78.3  78.6  78.9  79.2  79.6
 BACKG     50    50    50    49    50    48    46    47    47    47    47    47
 SIGMA      7     7     7     7     7     6     6     6     6     6     6     6
 NREJ      22    25    24    20     6     1     0     0     0     9    12     1
 RADIUS  79.9  80.2  80.5  80.9  81.2  81.5  81.8  82.2  82.5  82.8  83.2  83.5
 BACKG     46    47    47    47    47    47    45    46    45    44    44    44
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     0     0     0     2     4     2     0     0     0     0     0
 RADIUS  83.8  84.1  84.5
 BACKG     44    44    21
 SIGMA      6     6     3
 NREJ       0     0     0

 Starting spot search...
 sorting  637 spots

  Median spot size is  11 x  12 pixels

  Total number of spots found: 637
  Number rejected as too small on X: 164
  Number rejected as too small on Y:  18
  Number rejected as too big on X:  20
  Number rejected as too big on Y:  10
  Number too close (SEPARATION keyword):  94
  Number stored as OK: 409



             Number of spots found in each bin
               2   2   6   5   7   3   3   7
               9   7   9  15  10   8   5  15
              15  10   9  15  19   6  14  17
              17   9  14  19  17   5  12  20
              12   4  12  14  15   8   8  21

 FORMATTED      UNKNOWN file opened on unit  10

 Logical name: ref-mystery_1.spt, Filename: ref-mystery_1.spt


   387 spots written for image    1
   409 spots written for image    2
 A total of   796 spots were written to file

 FORMATTED      OLD     file opened on unit  10

 Logical name: ref-mystery_1.spt, Filename: ref-mystery_1.spt


DPS Indexing at Two-theta =    0.00 with  782 reflections (minimum spot separation = 0.90mm. Maximum expected cell edge  267.65, Beam position is   93.63   95.18
Generating direct lattice vectors (This may take some time):
|-----------------|
..................
 Refining  30 direct space vectors:
|----------------------------|
..............................
selected 4
 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    mI    37.10   178.82    77.93    64.0  89.9  77.8   C2
  43 902    oI    86.38    86.63   110.47    50.1  50.3  79.2   I222,I212121
  42 902    tI   110.47    86.63    86.38    79.2  50.3  50.1   I4,I41,I422,I4122
  41 902    tI    86.63    86.38   110.47    50.3  50.1  79.2   I4,I41,I422,I4122
  40 899    mC    86.25    86.38    86.63    79.2 100.6  50.9   C2
  39 899    oF    86.38    86.25   178.82   107.7 119.1  50.9   F222
  38 756    hR   178.28   110.27    37.10    90.1  78.2 107.9   H3,H32 (hexagonal settings of R3 and R32)
  37 654    cI    86.40    86.38   110.27    50.5  50.2  79.5   I23,I213,I432,I4132
  36 653    cF   116.38   116.31   116.41    95.9  95.6 142.8   F23,F432,F4132
  35 651    hR    37.10    86.25   249.62   102.6  98.4 115.4   H3,H32 (hexagonal settings of R3 and R32)
  34 550    tI    37.10    77.93   178.35    64.2  78.1  89.9   I4,I41,I422,I4122
  33 550    oI    37.10    77.93   178.35   115.8 101.9  89.9   I222,I212121
  32 453    hP    77.93    78.16    37.10    90.2  89.9  90.1   P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
                                                                P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
  31 452    hP    37.10    77.93    78.16    90.1  89.8  90.1   P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
                                                                P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
  30 450    mC    77.93   174.53    37.10    89.9  90.1  63.6   C2
  29 450    oC    77.93   174.53    37.10    89.9  89.9 116.4   C222,C2221
  28 450    mC   174.53    77.93    37.10    89.9  90.1  63.6   C2
  27 353    cP    37.10    77.93    78.16    90.1  90.2  89.9   P23,P213,P432,P4232,P4332,P4132
  26 353    hR    86.25    86.63   116.31   117.9  62.1 100.6   H3,H32 (hexagonal settings of R3 and R32)
  25 352    hR    86.25    86.40   116.67   118.0  62.2 100.6   H3,H32 (hexagonal settings of R3 and R32)
  24 351    tP    37.10    77.93    78.16    90.1  90.2  89.9   P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
  23 350    oC    86.38    86.25    78.16    90.0  90.2  50.9   C222,C2221
  22 349    mC    86.38    86.25    78.16    90.0  90.2  50.9   C2
  21 348    mC    86.38    86.25    78.16    90.0  90.2 129.1   C2
  20 303    tI   110.27   116.41    37.10    71.6  89.9  90.1   I4,I41,I422,I4122
  19 301    oF    37.10   160.15   160.53    86.9 103.2 103.3   F222
  18 205    oI    37.10   110.27   116.41    89.9  71.6  90.1   I222,I212121
  17 202    mC   160.15    37.10   110.27    90.1 133.4  76.7   C2
  16 104    oC    37.10   160.15    78.16    89.9  89.8 103.3   C222,C2221
  15 103    mC   160.15    37.10    78.16    89.8  90.1  76.7   C2
  14 102    oC    37.10   160.53    77.93    89.9  89.9 103.2   C222,C2221
  13 102    mC    37.10   160.53    77.93    89.9  90.1  76.8   C2
  12 102    mC    37.10   160.15    78.16    89.9  90.2  76.7   C2
  11 101    mC   160.53    37.10    77.93    89.9  90.1  76.8   C2
  10   5    tP    77.93    78.16    37.10    90.2  89.9  90.1   P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
   9   4    oC   110.27   110.47    37.10    90.2  90.1  89.8   C222,C2221
   8   4    mC   110.47   110.27    37.10    90.1  90.2  89.8   C2
   7   3    mC   110.47   110.27    37.10    89.9  90.2  90.2   C2
   6   2    mP    77.93    37.10    78.16    90.2  90.1  89.9   P2,P21
   5   2    mP    37.10    77.93    78.16    90.1  90.2  89.9   P2,P21
   4   2    oP    37.10    77.93    78.16    90.1  90.2  89.9   P222,P2221,P21212,P212121
   3   2    mP    37.10    78.16    77.93    90.1  89.9  90.2   P2,P21
   2   0    aP    37.10    77.93    78.16    89.9  89.8  89.9   P1
   1   0    aP    37.10    77.93    78.16    90.1  90.2  89.9   P1
 No PENALTY SDCELL FRACN LATT      a        b        c     alpha  beta gamma  Possible spacegroups

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

Refining solution #10 with P4     (number  75) symmetry imposed

Initial cell (before refinement) is   78.0439   78.0439   37.0999  90.000  90.000  90.000
Using  724 indexed reflections (out of  782 spots found, {delta(XY) <= 2.5 sigma}),
final sd in spot positions is 0.13mm and in phi 0.48 degrees
Refined cell parameters   78.17   78.17   37.19  90.00  90.00  90.00
Beam coordinates of  93.63  95.18 have been refined to  93.73  95.13
This is a shift of  0.11mm or  0.038 times the minimum spot separation of ca  2.99mm.
  Final cell (after refinement) is    78.1678   78.1678   37.1917  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   9363.000  9518.500 to   9427.895  9512.670

 ****** 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 ( 0.9340) 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-mystery_1.gen      Filename: ref-mystery_1.gen




 Title for MTZ and GENERATE Files (TITLE):
 .
 Crystal identifier (IDENT): ref-mystery_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=    21

 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          23    57    65    72    61    54    67    58    65    60    37    10     8     8     8    12    14     8    11
 No gained           8    21
 Total intensity 63095 68767 75524 83844 87050 90790 94994 96640 97802 99377 99999 99774 99706 99246 99029 98924 98712 98495 98266
 Total intensity 98033 97195
 SD of intensity    73    75    78    81    81    82    84    84    84    84    85    84    84    84    84    84    84    84    84
 SD of intensity    84    84
 The mosaicity has been estimated as ---> 0.62 <--- for this image only; 
This value can be used cautiously as an initial estimate.
Storing space group from DPS autoindexing: P4         number  75
Storing space group from DPS autoindexing: P4         number  75



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