Index results for ferritin_1

Symmetry and refined cell parameters

Image Symmetry a b c alpha beta gamma
1 F23 181.139 181.139 181.139 90.000 90.000 90.000
2 C2 222.549 128.091 181.958 90.000 144.919 90.000
1+2 F23 181.123 181.123 181.123 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
1 558 27 0.048 0.040 0.070 -0.085
2 536 23 0.043 0.040 0.060 -0.095
1+2 1093 50 0.046 0.050 0.070 -0.085

Image 1: /scisoft/pxsoft/data/dna_061202/ref-ferritin_1_001.img

Image 2: /scisoft/pxsoft/data/dna_061202/ref-ferritin_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-ferritin_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-ferritin_1_001.img      Filename: /scisoft/pxsoft/data/dna_061202/ref-ferritin_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-ferritin_1_001.img

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

 Logical Name: /scisoft/pxsoft/data/dna_061202/ref-ferritin_1_001.img      Filename: /scisoft/pxsoft/data/dna_061202/ref-ferritin_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  141 spots
 Threshold set to    4.1
 sorting  156 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     56    55    55    55    54    53    52    53    52    51    50    50
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     0     0     5    12    11     3     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    49    48    48    48    49    48    48    49    47    47    48
 SIGMA      7     6     6     6     6     7     6     6     7     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     48    48    49    48    48    48    49    48    47    47    47    46
 SIGMA      6     6     7     6     6     6     7     6     6     6     6     6
 NREJ       5     7     4    10     6     0     0     2     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     46    46    46    46    45    46    45    45    46    45    46    45
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     0     0     0     1     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     48    47    46    46    46    46    46    45    46    45    46    44
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       4     4    11    10     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     45    45    44    44    45    45    45    45    44    45    45    45
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     0     1     0     0     0     0     0     0     0     1     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     45    45    45    45    44    45    44    45    44    44    44    44
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     5     9     3     4     1     0     0     1     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     45    45    43    45    44    43    44    44    43    44    43    44
 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  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    43    44    44    44    45    46    45    44    45
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     0     0     0     0     0     0     0     2     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     45    45    45    46    46    45    45    45    46    45    47    46
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     0     0     0     0     0     0     2     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     46    47    46    47    47    47    48    47    49    50    48    47
 SIGMA      6     6     6     6     6     6     6     6     6     7     6     6
 NREJ       0     0     1     0     1     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     48    48    48    49    48    48    48    49    49    50    50    51
 SIGMA      6     6     6     6     6     6     6     7     7     7     7     7
 NREJ       0     0     0     0     0     0     0     0     1     8     7     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     51    50    50    50    50    49    49    50    51    51    51    50
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       3     1     0     0     0     0     0     0     0     0     2     9
 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     51    51    50    48    49    50    51    50    49    50    50    50
 SIGMA      7     7     7     6     7     7     7     7     7     7     7     7
 NREJ       3     0     0     0     0     0     3     0     1     1     6     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     49    49    48    49    50    50    49    49    50    50    49    48
 SIGMA      7     7     6     7     7     7     6     7     7     7     7     6
 NREJ       0     0     0     0     0     2     0     0     0     2     1     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    47    48    47    47    47    47    47    47    46    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     47    47    47    46    45    46    46    45    45    44    44    44
 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     45    44    45    44    44    43    44    43    44    43    44    43
 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  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     43    43    42    42    42    42    42    42    42    42    41    41
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       1     0     0     0     1     0     0     0     0     0     0     0
 RADIUS  83.8  84.1  84.5
 BACKG     41    41    20
 SIGMA      6     6     3
 NREJ       0     0     0

 Starting spot search...
 sorting  558 spots

  Median spot size is   5 x   5 pixels

  Total number of spots found: 558
  Number rejected as too small on X:  14
  Number rejected as too small on Y:  11
  Number rejected as too big on X:   2
  Number rejected as too big on Y:   0
  Number too close (SEPARATION keyword):   0
  Number stored as OK: 531



             Number of spots found in each bin
              22  15  17  22  27  10  15  27
              22  21  15  22  19  13  23  23
              27  23  19  20  29  18  12  13
              10  16   8   4   5   4   2   0
               2   1   1   0   1   1   0   2

 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  156 spots

 Based on a median spot size of  5 by  5 pixels in X and Y, the measurement box 
 parameters have been set to  17  17  10   5   5
 The overall size of the box has been fixed.
 To prevent this use keywords PROFILE NOFIXBOX.
 ***** WARNING ***** Lattice type not specified, so assumed primitive

 Based on a median spot size of  5 by  5 pixels in X and Y, the spot separation 
 parameters (in X and Y) have been set to  0.57  0.57mm.
 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-ferritin_1.spt, Filename: ref-ferritin_1.spt


   531 spots written for image    1
 A total of   531 spots were written to file

 FORMATTED      OLD     file opened on unit  10

 Logical name: ref-ferritin_1.spt, Filename: ref-ferritin_1.spt


DPS Indexing at Two-theta =    0.00 with  263 reflections (minimum spot separation = 0.41mm. 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 8
 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   128.09   180.84   128.28    90.0  90.0  89.8   I23,I213,I432,I4132
  43 505    cP   127.84   127.91   128.15    90.1 120.0 119.8   P23,P213,P432,P4232,P4332,P4132
  42 504    tP   127.91   128.15   127.84   120.0 119.8  90.1   P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
  41 503    tP   127.84   127.91   128.15    90.1 120.0 119.8   P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
  40 503    oP   127.84   127.91   128.15    90.1 120.0 119.8   P222,P2221,P21212,P212121
  39 502    tI   128.28   180.84   128.09    89.8  90.0  90.0   I4,I41,I422,I4122
  38 501    hR   221.79   181.30   127.84    90.1 106.6 114.1   H3,H32 (hexagonal settings of R3 and R32)
  37 501    oF   128.09   221.64   221.79    70.7  90.1  90.2   F222
  36 256    hP   128.15   128.20   127.84    90.1 120.0 119.9   P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
                                                                P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
  35 255    hP   127.84   128.15   127.91    90.1 119.8 120.0   P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
                                                                P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
  34 255    hR   181.30   221.64   128.20    73.3  90.0 114.3   H3,H32 (hexagonal settings of R3 and R32)
  33 254    oC   128.09   221.79   127.84    73.4 119.9  89.9   C222,C2221
  32 254    oC   128.28   221.25   128.15    73.3 120.0  90.0   C222,C2221
  31 254    oC   127.84   222.07   127.91    73.2 119.8  90.0   C222,C2221
  30 253    oC   127.84   222.07   127.91    73.2 119.8  90.0   C222,C2221
  29 253    mC   128.09   221.79   127.84    73.4 119.9  89.9   C2
  28 253    mC   128.09   221.79   127.84    73.4 119.9  89.9   C2
  27 253    mP   127.84   128.15   127.91    90.1 119.8 120.0   P2,P21
  26 252    mC   128.09   221.79   127.84    73.4 119.9  89.9   C2
  25 252    oC   127.84   222.07   127.91    73.2 119.8  90.0   C222,C2221
  24 252    mP   127.84   127.91   128.15    90.1 120.0 119.8   P2,P21
  23 251    mP   127.84   127.91   128.15    90.1 120.0 119.8   P2,P21
  22   9    tI   128.28   128.09   180.84    90.2  90.0  90.0   I4,I41,I422,I4122
  21   9    tI   128.09   128.28   180.84    90.0  89.8  90.0   I4,I41,I422,I4122
  20   8    oF   180.84   181.26   181.30    90.1  89.9  89.8   F222
  19   6    mC   180.84   181.30   128.20    90.0 135.0  89.9   C2
  18   6    cF   181.26   180.84   181.30    90.1  90.1  90.2   F23,F432,F4132
  17   5    oI   127.84   128.20   181.30    90.0  89.9  90.1   I222,I212121
  16   5    oI   127.84   128.20   181.30    90.0  89.9  90.1   I222,I212121
  15   5    tI   128.09   128.28   180.84    90.0  89.8  90.0   I4,I41,I422,I4122
  14   4    mI   127.84   181.30   128.20    90.0  90.1  89.9   C2
  13   4    mC   221.25   128.28   128.09    90.0 125.2  90.0   C2
  12   4    mC   221.25   128.28   128.09    90.0 125.2  90.0   C2
  11   4    hR   127.84   128.28   314.06    90.0  90.0 120.1   H3,H32 (hexagonal settings of R3 and R32)
  10   4    mC   180.84   181.30   127.84    90.1 134.9  89.9   C2
   9   4    mC   221.25   128.28   128.09    90.0 125.2  90.0   C2
   8   3    oI   128.28   128.09   180.84    89.8  90.0  90.0   I222,I212121
   7   3    hR   128.28   128.15   313.07    90.2  90.0 120.0   H3,H32 (hexagonal settings of R3 and R32)
   6   3    mC   222.02   127.84   128.20    90.1 125.3  89.8   C2
   5   3    mC   221.59   128.20   127.84    89.9 125.1  90.1   C2
   4   2    mC   221.25   128.28   128.09    90.0 125.2  90.0   C2
   3   1    mC   221.25   128.28   128.09    90.0 125.2  90.0   C2
   2   1    aP   127.84   127.91   128.15    90.1 120.0 119.8   P1
   1   0    aP   127.84   127.91   128.09    60.1  60.1  60.2   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  181.1299  181.1299  181.1299  90.000  90.000  90.000
Using  251 indexed reflections (out of  263 spots found, {delta(XY) <= 2.5 sigma}),
final sd in spot positions is 0.04mm and in phi 0.26 degrees
Refined cell parameters  181.14  181.14  181.14  90.00  90.00  90.00
Beam coordinates of  93.63  95.18 have been refined to  93.70  95.10
This is a shift of  0.11mm or  0.085 times the minimum spot separation of ca  1.29mm.
  Final cell (after refinement) is   181.1395  181.1395  181.1395  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   9431.107  9509.664

 ****** 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-ferritin_1.gen      Filename: ref-ferritin_1.gen




 Title for MTZ and GENERATE Files (TITLE):
 .
 Crystal identifier (IDENT): ref-ferritin_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=    63

 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         194   421   408   399   416   399   430   414   360   410   394     8     7     9    16    15    22    28    30
 No gained          39    38
 Total intensity 71369 78694 85766 89788 95256 96559 97974 98767 99327 99727 99991 99991 99997 99930 99942 99936 99911 99905 99886
 Total intensity 99868 99874
 SD of intensity   240   252   264   277   289   301   307   314   326   332   338   338   338   338   338   338   338   338   332
 SD of intensity   332   332
 The mosaicity has been estimated as ---> 0.49 <--- 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-ferritin_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-ferritin_1_002.img      Filename: /scisoft/pxsoft/data/dna_061202/ref-ferritin_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-ferritin_1_002.img

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

 Logical Name: /scisoft/pxsoft/data/dna_061202/ref-ferritin_1_002.img      Filename: /scisoft/pxsoft/data/dna_061202/ref-ferritin_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  140 spots
 Threshold set to    4.1
 sorting  148 spots
 Threshold set to    4.1


 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     62    61    61    59    59    57    57    56    55    54    54    53
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       6     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     54    53    52    52    52    53    51    51    51    51    52    51
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     0     0     0     0     0     0     0     0     1     5
 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     51    50    52    51    51    51    50    50    50    50    50    50
 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     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     50    49    50    50    50    50    51    49    51    50    51    52
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     0     5     4     0     0     0     0     9     7     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     50    51    50    50    50    49    49    49    49    50    50    49
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     0     1     2     0     0     0     0     2     1     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     50    50    50    48    50    49    49    49    50    50    50    49
 SIGMA      7     7     7     6     7     7     7     7     7     7     7     6
 NREJ       0     0     3    10     5     0     0     0     3     7     3     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     50    49    50    50    50    50    50    49    49    49    49    49
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     1     5     2     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     49    50    50    49    49    49    50    50    50    49    50    50
 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  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     51    51    52    52    51    52    52    53    53    52    51    51
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     8     3     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     53    53    53    53    54    54    54    56    56    56    56    56
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     5     3     0     0     0     0     3     6     1     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     57    58    58    58    56    58    58    59    58    59    59    59
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     7     8     0     0     0     0     0     2     0     1     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     60    61    60    60    60    61    61    62    63    60    62    62
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     1     0     0     0     0     0     3     3     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     63    63    64    63    62    62    64    65    64    63    63    63
 SIGMA      7     7     8     7     7     7     8     8     8     7     7     7
 NREJ       1     7     2     0     1     0     0     1     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     63    63    63    62    63    63    63    62    62    63    62    63
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       4     6     0     0     1     1     0     4     0     0     0     0
 RADIUS  64.2  64.5  64.9  65.2  65.5  65.9  66.2  66.5  66.8  67.2  67.5  67.8
 BACKG     64    64    63    63    63    61    64    62    61    60    61    61
 SIGMA      7     8     7     7     7     7     8     7     7     7     7     7
 NREJ       3     3     4     0     0     0     2     5     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     61    62    61    60    59    59    60    59    59    58    58    58
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       4     2     0     0     0     0     0     2     2     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     58    59    59    58    58    57    59    58    57    57    55    54
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       2     7     1     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     56    55    56    54    54    54    55    55    55    54    53    51
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     1     0     0     0     0     0     3     4     0     0     0
 RADIUS  79.9  80.2  80.5  80.9  81.2  81.5  81.8  82.2  82.5  82.8  83.2  83.5
 BACKG     53    54    54    52    52    52    52    54    52    52    50    51
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     0     1     0     0     0     0     0     0     0     0
 RADIUS  83.8  84.1  84.5
 BACKG     50    51    25
 SIGMA      7     7     3
 NREJ       0     0     0

 Starting spot search...
 sorting  536 spots

  Median spot size is   5 x   6 pixels

  Total number of spots found: 536
  Number rejected as too small on X:   6
  Number rejected as too small on Y:   9
  Number rejected as too big on X:   8
  Number rejected as too big on Y:   0
  Number too close (SEPARATION keyword):   0
  Number stored as OK: 513



             Number of spots found in each bin
              24  19   3  19  21  17  17  25
              20  20  25  22  25  15  15  28
              19  18  11  17  19  24  13  24
               8   8   2   3   4   5   8   7
               1   5   1   0   0   0   1   0

 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  148 spots

 Based on a median spot size of  5 by  5 pixels in X and Y, the measurement box 
 parameters have been set to  17  17  10   5   5
 The overall size of the box has been fixed.
 To prevent this use keywords PROFILE NOFIXBOX.
 ***** WARNING ***** Lattice type not specified, so assumed primitive

 Based on a median spot size of  5 by  5 pixels in X and Y, the spot separation 
 parameters (in X and Y) have been set to  0.57  0.57mm.
 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-ferritin_1.spt, Filename: ref-ferritin_1.spt


   513 spots written for image    2
 A total of   513 spots were written to file

 FORMATTED      OLD     file opened on unit  10

 Logical name: ref-ferritin_1.spt, Filename: ref-ferritin_1.spt


DPS Indexing at Two-theta =    0.00 with  277 reflections (minimum spot separation = 0.41mm. 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 16
 List of possible Laue groups, sorted on penalty index.
 The lower the PENALTY, the better
 No PENALTY LATT     a        b        c     alpha  beta gamma  Possible spacegroups

  44 999    cI   127.92   177.09   128.09    89.9  90.1  89.2   I23,I213,I432,I4132
  43 541    cP   125.93   126.10   127.22   119.3  91.2 118.9   P23,P213,P432,P4232,P4332,P4132
  42 539    tP   126.10   127.22   125.93    91.2 118.9 119.3   P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
  41 531    tP   125.93   126.10   127.22   119.3  91.2 118.9   P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
  40 530    oP   125.93   126.10   127.22   119.3  91.2 118.9   P222,P2221,P21212,P212121
  39 517    tI   128.09   177.09   127.92    89.2  90.1  89.9   I4,I41,I422,I4122
  38 516    oF   127.92   218.65   218.46    71.8  90.7  90.6   F222
  37 505    hR   218.65   181.15   125.93    90.4 105.5 114.1   H3,H32 (hexagonal settings of R3 and R32)
  36 291    hP   127.22   127.22   125.93   119.3  91.2 119.5   P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
                                                                P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
  35 284    oC   125.93   221.90   126.10    72.5 118.9  90.4   C222,C2221
  34 283    hP   126.10   127.22   125.93    91.2 118.9 119.3   P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
                                                                P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
  33 277    oC   127.92   218.65   125.93    74.5 119.9  89.4   C222,C2221
  32 275    oC   128.09   217.06   127.22   105.8 120.2  89.9   C222,C2221
  31 275    mC   128.09   219.85   125.93    74.3 120.5  90.0   C2
  30 274    mP   125.93   127.22   126.10   119.3 118.9  91.2   P2,P21
  29 274    oC   125.93   221.90   126.10    72.5 118.9  90.4   C222,C2221
  28 274    oC   126.10   221.80   125.93    72.6 118.9  90.4   C222,C2221
  27 269    mC   128.09   219.85   126.10    74.3 120.6  90.0   C2
  26 269    mC   128.09   219.85   126.10    74.3 120.6  90.0   C2
  25 268    mP   126.10   125.93   127.22    91.2 119.3 118.9   P2,P21
  24 268    hR   217.06   180.90   127.22    90.4 105.7 114.1   H3,H32 (hexagonal settings of R3 and R32)
  23 268    mP   125.93   126.10   127.22    91.3 119.3 118.9   P2,P21
  22  59    cF   180.90   177.09   181.15    90.5  90.1  90.6   F23,F432,F4132
  21  44    hR   126.10   128.09   313.10    90.0  89.2 120.6   H3,H32 (hexagonal settings of R3 and R32)
  20  42    hR   128.09   127.22   309.20    91.3  89.9 120.2   H3,H32 (hexagonal settings of R3 and R32)
  19  34    tI   128.09   127.92   177.09    90.8  89.9  89.9   I4,I41,I422,I4122
  18  34    oF   177.09   180.90   181.15    90.1  89.5  89.4   F222
  17  31    tI   127.92   128.09   177.09    89.9  89.2  90.1   I4,I41,I422,I4122
  16  31    oI   127.92   128.09   177.09    89.9  90.8  89.9   I222,I212121
  15  29    oI   128.09   127.92   177.09    89.2  90.1  89.9   I222,I212121
  14  27    mC   221.90   125.93   127.22    91.2 125.3  89.6   C2
  13  24    mC   177.09   181.15   127.22    90.3 134.7  89.5   C2
  12  23    mI   125.93   181.15   127.22    89.7  91.2  89.6   C2
  11  20    mC   217.06   128.09   127.92    90.1 125.3  89.9   C2
  10  20    mC   217.06   128.09   127.92    90.1 125.3  89.9   C2
   9  20    mC   217.06   128.09   127.92    89.9 125.3  90.1   C2
   8  19    mC   217.06   128.09   127.92    90.1 125.3  89.9   C2
   7  16    tI   127.92   128.09   177.09    89.9  89.2  90.1   I4,I41,I422,I4122
   6  15    mC   177.09   181.15   125.93    90.4 134.1  89.5   C2
   5  14    mC   217.06   128.09   127.92    89.9 125.3  90.1   C2
   4  11    oI   128.09   177.09   127.92    89.2  89.9  90.1   I222,I212121
   3  11    aP   125.93   126.10   127.22    60.7  91.2  61.1   P1
   2   1    mC   217.06   128.09   177.09    90.1 143.9  89.9   C2
   1   0    aP   125.93   126.10   127.22   119.3  91.2 118.9   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 # 2 with C2     (number   5) symmetry imposed

Initial cell (before refinement) is  217.0640  128.0856  177.0887  90.000 143.894  90.000
Using  259 indexed reflections (out of  277 spots found, {delta(XY) <= 2.5 sigma}),
final sd in spot positions is 0.04mm and in phi 0.25 degrees
Refined cell parameters  222.55  128.09  181.96  90.00 144.92  90.00
Beam coordinates of  93.63  95.18 have been refined to  93.69  95.09
This is a shift of  0.11mm or  0.062 times the minimum spot separation of ca  1.82mm.
  Final cell (after refinement) is   222.5495  128.0914  181.9577  90.000 144.919  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   9431.500  9509.074

 ****** 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-ferritin_1.gen      Filename: ref-ferritin_1.gen




 Title for MTZ and GENERATE Files (TITLE):
 .
 Crystal identifier (IDENT): ref-ferritin_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=    62

 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         214   374   403   385   416   376   394   406   396   402   418     7     6     6     8     5     2     7     4
 No gained           5     3
 Total intensity 78668 83547 88339 92026 93979 95542 97671 98627 99074 99583 99995 99974 99923 99928 99923 99918 99897 99871 99871
 Total intensity 99871 99820
 SD of intensity   267   278   283   293   298   308   314   319   329   334   339   339   339   339   339   339   339   339   339
 SD of intensity   339   339
 The mosaicity has been estimated as ---> 0.58 <--- for this image only; 
This value can be used cautiously as an initial estimate.
Storing space group from DPS autoindexing: C2         number   5



 *********** 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-ferritin_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-ferritin_1_001.img      Filename: /scisoft/pxsoft/data/dna_061202/ref-ferritin_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-ferritin_1_001.img

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

 Logical Name: /scisoft/pxsoft/data/dna_061202/ref-ferritin_1_001.img      Filename: /scisoft/pxsoft/data/dna_061202/ref-ferritin_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  141 spots
 Threshold set to    4.1
 sorting  156 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     56    55    55    55    54    53    52    53    52    51    50    50
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     0     0     5    12    11     3     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    49    48    48    48    49    48    48    49    47    47    48
 SIGMA      7     6     6     6     6     7     6     6     7     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     48    48    49    48    48    48    49    48    47    47    47    46
 SIGMA      6     6     7     6     6     6     7     6     6     6     6     6
 NREJ       5     7     4    10     6     0     0     2     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     46    46    46    46    45    46    45    45    46    45    46    45
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     0     0     0     1     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     48    47    46    46    46    46    46    45    46    45    46    44
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       4     4    11    10     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     45    45    44    44    45    45    45    45    44    45    45    45
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     0     1     0     0     0     0     0     0     0     1     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     45    45    45    45    44    45    44    45    44    44    44    44
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     5     9     3     4     1     0     0     1     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     45    45    43    45    44    43    44    44    43    44    43    44
 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  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    43    44    44    44    45    46    45    44    45
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     0     0     0     0     0     0     0     2     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     45    45    45    46    46    45    45    45    46    45    47    46
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       0     0     0     0     0     0     0     2     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     46    47    46    47    47    47    48    47    49    50    48    47
 SIGMA      6     6     6     6     6     6     6     6     6     7     6     6
 NREJ       0     0     1     0     1     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     48    48    48    49    48    48    48    49    49    50    50    51
 SIGMA      6     6     6     6     6     6     6     7     7     7     7     7
 NREJ       0     0     0     0     0     0     0     0     1     8     7     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     51    50    50    50    50    49    49    50    51    51    51    50
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       3     1     0     0     0     0     0     0     0     0     2     9
 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     51    51    50    48    49    50    51    50    49    50    50    50
 SIGMA      7     7     7     6     7     7     7     7     7     7     7     7
 NREJ       3     0     0     0     0     0     3     0     1     1     6     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     49    49    48    49    50    50    49    49    50    50    49    48
 SIGMA      7     7     6     7     7     7     6     7     7     7     7     6
 NREJ       0     0     0     0     0     2     0     0     0     2     1     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    47    48    47    47    47    47    47    47    46    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     47    47    47    46    45    46    46    45    45    44    44    44
 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     45    44    45    44    44    43    44    43    44    43    44    43
 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  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     43    43    42    42    42    42    42    42    42    42    41    41
 SIGMA      6     6     6     6     6     6     6     6     6     6     6     6
 NREJ       1     0     0     0     1     0     0     0     0     0     0     0
 RADIUS  83.8  84.1  84.5
 BACKG     41    41    20
 SIGMA      6     6     3
 NREJ       0     0     0

 Starting spot search...
 sorting  558 spots

  Median spot size is   5 x   5 pixels

  Total number of spots found: 558
  Number rejected as too small on X:  14
  Number rejected as too small on Y:  11
  Number rejected as too big on X:   2
  Number rejected as too big on Y:   0
  Number too close (SEPARATION keyword):   0
  Number stored as OK: 531



             Number of spots found in each bin
              22  15  17  22  27  10  15  27
              22  21  15  22  19  13  23  23
              27  23  19  20  29  18  12  13
              10  16   8   4   5   4   2   0
               2   1   1   0   1   1   0   2

 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  156 spots

 Based on a median spot size of  5 by  5 pixels in X and Y, the measurement box 
 parameters have been set to  17  17  10   5   5
 The overall size of the box has been fixed.
 To prevent this use keywords PROFILE NOFIXBOX.
 ***** WARNING ***** Lattice type not specified, so assumed primitive

 Based on a median spot size of  5 by  5 pixels in X and Y, the spot separation 
 parameters (in X and Y) have been set to  0.57  0.57mm.
 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-ferritin_1_002.img

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

 Logical Name: /scisoft/pxsoft/data/dna_061202/ref-ferritin_1_002.img      Filename: /scisoft/pxsoft/data/dna_061202/ref-ferritin_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     62    61    61    59    59    57    57    56    55    54    54    53
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       6     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     54    53    52    52    52    53    51    51    51    51    52    51
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     0     0     0     0     0     0     0     0     1     5
 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     51    50    52    51    51    51    50    50    50    50    50    50
 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     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     50    49    50    50    50    50    51    49    51    50    51    52
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     0     5     4     0     0     0     0     9     7     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     50    51    50    50    50    49    49    49    49    50    50    49
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     0     1     2     0     0     0     0     2     1     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     50    50    50    48    50    49    49    49    50    50    50    49
 SIGMA      7     7     7     6     7     7     7     7     7     7     7     6
 NREJ       0     0     3    10     5     0     0     0     3     7     3     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     50    49    50    50    50    50    50    49    49    49    49    49
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     1     5     2     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     49    50    50    49    49    49    50    50    50    49    50    50
 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  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     51    51    52    52    51    52    52    53    53    52    51    51
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     8     3     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     53    53    53    53    54    54    54    56    56    56    56    56
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     5     3     0     0     0     0     3     6     1     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     57    58    58    58    56    58    58    59    58    59    59    59
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     7     8     0     0     0     0     0     2     0     1     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     60    61    60    60    60    61    61    62    63    60    62    62
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     1     0     0     0     0     0     3     3     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     63    63    64    63    62    62    64    65    64    63    63    63
 SIGMA      7     7     8     7     7     7     8     8     8     7     7     7
 NREJ       1     7     2     0     1     0     0     1     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     63    63    63    62    63    63    63    62    62    63    62    63
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       4     6     0     0     1     1     0     4     0     0     0     0
 RADIUS  64.2  64.5  64.9  65.2  65.5  65.9  66.2  66.5  66.8  67.2  67.5  67.8
 BACKG     64    64    63    63    63    61    64    62    61    60    61    61
 SIGMA      7     8     7     7     7     7     8     7     7     7     7     7
 NREJ       3     3     4     0     0     0     2     5     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     61    62    61    60    59    59    60    59    59    58    58    58
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       4     2     0     0     0     0     0     2     2     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     58    59    59    58    58    57    59    58    57    57    55    54
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       2     7     1     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     56    55    56    54    54    54    55    55    55    54    53    51
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     1     0     0     0     0     0     3     4     0     0     0
 RADIUS  79.9  80.2  80.5  80.9  81.2  81.5  81.8  82.2  82.5  82.8  83.2  83.5
 BACKG     53    54    54    52    52    52    52    54    52    52    50    51
 SIGMA      7     7     7     7     7     7     7     7     7     7     7     7
 NREJ       0     0     0     1     0     0     0     0     0     0     0     0
 RADIUS  83.8  84.1  84.5
 BACKG     50    51    25
 SIGMA      7     7     3
 NREJ       0     0     0

 Starting spot search...
 sorting  535 spots

  Median spot size is   5 x   6 pixels

  Total number of spots found: 535
  Number rejected as too small on X:   6
  Number rejected as too small on Y:   9
  Number rejected as too big on X:   8
  Number rejected as too big on Y:   0
  Number too close (SEPARATION keyword):   0
  Number stored as OK: 512



             Number of spots found in each bin
              24  19   3  19  21  17  17  25
              20  20  25  22  25  15  15  28
              19  18  11  17  19  24  13  24
               8   8   2   3   4   5   8   7
               1   5   1   0   0   0   0   0

 FORMATTED      UNKNOWN file opened on unit  10

 Logical name: ref-ferritin_1.spt, Filename: ref-ferritin_1.spt


   531 spots written for image    1
   512 spots written for image    2
 A total of  1043 spots were written to file

 FORMATTED      OLD     file opened on unit  10

 Logical name: ref-ferritin_1.spt, Filename: ref-ferritin_1.spt


DPS Indexing at Two-theta =    0.00 with  540 reflections (minimum spot separation = 0.41mm. 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 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   128.10   180.97   128.33    89.9  89.8  89.9   I23,I213,I432,I4132
  43 501    cP   127.96   127.99   128.02   119.8 119.9  90.0   P23,P213,P432,P4232,P4332,P4132
  42 501    tP   127.96   127.99   128.02   119.8 119.9  90.0   P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
  41 501    tI   128.33   180.97   128.10    89.9  90.2  90.1   I4,I41,I422,I4122
  40 501    oF   128.10   221.62   222.07    70.7  90.2  90.0   F222
  39 500    hR   221.90   181.01   128.02    89.9 106.6 114.0   H3,H32 (hexagonal settings of R3 and R32)
  38 500    oP   127.96   127.99   128.02   119.8 119.9  90.0   P222,P2221,P21212,P212121
  37 500    tP   127.99   128.02   127.96   119.9  90.0 119.8   P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
  36 251    mC   128.10   221.62   127.99    73.3 119.8  90.0   C2
  35 251    mC   128.10   221.62   127.99   106.7 119.8  90.0   C2
  34 251    hP   127.96   128.02   127.99   119.8  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
  33 251    hP   127.96   128.02   127.99   119.8  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
  32 251    oC   127.96   221.85   127.99    55.0  90.0  90.0   C222,C2221
  31 251    oC   127.96   221.85   127.99    55.0  90.0  90.0   C222,C2221
  30 251    hR   181.01   221.62   128.38    73.4  89.9 114.1   H3,H32 (hexagonal settings of R3 and R32)
  29 251    mC   128.10   221.62   127.99   106.7 119.8  90.0   C2
  28 250    oC   128.10   221.62   127.99   106.7 119.8  90.0   C222,C2221
  27 250    mP   127.96   127.99   128.02   119.8 119.9  90.0   P2,P21
  26 250    mP   127.96   127.99   128.02   119.8 119.9  90.0   P2,P21
  25 250    mP   127.96   127.99   128.02   119.8 119.9  90.0   P2,P21
  24 250    oC   127.96   221.85   127.99    55.0  90.0  90.0   C222,C2221
  23 250    oC   128.10   221.62   127.99   106.7 119.8  90.0   C222,C2221
  22   8    cF   181.01   180.97   181.63    90.2  90.1  90.0   F23,F432,F4132
  21   7    hR   127.99   128.33   313.93    89.8  90.1 120.1   H3,H32 (hexagonal settings of R3 and R32)
  20   5    tI   128.33   128.10   180.97    89.9  89.9  89.8   I4,I41,I422,I4122
  19   4    tI   128.33   128.10   180.97    89.9  89.9  89.8   I4,I41,I422,I4122
  18   4    hR   127.96   128.38   313.39    89.9  90.0 119.9   H3,H32 (hexagonal settings of R3 and R32)
  17   4    oF   180.97   181.01   181.63    90.1  90.2  90.0   F222
  16   4    oI   128.02   181.01   128.38    90.1  89.8  90.1   I222,I212121
  15   3    mC   180.97   181.01   128.02    89.9 134.8  90.0   C2
  14   3    tI   127.96   127.99   181.63    89.8  90.0  90.0   I4,I41,I422,I4122
  13   3    mC   221.85   127.96   181.63    90.0 144.8  90.0   C2
  12   3    mI   127.99   181.63   127.96    90.0  90.0  89.8   C2
  11   3    oI   127.96   127.99   181.63    90.2  90.0  90.0   I222,I212121
  10   3    oI   180.97   128.10   128.33    89.8  89.9  89.9   I222,I212121
   9   2    mC   180.97   181.01   128.02    89.9 134.8  90.0   C2
   8   1    mC   221.85   127.96   127.99    90.0 125.0  90.0   C2
   7   1    mC   180.97   181.01   128.02    89.9 134.8  90.0   C2
   6   1    mC   180.97   181.01   128.02    90.1 134.8  90.0   C2
   5   1    mC   221.85   127.96   127.99    90.0 125.0  90.0   C2
   4   1    mC   221.85   127.96   127.99    90.0 125.0  90.0   C2
   3   1    mC   180.97   181.01   128.02    89.9 134.8  90.0   C2
   2   0    aP   127.96   127.99   128.02    60.2  60.1  90.0   P1
   1   0    aP   127.96   127.99   128.02   119.8 119.9  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  181.2012  181.2012  181.2012  90.000  90.000  90.000
Using  496 indexed reflections (out of  540 spots found, {delta(XY) <= 2.5 sigma}),
final sd in spot positions is 0.05mm and in phi 0.27 degrees
Refined cell parameters  181.12  181.12  181.12  90.00  90.00  90.00
Beam coordinates of  93.63  95.18 have been refined to  93.70  95.10
This is a shift of  0.11mm or  0.086 times the minimum spot separation of ca  1.29mm.
  Final cell (after refinement) is   181.1231  181.1231  181.1231  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   9430.712  9509.822

 ****** 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-ferritin_1.gen      Filename: ref-ferritin_1.gen




 Title for MTZ and GENERATE Files (TITLE):
 .
 Crystal identifier (IDENT): ref-ferritin_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=    62

 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         204   402   400   370   400   422   383   413   392   401   401     3     8     5     1     3     4     5     4
 No gained           9     8
 Total intensity 74879 82786 88193 90956 93326 95363 97582 98593 99251 99723 99988 99993 99998 99972 99977 99967 99967 99956 99946
 Total intensity 99708 99687
 SD of intensity   270   280   285   296   301   311   316   321   332   337   342   342   342   342   342   342   342   342   342
 SD of intensity   342   342
 The mosaicity has been estimated as ---> 0.57 <--- 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