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