Index results for ftest_1
Symmetry and refined cell parameters
Image |
Symmetry |
a |
b |
c |
alpha |
beta |
gamma |
1 |
F23 |
181.690 |
181.690 |
181.690 |
90.000 |
90.000 |
90.000 |
2 |
F23 |
181.587 |
181.587 |
181.587 |
90.000 |
90.000 |
90.000 |
1+2 |
F23 |
181.643 |
181.643 |
181.643 |
90.000 |
90.000 |
90.000 |
Spots found, rejected, RMS spot deviation, beamcentre shift
Image |
Spots found |
Spots rejected |
Fraction |
RMS spot deviation |
Beam shift x |
Beam shift y |
1 |
1579 |
115 |
0.073 |
0.080 |
0.025 |
-0.255 |
2 |
1439 |
73 |
0.051 |
0.080 |
0.025 |
-0.245 |
1+2 |
3025 |
187 |
0.062 |
0.110 |
0.015 |
-0.275 |
Image 1: /scisoft/pxsoft/data/dna_040402/ref-ftest_1_001.img
Image 2: /scisoft/pxsoft/data/dna_040402/ref-ftest_1_002.img
MOSFLM log
************ Version 6.2.3 (beta test 1.6) for Image plate and CCD data 4th November 2002 ***********
A.G.W. Leslie, MRC Laboratory Of Molecular Biology, HILLS ROAD, CAMBRIDGE CB2 2QH, UK
E-mail andrew@mrc-lmb.cam.ac.uk
New auto-indexing using DPS due to Ingo Steller Robert Bolotovsky and Michael Rossmann
(1998) J. Appl. Cryst. 30, 1036-1040
Original auto-indexing using REFIX due to Wolfgang Kabsch (Kabsch,W. (1993),
J.Appl.Cryst. 24,795-800.)
X-windows interface using xdl_view due to John Campbell (Daresbury Laboratory, UK.)
(Campbell,J.W. (1995) J. Appl. Cryst. 28, 236-242.
===> newmat autoindex.mat
===> template ref-ftest_1_###.img
===> directory /scisoft/pxsoft/data/dna_040402
===> detector adsc
===> beam 93.585000 92.245000
===> autoindex threshold 10 dps image 1
Using DPS code for background indexing
===> mosaic estimate
===> go
(Q)QOPEN: file opened on unit 1 Status: READONLY
Logical Name: /scisoft/pxsoft/data/dna_040402/ref-ftest_1_001.img Filename: /scisoft/pxsoft/data/dna_040402/ref-ftest_1_001.img
Crystal to detector distance of 249.95mm taken from image header
Wavelength of 0.93300A taken from image header
Pixel size of 0.0816mm taken from image header.
IBEAM = 2 it should be 2
Input beam coordinates 93.58mm 92.24mm will be used
Autoindexing image 1
=======================
image FILENAME: /scisoft/pxsoft/data/dna_040402/ref-ftest_1_001.img
(Q)QOPEN: file opened on unit 1 Status: READONLY
Logical Name: /scisoft/pxsoft/data/dna_040402/ref-ftest_1_001.img Filename: /scisoft/pxsoft/data/dna_040402/ref-ftest_1_001.img
Determining best threshold for spot finding.
Default parameters may be reset with SPOTS keyword.
Minimum radius 9.4mm, maximum radius 37.60mm, minimum number of spots 10
Background strip overlaps gap between detector tiles, so YOFFSET changed to 4.2mm
sorting 218 spots
Threshold set to 4.2
sorting 233 spots
Threshold set to 4.1
Finding spots on image 1 (Midpoint of phi 0.500 degrees)
Calculating radial background.....
The background is radial along the X (slow) direction
The average of 51 pixels, excluding outliers, is used
The scan is offset by 4.7mm from the image centre in Y to avoid any
backstop shadow
Radial Background calculation complete
RADIUS 9.4 9.7 10.0 10.4 10.7 11.0 11.3 11.7 12.0 12.3 12.6 13.0
BACKG 84 82 77 76 73 72 69 69 67 65 61 59
SIGMA 9 9 8 8 8 8 8 8 8 8 7 7
NREJ 18 11 8 0 3 5 0 0 1 4 1 0
RADIUS 13.3 13.6 14.0 14.3 14.6 14.9 15.3 15.6 15.9 16.2 16.6 16.9
BACKG 56 56 56 55 54 53 52 51 50 51 50 49
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 0 0 0 0 0 0 0 0 1 2 1
RADIUS 17.2 17.5 17.9 18.2 18.5 18.8 19.2 19.5 19.8 20.2 20.5 20.8
BACKG 50 51 50 50 49 48 47 46 46 46 46 46
SIGMA 7 7 7 7 7 6 6 6 6 6 6 6
NREJ 3 8 11 3 0 0 0 0 0 0 0 0
RADIUS 21.1 21.5 21.8 22.1 22.4 22.8 23.1 23.4 23.7 24.1 24.4 24.7
BACKG 45 46 46 45 45 44 44 45 45 45 45 44
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 0 0 0 0 0 0 0 0 2 8 1 0
RADIUS 25.1 25.4 25.7 26.0 26.4 26.7 27.0 27.3 27.7 28.0 28.3 28.6
BACKG 44 44 43 43 43 43 43 44 44 44 44 44
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 0 2 1 0 0 0 0 2 5 0 0 0
RADIUS 29.0 29.3 29.6 29.9 30.3 30.6 30.9 31.3 31.6 31.9 32.2 32.6
BACKG 43 44 43 43 43 44 43 43 44 44 44 44
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 3 0 1 0 0 0 0 0 0 0 0 0
RADIUS 32.9 33.2 33.5 33.9 34.2 34.5 34.8 35.2 35.5 35.8 36.1 36.5
BACKG 44 45 44 43 43 43 43 44 44 44 44 45
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 5 7 1 0 0 0 0 7 6 0 0 3
RADIUS 36.8 37.1 37.5 37.8 38.1 38.4 38.8 39.1 39.4 39.7 40.1 40.4
BACKG 44 44 43 44 44 44 45 44 44 44 44 44
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 6 1 8 3 0 0 4 4 0 0 0 0
RADIUS 40.7 41.0 41.4 41.7 42.0 42.4 42.7 43.0 43.3 43.7 44.0 44.3
BACKG 44 45 45 45 45 45 46 46 46 46 45 46
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 0 0 0 0 0 0 0 3 1 0 0 0
RADIUS 44.6 45.0 45.3 45.6 45.9 46.3 46.6 46.9 47.2 47.6 47.9 48.2
BACKG 46 47 46 46 47 47 47 48 48 49 47 48
SIGMA 6 6 6 6 6 6 6 6 6 7 6 6
NREJ 1 0 1 0 0 0 7 7 0 0 1 2
RADIUS 48.6 48.9 49.2 49.5 49.9 50.2 50.5 50.8 51.2 51.5 51.8 52.1
BACKG 50 50 50 49 49 50 51 50 51 51 51 51
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 4 3 0 0 0 3 0 0 1 0 0
RADIUS 52.5 52.8 53.1 53.4 53.8 54.1 54.4 54.8 55.1 55.4 55.7 56.1
BACKG 52 53 52 54 56 55 56 57 55 57 56 56
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 1 4 0 0 2 8 1 3 7 0 0 3
RADIUS 56.4 56.7 57.0 57.4 57.7 58.0 58.3 58.7 59.0 59.3 59.6 60.0
BACKG 58 58 58 58 59 60 60 62 61 62 65 64
SIGMA 7 7 7 7 7 7 7 7 7 7 8 8
NREJ 7 2 0 0 0 6 18 22 21 13 0 3
RADIUS 60.3 60.6 61.0 61.3 61.6 61.9 62.3 62.6 62.9 63.2 63.6 63.9
BACKG 64 63 64 64 65 66 67 68 68 68 69 71
SIGMA 8 7 8 8 8 8 8 8 8 8 8 8
NREJ 3 0 0 0 0 0 6 6 0 0 1 4
RADIUS 64.2 64.5 64.9 65.2 65.5 65.9 66.2 66.5 66.8 67.2 67.5 67.8
BACKG 73 73 71 71 72 73 72 73 73 72 72 72
SIGMA 8 8 8 8 8 8 8 8 8 8 8 8
NREJ 1 8 11 3 0 6 13 9 0 0 0 0
RADIUS 68.1 68.5 68.8 69.1 69.4 69.8 70.1 70.4 70.7 71.1 71.4 71.7
BACKG 73 73 73 74 74 72 71 72 70 69 69 69
SIGMA 8 8 8 8 8 8 8 8 8 8 8 8
NREJ 12 18 17 10 0 3 7 1 1 1 0 0
RADIUS 72.1 72.4 72.7 73.0 73.4 73.7 74.0 74.3 74.7 75.0 75.3 75.6
BACKG 70 68 68 66 67 66 67 68 66 66 66 66
SIGMA 8 8 8 8 8 8 8 8 8 8 8 8
NREJ 2 9 3 0 0 2 3 4 12 12 2 0
RADIUS 76.0 76.3 76.6 76.9 77.3 77.6 77.9 78.3 78.6 78.9 79.2 79.6
BACKG 66 65 64 63 62 61 62 64 63 62 61 60
SIGMA 8 8 7 7 7 7 7 8 7 7 7 7
NREJ 2 8 3 0 0 0 0 0 5 5 0 0
RADIUS 79.9 80.2 80.5 80.9 81.2 81.5 81.8 82.2 82.5 82.8 83.2 83.5
BACKG 61 60 60 58 59 59 60 59 60 59 59 59
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 1 6 1 0 1 0 0 0 3 5 0 0
RADIUS 83.8 84.1 84.5
BACKG 58 59 29
SIGMA 7 7 3
NREJ 0 0 0
Starting spot search...
sorting 1579 spots
Median spot size is 6 x 6 pixels
Total number of spots found:1579
Number rejected as too small on X: 29
Number rejected as too small on Y: 31
Number rejected as too big on X: 15
Number rejected as too big on Y: 8
Number too close (SEPARATION keyword): 0
Number stored as OK:1464
Number of spots found in each bin
36 26 26 37 32 17 22 35
44 27 32 51 56 28 34 51
49 29 41 68 56 28 45 48
49 30 39 49 45 26 33 46
44 26 36 41 31 26 22 35
Determining average spot size for spots in centre of image.
==========================================================
Finding spot size around direct beam position
Default parameters may be reset with SPOTS keyword.
Minimum radius 9.4mm, maximum radius 37.60mm, minimum number of spots 10
sorting 233 spots
Based on a median spot size of 6 by 6 pixels in X and Y, the measurement box
parameters have been set to 19 19 11 6 6
The overall size of the box has been fixed.
To prevent this use keywords PROFILE NOFIXBOX.
***** WARNING ***** Lattice type not specified, so assumed primitive
Based on a median spot size of 6 by 6 pixels in X and Y, the spot separation
parameters (in X and Y) have been set to 0.65 0.65mm.
Closest possible spot separation is 0.00mm.
Because the minimum possible spot separation is less than the estimated spot
size plus a safety margin of 2 pixels (set by keywords SPOTS SAFE) the
"CLOSE" option for integration has been set.
****************************************************
****************************************************
It is advisable to ensure that all images for this dataset are also
processed using the "CLOSE" option by explicitly including keywords:
SEPARATION CLOSE
****************************************************
****************************************************
FORMATTED UNKNOWN file opened on unit 10
Logical name: ref-ftest_1.spt, Filename: ref-ftest_1.spt
1464 spots written for image 1
A total of 1464 spots were written to file
FORMATTED OLD file opened on unit 10
Logical name: ref-ftest_1.spt, Filename: ref-ftest_1.spt
DPS Indexing at Two-theta = 0.00 with 1212 reflections (minimum spot separation = 0.49mm. Maximum expected cell edge 267.90, Beam position is 93.58 92.24
Generating direct lattice vectors (This may take some time):
|-----------------|
..................
Refining 30 direct space vectors:
|----------------------------|
..............................
selected 12
List of possible Laue groups, sorted on penalty index.
The lower the PENALTY, the better
No PENALTY LATT a b c alpha beta gamma Possible spacegroups
44 999 cI 128.42 128.95 181.23 89.7 89.6 89.8 I23,I213,I432,I4132
43 505 cP 128.03 128.16 128.41 90.1 119.9 119.6 P23,P213,P432,P4232,P4332,P4132
42 504 tP 128.16 128.41 128.03 119.9 119.6 90.1 P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
41 503 tI 128.95 181.23 128.42 89.6 90.2 90.3 I4,I41,I422,I4122
40 503 tP 128.03 128.16 128.41 90.1 119.9 119.6 P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
39 502 hR 222.88 181.61 128.03 90.2 106.3 114.0 H3,H32 (hexagonal settings of R3 and R32)
38 502 oF 128.42 221.96 222.88 70.9 90.5 90.2 F222
37 502 oP 128.03 128.16 128.41 90.1 119.9 119.6 P222,P2221,P21212,P212121
36 257 hR 181.61 221.96 129.07 73.5 89.9 114.4 H3,H32 (hexagonal settings of R3 and R32)
35 255 hP 128.03 128.41 128.16 90.1 119.6 119.9 P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
34 254 hP 128.03 128.41 128.16 90.1 119.6 119.9 P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
33 254 oC 128.42 221.96 128.16 73.5 119.6 89.8 C222,C2221
32 254 mC 128.03 222.64 128.16 73.4 119.6 90.0 C2
31 254 oC 128.95 221.36 128.41 73.3 119.8 89.9 C222,C2221
30 252 mP 128.03 128.16 128.41 90.1 119.9 119.6 P2,P21
29 252 oC 128.03 222.64 128.16 73.4 119.6 90.0 C222,C2221
28 252 mC 128.03 222.64 128.16 73.4 119.6 90.0 C2
27 251 oC 128.03 222.64 128.16 73.4 119.6 90.0 C222,C2221
26 251 mC 128.03 222.64 128.16 73.4 119.6 90.0 C2
25 251 mP 128.03 128.16 128.41 90.1 119.9 119.6 P2,P21
24 250 mP 128.03 128.16 128.41 90.1 119.9 119.6 P2,P21
23 250 oC 128.03 222.64 128.16 73.4 119.6 90.0 C222,C2221
22 16 tI 128.03 129.07 181.61 89.9 89.8 89.6 I4,I41,I422,I4122
21 15 oF 181.61 181.23 182.37 89.5 90.2 89.9 F222
20 14 tI 128.16 128.41 182.37 89.8 89.5 90.1 I4,I41,I422,I4122
19 14 oI 128.16 128.41 182.37 89.8 90.5 89.9 I222,I212121
18 14 cF 182.37 181.23 181.61 90.1 90.2 90.5 F23,F432,F4132
17 12 hR 128.03 128.95 315.40 90.3 89.8 120.2 H3,H32 (hexagonal settings of R3 and R32)
16 11 tI 128.42 128.95 181.23 89.7 89.6 89.8 I4,I41,I422,I4122
15 10 mI 128.16 182.37 128.41 90.2 89.9 89.5 C2
14 9 oI 128.03 129.07 181.61 90.1 89.8 90.4 I222,I212121
13 8 mC 181.23 181.61 128.03 90.2 134.6 89.9 C2
12 8 oI 128.95 128.42 181.23 89.6 89.7 89.8 I222,I212121
11 7 mC 222.96 128.03 129.07 90.4 125.5 89.6 C2
10 7 mC 221.99 128.41 128.16 90.1 124.8 89.8 C2
9 7 mC 221.99 128.41 128.16 90.1 124.8 89.8 C2
8 7 mC 221.99 128.41 128.16 90.1 124.8 89.8 C2
7 6 hR 128.95 128.41 313.28 90.2 90.1 119.8 H3,H32 (hexagonal settings of R3 and R32)
6 6 mC 221.36 128.95 128.42 89.8 125.0 89.9 C2
5 5 mC 181.23 181.61 128.03 90.2 134.6 89.9 C2
4 5 mC 221.99 128.41 128.16 89.9 124.8 90.2 C2
3 3 mC 221.36 128.95 128.42 90.2 125.0 90.1 C2
2 0 aP 128.03 128.16 128.42 60.4 60.1 60.4 P1
1 0 aP 128.03 128.16 128.41 90.1 119.9 119.6 P1
No PENALTY SDCELL FRACN LATT a b c alpha beta gamma Possible spacegroups
The solution and direct beam position will now be refined; reflections which deviate by more
than the sigma cutoff from their calculated position will be excluded from the refinement.
Refining solution #18 with F23 (number 196) symmetry imposed
Initial cell (before refinement) is 181.7338 181.7338 181.7338 90.000 90.000 90.000
Using 1154 indexed reflections (out of 1212 spots found, {delta(XY) <= 2.5 sigma}),
final sd in spot positions is 0.08mm and in phi 0.27 degrees
Refined cell parameters 181.69 181.69 181.69 90.00 90.00 90.00
Beam coordinates of 93.58 92.24 have been refined to 93.61 91.99
This is a shift of 0.25mm or 0.196 times the minimum spot separation of ca 1.28mm.
Final cell (after refinement) is 181.6902 181.6901 181.6902 90.000 90.000 90.000
FORMATTED UNKNOWN file opened on unit 12
Logical name: autoindex.mat, Filename: autoindex.mat
Updating the stored central beam position from 9358.500 9224.500 to 9440.142 9199.460
****** INFORMATION *****
****** INFORMATION *****
****** INFORMATION *****
The cell derived from autoindexing will override that given on the CELL keyword.
To force the program to use the input cell, add the keyword KEEP. eg:
CELL KEEP 74.2 74.2 35.1 90 90 90
**** WARNING ****
Because input wavelength ( 0.9330) is not CuKa (1.5418) or Mo (0.7107),
source is assumed to be a synchrotron and synchrotron defaults for polarisation and beam divergence
will be used if these have not been defined explicitly (SYNCH POLAR and DIVH/DIVV keywords.
(Q)QOPEN: file opened on unit 1 Status: UNKNOWN
Logical Name: ref-ftest_1.gen Filename: ref-ftest_1.gen
Title for MTZ and GENERATE Files (TITLE):
.
Crystal identifier (IDENT): ref-ftest_1
********************************************************************************
Warning!! No PROTEIN NAME GIVEN by KeyWord PNAME
It has been set to be "Unspecified"
********************************************************************************
********************************************************************************
Warning!! No DATA SET NAME GIVEN by KeyWord DNAME
It has been set to be "Unspecified"
********************************************************************************
PSIX changed by 0.00 Degrees and CCOMEGA set to 0.000
MAX. No. of Active Reflections= 51
Beam divergence refinement
Beam divergence refinement
Refining DIV with stepsize 0.01 Degrees
Divergence 0.000 0.100 0.200 0.300 0.400 0.500 0.600 0.700 0.800 0.900 1.000 1.100 1.200 1.300 1.400 1.500 1.600 1.700 1.800
Divergence 1.900 2.000
No gained 153 421 393 351 388 358 336 343 353 347 324 78 94 99 107 121 113 128 124
No gained 135 114
Total intensity 83518 89923 94167 96080 97472 98336 98966 99364 99633 99825 99998 99930 99856 99745 99583 98957 98617 98225 97749
Total intensity 97171 96424
SD of intensity 111 115 117 118 119 121 121 122 123 123 124 124 124 124 123 123 122 122 122
SD of intensity 122 121
The mosaicity has been estimated as ---> 0.45 <--- for this image only;
This value can be used cautiously as an initial estimate.
Storing space group from DPS autoindexing: F23 number 196
*********** END OF PROCESSING *****************
************ Version 6.2.3 (beta test 1.6) for Image plate and CCD data 4th November 2002 ***********
A.G.W. Leslie, MRC Laboratory Of Molecular Biology, HILLS ROAD, CAMBRIDGE CB2 2QH, UK
E-mail andrew@mrc-lmb.cam.ac.uk
New auto-indexing using DPS due to Ingo Steller Robert Bolotovsky and Michael Rossmann
(1998) J. Appl. Cryst. 30, 1036-1040
Original auto-indexing using REFIX due to Wolfgang Kabsch (Kabsch,W. (1993),
J.Appl.Cryst. 24,795-800.)
X-windows interface using xdl_view due to John Campbell (Daresbury Laboratory, UK.)
(Campbell,J.W. (1995) J. Appl. Cryst. 28, 236-242.
===> newmat autoindex.mat
===> template ref-ftest_1_###.img
===> directory /scisoft/pxsoft/data/dna_040402
===> detector adsc
===> beam 93.585000 92.245000
===> autoindex threshold 10 dps image 2
Using DPS code for background indexing
===> mosaic estimate
===> go
(Q)QOPEN: file opened on unit 1 Status: READONLY
Logical Name: /scisoft/pxsoft/data/dna_040402/ref-ftest_1_002.img Filename: /scisoft/pxsoft/data/dna_040402/ref-ftest_1_002.img
Crystal to detector distance of 249.95mm taken from image header
Wavelength of 0.93300A taken from image header
Pixel size of 0.0816mm taken from image header.
IBEAM = 2 it should be 2
Input beam coordinates 93.58mm 92.24mm will be used
Autoindexing image 2
=======================
image FILENAME: /scisoft/pxsoft/data/dna_040402/ref-ftest_1_002.img
(Q)QOPEN: file opened on unit 1 Status: READONLY
Logical Name: /scisoft/pxsoft/data/dna_040402/ref-ftest_1_002.img Filename: /scisoft/pxsoft/data/dna_040402/ref-ftest_1_002.img
Determining best threshold for spot finding.
Default parameters may be reset with SPOTS keyword.
Minimum radius 9.4mm, maximum radius 37.60mm, minimum number of spots 10
Background strip overlaps gap between detector tiles, so YOFFSET changed to 4.2mm
sorting 184 spots
Threshold set to 4.2
sorting 194 spots
Threshold set to 4.2
Finding spots on image 2 (Midpoint of phi 90.500 degrees)
Calculating radial background.....
The background is radial along the X (slow) direction
The average of 51 pixels, excluding outliers, is used
The scan is offset by 4.7mm from the image centre in Y to avoid any
backstop shadow
Radial Background calculation complete
RADIUS 9.4 9.7 10.0 10.4 10.7 11.0 11.3 11.7 12.0 12.3 12.6 13.0
BACKG 70 68 66 63 61 58 57 57 55 54 52 51
SIGMA 8 8 8 7 7 7 7 7 7 7 7 7
NREJ 10 6 1 1 0 1 0 0 0 0 0 0
RADIUS 13.3 13.6 14.0 14.3 14.6 14.9 15.3 15.6 15.9 16.2 16.6 16.9
BACKG 50 50 49 49 48 48 48 46 46 45 45 44
SIGMA 7 7 7 7 6 6 6 6 6 6 6 6
NREJ 0 0 7 8 4 0 0 0 0 0 0 0
RADIUS 17.2 17.5 17.9 18.2 18.5 18.8 19.2 19.5 19.8 20.2 20.5 20.8
BACKG 43 45 44 44 43 44 43 43 43 43 42 42
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 0 0 3 1 0 1 1 0 0 1 4 4
RADIUS 21.1 21.5 21.8 22.1 22.4 22.8 23.1 23.4 23.7 24.1 24.4 24.7
BACKG 42 42 43 41 41 41 42 41 41 41 40 40
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 0 0 6 8 0 0 3 7 1 0 0 0
RADIUS 25.1 25.4 25.7 26.0 26.4 26.7 27.0 27.3 27.7 28.0 28.3 28.6
BACKG 41 41 40 41 41 40 40 40 40 40 40 40
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 0 0 8 7 1 0 0 0 0 0 0 0
RADIUS 29.0 29.3 29.6 29.9 30.3 30.6 30.9 31.3 31.6 31.9 32.2 32.6
BACKG 39 39 39 39 40 39 40 39 39 39 39 40
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 0 0 0 0 0 0 0 0 0 0 0 0
RADIUS 32.9 33.2 33.5 33.9 34.2 34.5 34.8 35.2 35.5 35.8 36.1 36.5
BACKG 38 39 39 39 39 39 38 39 39 39 39 39
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 1 0 0 4 1 0 0 0 0 0 1 4
RADIUS 36.8 37.1 37.5 37.8 38.1 38.4 38.8 39.1 39.4 39.7 40.1 40.4
BACKG 39 39 40 39 40 40 40 40 39 39 39 40
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 0 0 1 8 5 0 0 0 0 0 0 2
RADIUS 40.7 41.0 41.4 41.7 42.0 42.4 42.7 43.0 43.3 43.7 44.0 44.3
BACKG 40 39 40 40 40 40 40 40 40 40 40 41
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 1 0 1 6 5 0 0 2 0 0 0 0
RADIUS 44.6 45.0 45.3 45.6 45.9 46.3 46.6 46.9 47.2 47.6 47.9 48.2
BACKG 41 40 40 41 41 41 41 41 41 42 41 42
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 1 0 0 5 2 0 0 0 0 0 0 0
RADIUS 48.6 48.9 49.2 49.5 49.9 50.2 50.5 50.8 51.2 51.5 51.8 52.1
BACKG 42 42 43 43 44 44 45 45 46 44 44 45
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 0 0 0 5 8 2 0 1 1 0 0 0
RADIUS 52.5 52.8 53.1 53.4 53.8 54.1 54.4 54.8 55.1 55.4 55.7 56.1
BACKG 45 44 45 45 45 45 46 47 49 48 48 47
SIGMA 6 6 6 6 6 6 6 6 7 6 6 6
NREJ 0 0 0 0 0 0 0 0 1 1 0 0
RADIUS 56.4 56.7 57.0 57.4 57.7 58.0 58.3 58.7 59.0 59.3 59.6 60.0
BACKG 48 47 48 50 51 51 51 52 51 51 50 50
SIGMA 6 6 6 7 7 7 7 7 7 7 7 7
NREJ 0 0 0 0 6 10 5 0 1 0 0 0
RADIUS 60.3 60.6 61.0 61.3 61.6 61.9 62.3 62.6 62.9 63.2 63.6 63.9
BACKG 52 53 53 52 54 55 56 54 54 57 58 57
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 0 0 0 0 0 0 0 0 2 0 0
RADIUS 64.2 64.5 64.9 65.2 65.5 65.9 66.2 66.5 66.8 67.2 67.5 67.8
BACKG 57 56 57 56 56 56 58 58 57 57 56 56
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 0 0 0 0 0 1 0 0 0 0 0
RADIUS 68.1 68.5 68.8 69.1 69.4 69.8 70.1 70.4 70.7 71.1 71.4 71.7
BACKG 55 56 54 55 55 54 54 55 54 53 54 54
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 0 1 1 0 0 0 0 0 0 1 4
RADIUS 72.1 72.4 72.7 73.0 73.4 73.7 74.0 74.3 74.7 75.0 75.3 75.6
BACKG 53 53 53 53 52 52 52 52 51 52 52 52
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 0 0 0 0 0 0 2 3 0 0 1
RADIUS 76.0 76.3 76.6 76.9 77.3 77.6 77.9 78.3 78.6 78.9 79.2 79.6
BACKG 54 52 52 51 53 51 51 51 51 50 49 48
SIGMA 7 7 7 7 7 7 7 7 7 7 7 6
NREJ 2 0 0 0 3 1 0 0 6 3 0 0
RADIUS 79.9 80.2 80.5 80.9 81.2 81.5 81.8 82.2 82.5 82.8 83.2 83.5
BACKG 48 48 48 47 49 48 48 47 47 47 46 46
SIGMA 6 6 6 6 7 6 6 6 6 6 6 6
NREJ 0 0 0 0 1 7 2 1 0 1 3 0
RADIUS 83.8 84.1 84.5
BACKG 46 46 23
SIGMA 6 6 3
NREJ 0 0 1
Starting spot search...
sorting 1439 spots
Median spot size is 6 x 6 pixels
Total number of spots found:1439
Number rejected as too small on X: 24
Number rejected as too small on Y: 24
Number rejected as too big on X: 14
Number rejected as too big on Y: 1
Number too close (SEPARATION keyword): 0
Number stored as OK:1366
Number of spots found in each bin
34 22 16 29 26 18 16 30
39 34 27 39 46 27 33 43
52 32 33 48 53 37 29 53
51 33 26 48 50 32 31 51
45 24 27 28 30 20 25 39
Determining average spot size for spots in centre of image.
==========================================================
Finding spot size around direct beam position
Default parameters may be reset with SPOTS keyword.
Minimum radius 9.4mm, maximum radius 37.60mm, minimum number of spots 10
sorting 194 spots
Based on a median spot size of 7 by 6 pixels in X and Y, the measurement box
parameters have been set to 21 19 11 6 6
The overall size of the box has been fixed.
To prevent this use keywords PROFILE NOFIXBOX.
***** WARNING ***** Lattice type not specified, so assumed primitive
Based on a median spot size of 7 by 6 pixels in X and Y, the spot separation
parameters (in X and Y) have been set to 0.73 0.65mm.
Closest possible spot separation is 0.00mm.
Because the minimum possible spot separation is less than the estimated spot
size plus a safety margin of 2 pixels (set by keywords SPOTS SAFE) the
"CLOSE" option for integration has been set.
****************************************************
****************************************************
It is advisable to ensure that all images for this dataset are also
processed using the "CLOSE" option by explicitly including keywords:
SEPARATION CLOSE
****************************************************
****************************************************
FORMATTED UNKNOWN file opened on unit 10
Logical name: ref-ftest_1.spt, Filename: ref-ftest_1.spt
1366 spots written for image 2
A total of 1366 spots were written to file
FORMATTED OLD file opened on unit 10
Logical name: ref-ftest_1.spt, Filename: ref-ftest_1.spt
DPS Indexing at Two-theta = 0.00 with 1108 reflections (minimum spot separation = 0.49mm. Maximum expected cell edge 267.90, Beam position is 93.58 92.24
Generating direct lattice vectors (This may take some time):
|-----------------|
..................
Refining 30 direct space vectors:
|----------------------------|
..............................
selected 2
List of possible Laue groups, sorted on penalty index.
The lower the PENALTY, the better
No PENALTY LATT a b c alpha beta gamma Possible spacegroups
44 999 cI 130.05 181.20 128.25 89.9 89.9 89.8 I23,I213,I432,I4132
43 513 cP 128.46 128.57 128.60 90.4 119.2 120.1 P23,P213,P432,P4232,P4332,P4132
42 512 tP 128.57 128.60 128.46 119.2 120.1 90.4 P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
41 512 tP 128.57 128.60 128.46 119.2 120.1 90.4 P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
40 512 oP 128.57 128.46 128.60 119.2 90.4 120.1 P222,P2221,P21212,P212121
39 502 hR 222.25 182.50 128.46 89.4 106.6 113.9 H3,H32 (hexagonal settings of R3 and R32)
38 493 tI 130.05 181.20 128.25 89.9 90.1 90.2 I4,I41,I422,I4122
37 492 oF 128.25 222.76 223.32 71.3 90.2 90.1 F222
36 258 hP 128.57 128.46 128.60 119.2 90.4 120.1 P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
35 258 oC 128.57 222.19 128.60 55.4 90.4 89.9 C222,C2221
34 258 hP 128.57 128.46 128.60 119.2 90.4 120.1 P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
33 258 oC 128.57 222.19 128.60 55.4 90.4 89.9 C222,C2221
32 257 oC 128.25 222.76 128.60 106.1 119.7 90.1 C222,C2221
31 257 hR 182.50 222.76 128.93 73.9 89.4 114.5 H3,H32 (hexagonal settings of R3 and R32)
30 257 oC 128.57 222.19 128.60 55.4 90.4 89.9 C222,C2221
29 256 mP 128.57 128.60 128.46 119.2 120.1 90.4 P2,P21
28 256 mP 128.57 128.60 128.46 119.2 120.1 90.4 P2,P21
27 256 oC 128.25 222.76 128.60 106.1 119.7 90.1 C222,C2221
26 256 mP 128.57 128.60 128.46 119.2 120.1 90.4 P2,P21
25 249 mC 128.25 223.32 128.46 74.0 119.9 89.8 C2
24 247 mC 128.25 222.76 128.60 73.9 119.7 89.9 C2
23 247 mC 128.25 223.32 128.46 74.0 119.9 89.8 C2
22 17 tI 128.57 128.60 182.81 89.3 89.6 89.6 I4,I41,I422,I4122
21 16 cF 182.50 182.81 181.20 90.2 90.0 90.8 F23,F432,F4132
20 16 oI 128.25 130.05 181.20 90.2 90.1 89.9 I222,I212121
19 15 tI 128.25 130.05 181.20 89.8 89.9 89.9 I4,I41,I422,I4122
18 15 hR 128.25 128.57 317.40 90.6 90.2 120.0 H3,H32 (hexagonal settings of R3 and R32)
17 14 oF 181.20 182.50 182.81 90.8 90.2 90.0 F222
16 13 tI 130.05 128.25 181.20 89.9 89.8 89.9 I4,I41,I422,I4122
15 12 mI 128.60 182.81 128.57 90.4 90.4 89.3 C2
14 11 hR 128.57 130.05 313.68 90.0 89.9 120.2 H3,H32 (hexagonal settings of R3 and R32)
13 9 mC 182.50 181.20 128.25 90.1 134.6 90.0 C2
12 9 mC 182.50 181.20 128.25 89.9 134.6 90.0 C2
11 8 mC 222.19 128.57 128.60 90.4 124.6 90.1 C2
10 8 mC 222.19 128.57 128.60 90.4 124.6 90.1 C2
9 8 mC 222.19 128.57 128.60 90.4 124.6 90.1 C2
8 6 oI 128.25 130.05 181.20 89.8 89.9 89.9 I222,I212121
7 6 mC 222.76 128.25 181.20 89.9 144.3 90.1 C2
6 5 mC 182.50 181.20 128.25 90.1 134.6 90.0 C2
5 5 oI 128.25 181.20 130.05 89.8 89.9 89.9 I222,I212121
4 4 mC 222.76 128.25 130.05 89.9 125.6 89.9 C2
3 3 aP 128.57 128.46 128.60 119.2 90.4 120.1 P1
2 2 mC 221.74 130.05 128.25 90.1 125.2 90.1 C2
1 0 aP 128.25 128.46 128.60 60.8 60.3 60.1 P1
No PENALTY SDCELL FRACN LATT a b c alpha beta gamma Possible spacegroups
The solution and direct beam position will now be refined; reflections which deviate by more
than the sigma cutoff from their calculated position will be excluded from the refinement.
Refining solution #21 with F23 (number 196) symmetry imposed
Initial cell (before refinement) is 182.1671 182.1671 182.1671 90.000 90.000 90.000
Using 1051 indexed reflections (out of 1108 spots found, {delta(XY) <= 2.5 sigma}),
final sd in spot positions is 0.08mm and in phi 0.24 degrees
Refined cell parameters 181.59 181.59 181.59 90.00 90.00 90.00
Beam coordinates of 93.58 92.24 have been refined to 93.61 92.00
This is a shift of 0.25mm or 0.193 times the minimum spot separation of ca 1.28mm.
Final cell (after refinement) is 181.5874 181.5874 181.5874 90.000 90.000 90.000
FORMATTED UNKNOWN file opened on unit 12
Logical name: autoindex.mat, Filename: autoindex.mat
Updating the stored central beam position from 9358.500 9224.500 to 9440.112 9199.854
****** INFORMATION *****
****** INFORMATION *****
****** INFORMATION *****
The cell derived from autoindexing will override that given on the CELL keyword.
To force the program to use the input cell, add the keyword KEEP. eg:
CELL KEEP 74.2 74.2 35.1 90 90 90
**** WARNING ****
Because input wavelength ( 0.9330) is not CuKa (1.5418) or Mo (0.7107),
source is assumed to be a synchrotron and synchrotron defaults for polarisation and beam divergence
will be used if these have not been defined explicitly (SYNCH POLAR and DIVH/DIVV keywords.
(Q)QOPEN: file opened on unit 1 Status: UNKNOWN
Logical Name: ref-ftest_1.gen Filename: ref-ftest_1.gen
Title for MTZ and GENERATE Files (TITLE):
.
Crystal identifier (IDENT): ref-ftest_1
********************************************************************************
Warning!! No PROTEIN NAME GIVEN by KeyWord PNAME
It has been set to be "Unspecified"
********************************************************************************
********************************************************************************
Warning!! No DATA SET NAME GIVEN by KeyWord DNAME
It has been set to be "Unspecified"
********************************************************************************
PSIX changed by 0.00 Degrees and CCOMEGA set to 0.000
MAX. No. of Active Reflections= 46
Beam divergence refinement
Refining DIV with stepsize 0.01 Degrees
Divergence 0.000 0.050 0.100 0.150 0.200 0.250 0.300 0.350 0.400 0.450 0.500 0.550 0.600 0.650 0.700 0.750 0.800 0.850 0.900
Divergence 0.950 1.000
No gained 0 160 191 161 173 168 184 178 188 184 169 161 154 172 155 144 176 149 139
No gained 146 159
Total intensity 81796 86595 91136 93370 94433 95218 97211 97717 98329 98644 98904 99132 99276 99433 99533 99593 99696 99765 99877
Total intensity 99936 99998
SD of intensity 93 96 98 99 101 101 106 107 108 108 109 109 109 110 110 112 112 112 113
SD of intensity 113 114
The mosaicity has been estimated as ---> 0.35 <--- for this image only;
This value can be used cautiously as an initial estimate.
Storing space group from DPS autoindexing: F23 number 196
*********** END OF PROCESSING *****************
************ Version 6.2.3 (beta test 1.6) for Image plate and CCD data 4th November 2002 ***********
A.G.W. Leslie, MRC Laboratory Of Molecular Biology, HILLS ROAD, CAMBRIDGE CB2 2QH, UK
E-mail andrew@mrc-lmb.cam.ac.uk
New auto-indexing using DPS due to Ingo Steller Robert Bolotovsky and Michael Rossmann
(1998) J. Appl. Cryst. 30, 1036-1040
Original auto-indexing using REFIX due to Wolfgang Kabsch (Kabsch,W. (1993),
J.Appl.Cryst. 24,795-800.)
X-windows interface using xdl_view due to John Campbell (Daresbury Laboratory, UK.)
(Campbell,J.W. (1995) J. Appl. Cryst. 28, 236-242.
===> newmat autoindex.mat
===> template ref-ftest_1_###.img
===> directory /scisoft/pxsoft/data/dna_040402
===> detector adsc
===> beam 93.585000 92.245000
===> autoindex threshold 10 dps image 1
Using DPS code for background indexing
===> autoindex threshold 10 dps image 2
Using DPS code for background indexing
===> mosaic estimate
===> go
(Q)QOPEN: file opened on unit 1 Status: READONLY
Logical Name: /scisoft/pxsoft/data/dna_040402/ref-ftest_1_001.img Filename: /scisoft/pxsoft/data/dna_040402/ref-ftest_1_001.img
Crystal to detector distance of 249.95mm taken from image header
Wavelength of 0.93300A taken from image header
Pixel size of 0.0816mm taken from image header.
IBEAM = 2 it should be 2
Input beam coordinates 93.58mm 92.24mm will be used
Autoindexing using 2 images
Image numbers: 1 2
image FILENAME: /scisoft/pxsoft/data/dna_040402/ref-ftest_1_001.img
(Q)QOPEN: file opened on unit 1 Status: READONLY
Logical Name: /scisoft/pxsoft/data/dna_040402/ref-ftest_1_001.img Filename: /scisoft/pxsoft/data/dna_040402/ref-ftest_1_001.img
Determining best threshold for spot finding.
Default parameters may be reset with SPOTS keyword.
Minimum radius 9.4mm, maximum radius 37.60mm, minimum number of spots 10
Background strip overlaps gap between detector tiles, so YOFFSET changed to 4.2mm
sorting 218 spots
Threshold set to 4.2
sorting 233 spots
Threshold set to 4.1
Finding spots on image 1 (Midpoint of phi 0.500 degrees)
Calculating radial background.....
The background is radial along the X (slow) direction
The average of 51 pixels, excluding outliers, is used
The scan is offset by 4.7mm from the image centre in Y to avoid any
backstop shadow
Radial Background calculation complete
RADIUS 9.4 9.7 10.0 10.4 10.7 11.0 11.3 11.7 12.0 12.3 12.6 13.0
BACKG 84 82 77 76 73 72 69 69 67 65 61 59
SIGMA 9 9 8 8 8 8 8 8 8 8 7 7
NREJ 18 11 8 0 3 5 0 0 1 4 1 0
RADIUS 13.3 13.6 14.0 14.3 14.6 14.9 15.3 15.6 15.9 16.2 16.6 16.9
BACKG 56 56 56 55 54 53 52 51 50 51 50 49
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 0 0 0 0 0 0 0 0 1 2 1
RADIUS 17.2 17.5 17.9 18.2 18.5 18.8 19.2 19.5 19.8 20.2 20.5 20.8
BACKG 50 51 50 50 49 48 47 46 46 46 46 46
SIGMA 7 7 7 7 7 6 6 6 6 6 6 6
NREJ 3 8 11 3 0 0 0 0 0 0 0 0
RADIUS 21.1 21.5 21.8 22.1 22.4 22.8 23.1 23.4 23.7 24.1 24.4 24.7
BACKG 45 46 46 45 45 44 44 45 45 45 45 44
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 0 0 0 0 0 0 0 0 2 8 1 0
RADIUS 25.1 25.4 25.7 26.0 26.4 26.7 27.0 27.3 27.7 28.0 28.3 28.6
BACKG 44 44 43 43 43 43 43 44 44 44 44 44
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 0 2 1 0 0 0 0 2 5 0 0 0
RADIUS 29.0 29.3 29.6 29.9 30.3 30.6 30.9 31.3 31.6 31.9 32.2 32.6
BACKG 43 44 43 43 43 44 43 43 44 44 44 44
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 3 0 1 0 0 0 0 0 0 0 0 0
RADIUS 32.9 33.2 33.5 33.9 34.2 34.5 34.8 35.2 35.5 35.8 36.1 36.5
BACKG 44 45 44 43 43 43 43 44 44 44 44 45
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 5 7 1 0 0 0 0 7 6 0 0 3
RADIUS 36.8 37.1 37.5 37.8 38.1 38.4 38.8 39.1 39.4 39.7 40.1 40.4
BACKG 44 44 43 44 44 44 45 44 44 44 44 44
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 6 1 8 3 0 0 4 4 0 0 0 0
RADIUS 40.7 41.0 41.4 41.7 42.0 42.4 42.7 43.0 43.3 43.7 44.0 44.3
BACKG 44 45 45 45 45 45 46 46 46 46 45 46
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 0 0 0 0 0 0 0 3 1 0 0 0
RADIUS 44.6 45.0 45.3 45.6 45.9 46.3 46.6 46.9 47.2 47.6 47.9 48.2
BACKG 46 47 46 46 47 47 47 48 48 49 47 48
SIGMA 6 6 6 6 6 6 6 6 6 7 6 6
NREJ 1 0 1 0 0 0 7 7 0 0 1 2
RADIUS 48.6 48.9 49.2 49.5 49.9 50.2 50.5 50.8 51.2 51.5 51.8 52.1
BACKG 50 50 50 49 49 50 51 50 51 51 51 51
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 4 3 0 0 0 3 0 0 1 0 0
RADIUS 52.5 52.8 53.1 53.4 53.8 54.1 54.4 54.8 55.1 55.4 55.7 56.1
BACKG 52 53 52 54 56 55 56 57 55 57 56 56
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 1 4 0 0 2 8 1 3 7 0 0 3
RADIUS 56.4 56.7 57.0 57.4 57.7 58.0 58.3 58.7 59.0 59.3 59.6 60.0
BACKG 58 58 58 58 59 60 60 62 61 62 65 64
SIGMA 7 7 7 7 7 7 7 7 7 7 8 8
NREJ 7 2 0 0 0 6 18 22 21 13 0 3
RADIUS 60.3 60.6 61.0 61.3 61.6 61.9 62.3 62.6 62.9 63.2 63.6 63.9
BACKG 64 63 64 64 65 66 67 68 68 68 69 71
SIGMA 8 7 8 8 8 8 8 8 8 8 8 8
NREJ 3 0 0 0 0 0 6 6 0 0 1 4
RADIUS 64.2 64.5 64.9 65.2 65.5 65.9 66.2 66.5 66.8 67.2 67.5 67.8
BACKG 73 73 71 71 72 73 72 73 73 72 72 72
SIGMA 8 8 8 8 8 8 8 8 8 8 8 8
NREJ 1 8 11 3 0 6 13 9 0 0 0 0
RADIUS 68.1 68.5 68.8 69.1 69.4 69.8 70.1 70.4 70.7 71.1 71.4 71.7
BACKG 73 73 73 74 74 72 71 72 70 69 69 69
SIGMA 8 8 8 8 8 8 8 8 8 8 8 8
NREJ 12 18 17 10 0 3 7 1 1 1 0 0
RADIUS 72.1 72.4 72.7 73.0 73.4 73.7 74.0 74.3 74.7 75.0 75.3 75.6
BACKG 70 68 68 66 67 66 67 68 66 66 66 66
SIGMA 8 8 8 8 8 8 8 8 8 8 8 8
NREJ 2 9 3 0 0 2 3 4 12 12 2 0
RADIUS 76.0 76.3 76.6 76.9 77.3 77.6 77.9 78.3 78.6 78.9 79.2 79.6
BACKG 66 65 64 63 62 61 62 64 63 62 61 60
SIGMA 8 8 7 7 7 7 7 8 7 7 7 7
NREJ 2 8 3 0 0 0 0 0 5 5 0 0
RADIUS 79.9 80.2 80.5 80.9 81.2 81.5 81.8 82.2 82.5 82.8 83.2 83.5
BACKG 61 60 60 58 59 59 60 59 60 59 59 59
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 1 6 1 0 1 0 0 0 3 5 0 0
RADIUS 83.8 84.1 84.5
BACKG 58 59 29
SIGMA 7 7 3
NREJ 0 0 0
Starting spot search...
sorting 1579 spots
Median spot size is 6 x 6 pixels
Total number of spots found:1579
Number rejected as too small on X: 29
Number rejected as too small on Y: 31
Number rejected as too big on X: 15
Number rejected as too big on Y: 8
Number too close (SEPARATION keyword): 0
Number stored as OK:1464
Number of spots found in each bin
36 26 26 37 32 17 22 35
44 27 32 51 56 28 34 51
49 29 41 68 56 28 45 48
49 30 39 49 45 26 33 46
44 26 36 41 31 26 22 35
Determining average spot size for spots in centre of image.
==========================================================
Finding spot size around direct beam position
Default parameters may be reset with SPOTS keyword.
Minimum radius 9.4mm, maximum radius 37.60mm, minimum number of spots 10
sorting 233 spots
Based on a median spot size of 6 by 6 pixels in X and Y, the measurement box
parameters have been set to 19 19 11 6 6
The overall size of the box has been fixed.
To prevent this use keywords PROFILE NOFIXBOX.
***** WARNING ***** Lattice type not specified, so assumed primitive
Based on a median spot size of 6 by 6 pixels in X and Y, the spot separation
parameters (in X and Y) have been set to 0.65 0.65mm.
Closest possible spot separation is 0.00mm.
Because the minimum possible spot separation is less than the estimated spot
size plus a safety margin of 2 pixels (set by keywords SPOTS SAFE) the
"CLOSE" option for integration has been set.
****************************************************
****************************************************
It is advisable to ensure that all images for this dataset are also
processed using the "CLOSE" option by explicitly including keywords:
SEPARATION CLOSE
****************************************************
****************************************************
image FILENAME: /scisoft/pxsoft/data/dna_040402/ref-ftest_1_002.img
(Q)QOPEN: file opened on unit 1 Status: READONLY
Logical Name: /scisoft/pxsoft/data/dna_040402/ref-ftest_1_002.img Filename: /scisoft/pxsoft/data/dna_040402/ref-ftest_1_002.img
Finding spots on image 2 (Midpoint of phi 90.500 degrees)
Calculating radial background.....
The background is radial along the X (slow) direction
The average of 51 pixels, excluding outliers, is used
The scan is offset by 4.7mm from the image centre in Y to avoid any
backstop shadow
Radial Background calculation complete
RADIUS 9.4 9.7 10.0 10.4 10.7 11.0 11.3 11.7 12.0 12.3 12.6 13.0
BACKG 70 68 66 63 61 58 57 57 55 54 52 51
SIGMA 8 8 8 7 7 7 7 7 7 7 7 7
NREJ 10 6 1 1 0 1 0 0 0 0 0 0
RADIUS 13.3 13.6 14.0 14.3 14.6 14.9 15.3 15.6 15.9 16.2 16.6 16.9
BACKG 50 50 49 49 48 48 48 46 46 45 45 44
SIGMA 7 7 7 7 6 6 6 6 6 6 6 6
NREJ 0 0 7 8 4 0 0 0 0 0 0 0
RADIUS 17.2 17.5 17.9 18.2 18.5 18.8 19.2 19.5 19.8 20.2 20.5 20.8
BACKG 43 45 44 44 43 44 43 43 43 43 42 42
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 0 0 3 1 0 1 1 0 0 1 4 4
RADIUS 21.1 21.5 21.8 22.1 22.4 22.8 23.1 23.4 23.7 24.1 24.4 24.7
BACKG 42 42 43 41 41 41 42 41 41 41 40 40
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 0 0 6 8 0 0 3 7 1 0 0 0
RADIUS 25.1 25.4 25.7 26.0 26.4 26.7 27.0 27.3 27.7 28.0 28.3 28.6
BACKG 41 41 40 41 41 40 40 40 40 40 40 40
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 0 0 8 7 1 0 0 0 0 0 0 0
RADIUS 29.0 29.3 29.6 29.9 30.3 30.6 30.9 31.3 31.6 31.9 32.2 32.6
BACKG 39 39 39 39 40 39 40 39 39 39 39 40
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 0 0 0 0 0 0 0 0 0 0 0 0
RADIUS 32.9 33.2 33.5 33.9 34.2 34.5 34.8 35.2 35.5 35.8 36.1 36.5
BACKG 38 39 39 39 39 39 38 39 39 39 39 39
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 1 0 0 4 1 0 0 0 0 0 1 4
RADIUS 36.8 37.1 37.5 37.8 38.1 38.4 38.8 39.1 39.4 39.7 40.1 40.4
BACKG 39 39 40 39 40 40 40 40 39 39 39 40
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 0 0 1 8 5 0 0 0 0 0 0 2
RADIUS 40.7 41.0 41.4 41.7 42.0 42.4 42.7 43.0 43.3 43.7 44.0 44.3
BACKG 40 39 40 40 40 40 40 40 40 40 40 41
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 1 0 1 6 5 0 0 2 0 0 0 0
RADIUS 44.6 45.0 45.3 45.6 45.9 46.3 46.6 46.9 47.2 47.6 47.9 48.2
BACKG 41 40 40 41 41 41 41 41 41 42 41 42
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 1 0 0 5 2 0 0 0 0 0 0 0
RADIUS 48.6 48.9 49.2 49.5 49.9 50.2 50.5 50.8 51.2 51.5 51.8 52.1
BACKG 42 42 43 43 44 44 45 45 46 44 44 45
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 0 0 0 5 8 2 0 1 1 0 0 0
RADIUS 52.5 52.8 53.1 53.4 53.8 54.1 54.4 54.8 55.1 55.4 55.7 56.1
BACKG 45 44 45 45 45 45 46 47 49 48 48 47
SIGMA 6 6 6 6 6 6 6 6 7 6 6 6
NREJ 0 0 0 0 0 0 0 0 1 1 0 0
RADIUS 56.4 56.7 57.0 57.4 57.7 58.0 58.3 58.7 59.0 59.3 59.6 60.0
BACKG 48 47 48 50 51 51 51 52 51 51 50 50
SIGMA 6 6 6 7 7 7 7 7 7 7 7 7
NREJ 0 0 0 0 6 10 5 0 1 0 0 0
RADIUS 60.3 60.6 61.0 61.3 61.6 61.9 62.3 62.6 62.9 63.2 63.6 63.9
BACKG 52 53 53 52 54 55 56 54 54 57 58 57
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 0 0 0 0 0 0 0 0 2 0 0
RADIUS 64.2 64.5 64.9 65.2 65.5 65.9 66.2 66.5 66.8 67.2 67.5 67.8
BACKG 57 56 57 56 56 56 58 58 57 57 56 56
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 0 0 0 0 0 1 0 0 0 0 0
RADIUS 68.1 68.5 68.8 69.1 69.4 69.8 70.1 70.4 70.7 71.1 71.4 71.7
BACKG 55 56 54 55 55 54 54 55 54 53 54 54
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 0 1 1 0 0 0 0 0 0 1 4
RADIUS 72.1 72.4 72.7 73.0 73.4 73.7 74.0 74.3 74.7 75.0 75.3 75.6
BACKG 53 53 53 53 52 52 52 52 51 52 52 52
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 0 0 0 0 0 0 2 3 0 0 1
RADIUS 76.0 76.3 76.6 76.9 77.3 77.6 77.9 78.3 78.6 78.9 79.2 79.6
BACKG 54 52 52 51 53 51 51 51 51 50 49 48
SIGMA 7 7 7 7 7 7 7 7 7 7 7 6
NREJ 2 0 0 0 3 1 0 0 6 3 0 0
RADIUS 79.9 80.2 80.5 80.9 81.2 81.5 81.8 82.2 82.5 82.8 83.2 83.5
BACKG 48 48 48 47 49 48 48 47 47 47 46 46
SIGMA 6 6 6 6 7 6 6 6 6 6 6 6
NREJ 0 0 0 0 1 7 2 1 0 1 3 0
RADIUS 83.8 84.1 84.5
BACKG 46 46 23
SIGMA 6 6 3
NREJ 0 0 1
Starting spot search...
sorting 1446 spots
Median spot size is 6 x 6 pixels
Total number of spots found:1446
Number rejected as too small on X: 25
Number rejected as too small on Y: 21
Number rejected as too big on X: 14
Number rejected as too big on Y: 1
Number too close (SEPARATION keyword): 1
Number stored as OK:1374
Number of spots found in each bin
34 22 16 30 27 18 16 30
39 34 27 39 47 28 33 43
53 33 33 48 53 37 29 53
51 33 26 48 50 32 31 51
45 24 28 29 30 20 25 40
FORMATTED UNKNOWN file opened on unit 10
Logical name: ref-ftest_1.spt, Filename: ref-ftest_1.spt
1464 spots written for image 1
1374 spots written for image 2
A total of 2838 spots were written to file
FORMATTED OLD file opened on unit 10
Logical name: ref-ftest_1.spt, Filename: ref-ftest_1.spt
DPS Indexing at Two-theta = 0.00 with 2321 reflections (minimum spot separation = 0.49mm. Maximum expected cell edge 267.90, Beam position is 93.58 92.24
Generating direct lattice vectors (This may take some time):
|-----------------|
..................
Refining 30 direct space vectors:
|----------------------------|
..............................
selected 0
List of possible Laue groups, sorted on penalty index.
The lower the PENALTY, the better
No PENALTY LATT a b c alpha beta gamma Possible spacegroups
44 999 cI 128.56 181.50 128.57 89.9 89.8 89.9 I23,I213,I432,I4132
43 503 tI 128.57 181.50 128.56 89.9 90.2 90.1 I4,I41,I422,I4122
42 502 oF 128.56 222.25 222.59 70.6 90.2 90.0 F222
41 501 cP 128.34 128.36 128.41 119.9 119.9 90.0 P23,P213,P432,P4232,P4332,P4132
40 500 hR 222.57 181.54 128.41 90.0 106.6 114.1 H3,H32 (hexagonal settings of R3 and R32)
39 500 tP 128.34 128.36 128.41 119.9 119.9 90.0 P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
38 500 oP 128.34 128.36 128.41 119.9 119.9 90.0 P222,P2221,P21212,P212121
37 500 tP 128.36 128.41 128.34 119.9 90.0 119.9 P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
36 252 hP 128.36 128.41 128.34 119.9 90.0 119.9 P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
35 252 mC 128.57 222.26 128.34 106.7 119.9 90.0 C2
34 252 mC 128.57 222.26 128.34 106.7 119.9 90.0 C2
33 252 mC 128.57 222.26 128.34 106.7 119.9 90.0 C2
32 252 hP 128.34 128.41 128.36 119.9 90.0 119.9 P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
31 252 oC 128.34 222.62 128.36 54.9 90.0 90.1 C222,C2221
30 251 oC 128.57 222.26 128.34 106.7 119.9 90.0 C222,C2221
29 251 oC 128.36 222.62 128.34 54.9 90.0 90.1 C222,C2221
28 251 oC 128.34 222.62 128.36 54.9 90.0 90.1 C222,C2221
27 250 mP 128.34 128.36 128.41 119.9 119.9 90.0 P2,P21
26 250 mP 128.34 128.36 128.41 119.9 119.9 90.0 P2,P21
25 250 mP 128.36 128.34 128.41 119.9 119.9 90.0 P2,P21
24 250 hR 181.54 222.25 128.69 73.3 90.0 114.1 H3,H32 (hexagonal settings of R3 and R32)
23 250 oC 128.57 222.26 128.34 106.7 119.9 90.0 C222,C2221
22 8 cF 181.54 181.50 182.09 90.1 90.0 90.0 F23,F432,F4132
21 6 hR 128.36 128.57 314.93 89.8 90.0 120.0 H3,H32 (hexagonal settings of R3 and R32)
20 5 hR 128.34 128.69 314.51 89.9 90.1 120.0 H3,H32 (hexagonal settings of R3 and R32)
19 4 oI 128.41 181.54 128.69 90.0 89.8 90.0 I222,I212121
18 4 mC 222.51 128.41 181.54 90.0 144.7 89.9 C2
17 4 tI 128.56 128.57 181.50 89.9 89.9 89.8 I4,I41,I422,I4122
16 3 mI 128.69 181.54 128.41 90.0 90.2 90.0 C2
15 3 tI 128.57 128.56 181.50 89.9 89.9 89.8 I4,I41,I422,I4122
14 3 oI 128.34 128.36 182.09 90.1 90.1 90.0 I222,I212121
13 3 oI 181.50 128.56 128.57 89.8 89.9 89.9 I222,I212121
12 3 tI 128.34 128.36 182.09 89.9 89.9 90.0 I4,I41,I422,I4122
11 2 oF 181.50 181.54 182.09 90.0 90.1 90.0 F222
10 2 mC 182.09 181.54 128.69 90.0 135.2 90.0 C2
9 2 mC 222.62 128.34 128.36 90.0 125.1 89.9 C2
8 1 mC 222.62 128.36 128.34 90.0 125.1 89.9 C2
7 1 mC 181.50 181.54 128.41 90.0 134.8 90.0 C2
6 1 mC 222.62 128.34 128.36 90.0 125.1 89.9 C2
5 1 mC 181.50 181.54 128.41 90.0 134.8 90.0 C2
4 0 mC 181.50 181.54 128.41 90.0 134.8 90.0 C2
3 0 mC 181.50 181.54 128.41 90.0 134.8 90.0 C2
2 0 aP 128.34 128.36 128.41 60.1 60.1 90.0 P1
1 0 aP 128.34 128.36 128.41 119.9 119.9 90.0 P1
No PENALTY SDCELL FRACN LATT a b c alpha beta gamma Possible spacegroups
The solution and direct beam position will now be refined; reflections which deviate by more
than the sigma cutoff from their calculated position will be excluded from the refinement.
Refining solution #22 with F23 (number 196) symmetry imposed
Initial cell (before refinement) is 181.7087 181.7087 181.7087 90.000 90.000 90.000
Using 2191 indexed reflections (out of 2321 spots found, {delta(XY) <= 2.5 sigma}),
final sd in spot positions is 0.11mm and in phi 0.30 degrees
Refined cell parameters 181.64 181.64 181.64 90.00 90.00 90.00
Beam coordinates of 93.58 92.24 have been refined to 93.60 91.97
This is a shift of 0.28mm or 0.215 times the minimum spot separation of ca 1.28mm.
Final cell (after refinement) is 181.6432 181.6432 181.6432 90.000 90.000 90.000
FORMATTED UNKNOWN file opened on unit 12
Logical name: autoindex.mat, Filename: autoindex.mat
Updating the stored central beam position from 9358.500 9224.500 to 9440.320 9196.946
****** INFORMATION *****
****** INFORMATION *****
****** INFORMATION *****
The cell derived from autoindexing will override that given on the CELL keyword.
To force the program to use the input cell, add the keyword KEEP. eg:
CELL KEEP 74.2 74.2 35.1 90 90 90
**** WARNING ****
Because input wavelength ( 0.9330) is not CuKa (1.5418) or Mo (0.7107),
source is assumed to be a synchrotron and synchrotron defaults for polarisation and beam divergence
will be used if these have not been defined explicitly (SYNCH POLAR and DIVH/DIVV keywords.
(Q)QOPEN: file opened on unit 1 Status: UNKNOWN
Logical Name: ref-ftest_1.gen Filename: ref-ftest_1.gen
Title for MTZ and GENERATE Files (TITLE):
.
Crystal identifier (IDENT): ref-ftest_1
********************************************************************************
Warning!! No PROTEIN NAME GIVEN by KeyWord PNAME
It has been set to be "Unspecified"
********************************************************************************
********************************************************************************
Warning!! No DATA SET NAME GIVEN by KeyWord DNAME
It has been set to be "Unspecified"
********************************************************************************
PSIX changed by 0.00 Degrees and CCOMEGA set to 0.000
MAX. No. of Active Reflections= 51
Beam divergence refinement
Beam divergence refinement
Refining DIV with stepsize 0.01 Degrees
Divergence 0.000 0.100 0.200 0.300 0.400 0.500 0.600 0.700 0.800 0.900 1.000 1.100 1.200 1.300 1.400 1.500 1.600 1.700 1.800
Divergence 1.900 2.000
No gained 148 398 331 382 354 324 317 294 322 329 307 116 111 113 107 119 127 96 91
No gained 86 87
Total intensity 65118 72576 78272 82694 86397 90074 93383 96338 97853 99814 99999 99704 99347 98876 98495 97920 97240 96691 96093
Total intensity 95473 94309
SD of intensity 117 123 137 140 143 145 147 151 152 161 161 161 161 161 159 159 159 159 158
SD of intensity 158 158
The mosaicity has been estimated as ---> 0.68 <--- for this image only;
This value can be used cautiously as an initial estimate.
Storing space group from DPS autoindexing: F23 number 196
Storing space group from DPS autoindexing: F23 number 196
*********** END OF PROCESSING *****************
/n