Index results for ntest2_1
Symmetry and refined cell parameters
Image |
Symmetry |
a |
b |
c |
alpha |
beta |
gamma |
1 |
F23 |
180.970 |
180.970 |
180.970 |
90.000 |
90.000 |
90.000 |
2 |
F23 |
180.931 |
180.931 |
180.931 |
90.000 |
90.000 |
90.000 |
1+2 |
F23 |
180.952 |
180.952 |
180.952 |
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 |
957 |
9 |
0.009 |
0.080 |
0.025 |
-0.235 |
2 |
1124 |
23 |
0.020 |
0.080 |
0.015 |
-0.245 |
1+2 |
2106 |
48 |
0.023 |
0.100 |
0.015 |
-0.275 |
Image 1: /scisoft/pxsoft/data/dna_040402/ref-ntest2_1_001.img
Image 2: /scisoft/pxsoft/data/dna_040402/ref-ntest2_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-ntest2_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-ntest2_1_001.img Filename: /scisoft/pxsoft/data/dna_040402/ref-ntest2_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-ntest2_1_001.img
(Q)QOPEN: file opened on unit 1 Status: READONLY
Logical Name: /scisoft/pxsoft/data/dna_040402/ref-ntest2_1_001.img Filename: /scisoft/pxsoft/data/dna_040402/ref-ntest2_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 116 spots
Threshold set to 4.5
sorting 118 spots
Threshold set to 4.5
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 357 349 345 338 331 322 317 310 303 295 290 284
SIGMA 18 18 18 18 18 17 17 17 17 17 17 16
NREJ 19 16 10 10 8 9 3 2 2 4 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 276 273 265 259 252 248 244 240 235 229 225 220
SIGMA 16 16 16 16 15 15 15 15 15 15 14 14
NREJ 1 0 1 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 217 214 209 206 202 198 194 191 189 186 182 180
SIGMA 14 14 14 14 14 14 13 13 13 13 13 13
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 177 176 173 169 167 165 165 162 157 156 152 151
SIGMA 13 13 13 13 12 12 12 12 12 12 12 12
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 149 146 142 141 141 140 136 134 133 132 130 127
SIGMA 12 12 11 11 11 11 11 11 11 11 11 11
NREJ 0 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 127 125 123 123 122 121 122 120 116 115 113 112
SIGMA 11 11 11 11 11 10 11 10 10 10 10 10
NREJ 0 0 0 0 0 1 6 4 4 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 110 109 108 107 106 104 104 101 100 99 97 98
SIGMA 10 10 10 10 10 10 10 10 10 9 9 9
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 98 96 95 95 93 92 93 92 90 88 88 87
SIGMA 9 9 9 9 9 9 9 9 9 9 9 9
NREJ 1 0 0 0 0 0 2 6 7 2 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 88 86 86 85 84 84 83 82 82 81 81 80
SIGMA 9 9 9 9 9 9 9 9 9 9 9 8
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 79 79 79 78 77 78 79 80 79 76 75 75
SIGMA 8 8 8 8 8 8 8 8 8 8 8 8
NREJ 1 0 0 0 0 0 5 8 8 5 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 75 74 75 75 74 74 73 72 73 72 72 71
SIGMA 8 8 8 8 8 8 8 8 8 8 8 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 72 71 70 69 68 69 69 70 69 68 67 67
SIGMA 8 8 8 8 8 8 8 8 8 8 8 8
NREJ 0 2 0 0 0 0 0 2 4 2 1 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 68 67 68 67 68 66 67 66 67 68 67 68
SIGMA 8 8 8 8 8 8 8 8 8 8 8 8
NREJ 0 0 4 2 2 0 0 0 0 0 7 7
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 67 68 66 66 66 65 66 65 66 65 67 66
SIGMA 8 8 8 8 8 8 8 8 8 8 8 8
NREJ 5 0 0 0 0 0 0 0 0 0 0 0
RADIUS 64.2 64.5 64.9 65.2 65.5 65.9 66.2 66.5 66.8 67.2 67.5 67.8
BACKG 66 65 65 66 66 66 66 65 64 65 65 65
SIGMA 8 8 8 8 8 8 8 8 8 8 8 8
NREJ 0 0 0 0 2 2 0 0 0 0 0 2
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 65 65 63 63 63 63 63 63 61 62 62 62
SIGMA 8 8 7 7 7 7 7 7 7 7 7 7
NREJ 0 1 0 0 1 0 3 0 0 0 0 2
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 61 61 60 59 59 58 58 59 60 58 57 57
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 4 4 2 0 0 0 0 2 1 3 0 0
RADIUS 76.0 76.3 76.6 76.9 77.3 77.6 77.9 78.3 78.6 78.9 79.2 79.6
BACKG 56 56 55 55 55 54 54 54 54 53 53 53
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 79.9 80.2 80.5 80.9 81.2 81.5 81.8 82.2 82.5 82.8 83.2 83.5
BACKG 53 52 51 50 50 49 50 50 50 50 49 49
SIGMA 7 7 7 7 7 7 7 7 7 7 7 6
NREJ 0 0 1 1 0 0 0 1 0 3 4 3
RADIUS 83.8 84.1 84.5
BACKG 49 48 24
SIGMA 7 6 3
NREJ 0 0 0
Starting spot search...
sorting 957 spots
Median spot size is 4 x 4 pixels
Total number of spots found: 957
Number rejected as too small on X: 0
Number rejected as too small on Y: 0
Number rejected as too big on X: 7
Number rejected as too big on Y: 2
Number too close (SEPARATION keyword): 0
Number stored as OK: 948
Number of spots found in each bin
21 14 7 22 24 8 9 17
36 19 13 29 34 17 19 33
38 27 21 39 42 19 20 37
35 20 20 31 38 16 20 36
21 21 14 35 21 20 14 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 118 spots
Based on a median spot size of 4 by 4 pixels in X and Y, the measurement box
parameters have been set to 15 15 9 5 5
The overall size of the box has been fixed.
To prevent this use keywords PROFILE NOFIXBOX.
***** WARNING ***** Lattice type not specified, so assumed primitive
Based on a median spot size of 4 by 4 pixels in X and Y, the spot separation
parameters (in X and Y) have been set to 0.48 0.48mm.
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-ntest2_1.spt, Filename: ref-ntest2_1.spt
948 spots written for image 1
A total of 948 spots were written to file
FORMATTED OLD file opened on unit 10
Logical name: ref-ntest2_1.spt, Filename: ref-ntest2_1.spt
DPS Indexing at Two-theta = 0.00 with 815 reflections (minimum spot separation = 0.33mm. Maximum expected cell edge 297.43, Beam position is 93.58 92.24
Generating direct lattice vectors (This may take some time):
|-----------------|
..................
Refining 30 direct space vectors:
|----------------------------|
..............................
selected 7
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 128.65 180.74 127.97 89.9 90.1 89.8 I23,I213,I432,I4132
43 509 cP 127.74 128.08 128.16 90.3 119.6 120.0 P23,P213,P432,P4232,P4332,P4132
42 508 tP 127.74 128.08 128.16 90.3 119.6 120.0 P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
41 506 oP 127.74 128.08 128.16 90.3 119.6 120.0 P222,P2221,P21212,P212121
40 506 tP 128.08 128.16 127.74 119.6 120.0 90.3 P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
39 502 hR 221.71 181.64 127.74 89.8 106.7 114.0 H3,H32 (hexagonal settings of R3 and R32)
38 502 tI 180.74 128.65 127.97 90.1 90.1 90.2 I4,I41,I422,I4122
37 499 oF 127.97 221.52 222.19 70.9 90.0 90.2 F222
36 257 hP 128.25 128.16 127.74 119.6 90.2 120.1 P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
35 257 hR 221.52 181.28 128.16 90.4 106.4 114.1 H3,H32 (hexagonal settings of R3 and R32)
34 257 hP 127.74 128.08 128.16 90.3 119.6 120.0 P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
33 256 oC 128.25 221.70 127.74 55.0 90.2 89.9 C222,C2221
32 256 oC 127.97 221.52 128.16 73.6 119.9 89.8 C222,C2221
31 255 oC 127.74 221.91 128.16 73.1 119.6 89.9 C222,C2221
30 255 oC 127.97 222.19 127.74 106.5 119.9 90.0 C222,C2221
29 254 mP 127.74 128.16 128.08 90.3 120.0 119.6 P2,P21
28 254 mP 128.25 127.74 128.16 119.6 120.1 90.2 P2,P21
27 254 oC 127.74 221.91 128.16 73.1 119.6 89.9 C222,C2221
26 253 mP 127.74 128.16 128.08 90.3 120.0 119.6 P2,P21
25 252 mC 127.97 221.52 128.16 73.6 119.9 89.8 C2
24 251 mC 127.97 222.19 127.74 73.5 119.9 90.0 C2
23 249 mC 127.97 222.19 127.74 73.5 119.9 90.0 C2
22 9 tI 127.74 128.25 181.64 89.8 90.2 90.2 I4,I41,I422,I4122
21 9 tI 128.65 127.97 180.74 90.1 89.8 89.9 I4,I41,I422,I4122
20 9 cF 180.74 181.28 181.64 90.3 90.0 90.2 F23,F432,F4132
19 8 oI 127.74 128.25 181.64 90.2 90.2 89.8 I222,I212121
18 8 hR 127.74 128.08 314.92 89.7 90.2 120.0 H3,H32 (hexagonal settings of R3 and R32)
17 8 oF 180.74 181.28 181.64 90.3 90.0 89.8 F222
16 7 tI 128.65 127.97 180.74 89.9 89.8 90.1 I4,I41,I422,I4122
15 7 hR 128.08 128.65 312.97 90.2 89.8 120.1 H3,H32 (hexagonal settings of R3 and R32)
14 6 mC 180.74 181.64 127.74 89.8 134.8 90.0 C2
13 6 mI 127.74 181.64 128.25 89.8 90.2 90.2 C2
12 6 oI 127.74 128.25 181.64 89.8 89.8 89.8 I222,I212121
11 6 mC 221.70 128.25 127.74 90.2 125.0 90.1 C2
10 5 mC 221.91 127.74 128.25 89.8 125.1 89.9 C2
9 5 mC 221.91 127.74 128.25 90.2 125.1 90.1 C2
8 5 oI 127.97 128.65 180.74 89.8 89.9 90.1 I222,I212121
7 4 mC 180.74 181.64 127.74 89.8 134.8 90.0 C2
6 4 mC 221.52 127.97 128.65 90.1 125.3 89.8 C2
5 4 mC 221.91 127.74 128.25 90.2 125.1 90.1 C2
4 4 mC 221.31 128.08 128.16 89.7 125.0 90.1 C2
3 3 mC 221.70 128.25 127.74 90.2 125.0 90.1 C2
2 1 aP 127.74 128.08 128.16 90.3 119.6 120.0 P1
1 0 aP 127.74 127.97 128.16 60.1 60.4 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 #20 with F23 (number 196) symmetry imposed
Initial cell (before refinement) is 181.2189 181.2189 181.2189 90.000 90.000 90.000
Using 782 indexed reflections (out of 815 spots found, {delta(XY) <= 2.5 sigma}),
final sd in spot positions is 0.08mm and in phi 0.22 degrees
Refined cell parameters 180.97 180.97 180.97 90.00 90.00 90.00
Beam coordinates of 93.58 92.24 have been refined to 93.61 92.01
This is a shift of 0.24mm or 0.187 times the minimum spot separation of ca 1.29mm.
Final cell (after refinement) is 180.9697 180.9697 180.9697 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 9439.999 9200.513
****** 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-ntest2_1.gen Filename: ref-ntest2_1.gen
Title for MTZ and GENERATE Files (TITLE):
.
Crystal identifier (IDENT): ref-ntest2_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= 72
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 0 193 180 199 218 211 221 205 187 204 160 180 199 186 197 204 201 219 216
No gained 212 170
Total intensity 91745 96654 98252 98889 99116 99298 99397 99566 99524 99701 99751 99795 99838 99858 99895 99940 99945 99970 99987
Total intensity 99997 99997
SD of intensity 319 331 334 334 334 334 334 334 336 336 336 336 336 336 336 336 339 339 339
SD of intensity 339 339
The mosaicity has been estimated as ---> 0.17 <--- 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-ntest2_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-ntest2_1_002.img Filename: /scisoft/pxsoft/data/dna_040402/ref-ntest2_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-ntest2_1_002.img
(Q)QOPEN: file opened on unit 1 Status: READONLY
Logical Name: /scisoft/pxsoft/data/dna_040402/ref-ntest2_1_002.img Filename: /scisoft/pxsoft/data/dna_040402/ref-ntest2_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 130 spots
Threshold set to 4.7
sorting 130 spots
Threshold set to 4.7
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 354 349 342 339 329 321 314 306 301 290 286 281
SIGMA 18 18 18 18 18 17 17 17 17 17 16 16
NREJ 19 13 13 4 7 3 6 3 1 6 3 1
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 275 269 263 256 253 247 240 235 231 227 224 219
SIGMA 16 16 16 16 15 15 15 15 15 15 14 14
NREJ 0 0 0 2 0 0 1 0 0 0 1 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 213 208 206 203 202 198 194 189 188 184 181 178
SIGMA 14 14 14 14 14 14 13 13 13 13 13 13
NREJ 2 0 0 0 3 7 3 0 0 0 2 8
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 175 173 170 168 164 162 160 158 154 152 150 149
SIGMA 13 13 13 12 12 12 12 12 12 12 12 12
NREJ 10 4 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 146 145 143 141 140 136 134 133 130 130 128 127
SIGMA 12 12 11 11 11 11 11 11 11 11 11 11
NREJ 0 0 0 0 2 0 0 0 0 0 0 3
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 124 122 121 120 119 117 116 115 114 114 111 111
SIGMA 11 11 11 10 10 10 10 10 10 10 10 10
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 108 107 107 105 104 103 101 100 99 98 98 97
SIGMA 10 10 10 10 10 10 10 10 9 9 9 9
NREJ 0 0 0 2 2 0 0 0 0 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 95 94 95 91 91 91 91 89 88 86 87 87
SIGMA 9 9 9 9 9 9 9 9 9 9 9 9
NREJ 0 0 0 0 0 2 1 0 0 0 0 0
RADIUS 40.7 41.0 41.4 41.7 42.0 42.4 42.7 43.0 43.3 43.7 44.0 44.3
BACKG 85 84 83 83 83 82 81 80 80 80 80 80
SIGMA 9 9 9 9 9 9 9 8 8 8 8 8
NREJ 0 0 0 2 4 0 0 0 0 0 4 7
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 79 77 76 76 75 75 74 74 74 74 73 73
SIGMA 8 8 8 8 8 8 8 8 8 8 8 8
NREJ 1 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 72 72 73 73 74 72 71 70 70 70 70 69
SIGMA 8 8 8 8 8 8 8 8 8 8 8 8
NREJ 0 0 0 4 8 5 0 0 0 0 0 3
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 69 69 68 68 67 68 66 66 67 68 66 66
SIGMA 8 8 8 8 8 8 8 8 8 8 8 8
NREJ 2 0 0 0 0 0 0 0 0 1 5 2
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 66 66 66 65 66 67 66 66 65 64 65 65
SIGMA 8 8 8 8 8 8 8 8 8 8 8 8
NREJ 0 0 0 0 0 5 2 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 65 65 65 64 65 66 64 65 65 63 64 64
SIGMA 8 8 8 7 8 8 8 8 8 7 8 7
NREJ 0 0 0 0 0 1 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 63 63 63 62 62 62 61 62 62 61 63 63
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 4
RADIUS 68.1 68.5 68.8 69.1 69.4 69.8 70.1 70.4 70.7 71.1 71.4 71.7
BACKG 61 60 60 61 61 60 61 60 59 58 58 59
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 2 0 0 0 0 3 6 2 0 0 2 2
RADIUS 72.1 72.4 72.7 73.0 73.4 73.7 74.0 74.3 74.7 75.0 75.3 75.6
BACKG 58 57 56 56 56 56 56 56 54 55 54 54
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 0 0 0 0 0 5 3 1 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 53 53 52 51 52 52 52 50 50 50 50 49
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 0 0 0 0 2 2 0 0 0 0 0
RADIUS 79.9 80.2 80.5 80.9 81.2 81.5 81.8 82.2 82.5 82.8 83.2 83.5
BACKG 51 49 49 48 48 49 47 48 48 47 47 47
SIGMA 7 7 7 6 6 6 6 6 6 6 6 6
NREJ 0 1 0 0 0 0 2 1 0 0 0 0
RADIUS 83.8 84.1 84.5
BACKG 48 47 24
SIGMA 6 6 3
NREJ 1 6 1
Starting spot search...
sorting 1124 spots
Median spot size is 4 x 4 pixels
Total number of spots found:1124
Number rejected as too small on X: 0
Number rejected as too small on Y: 0
Number rejected as too big on X: 16
Number rejected as too big on Y: 7
Number too close (SEPARATION keyword): 0
Number stored as OK:1101
Number of spots found in each bin
26 12 10 17 21 11 13 19
37 23 17 40 33 21 19 32
44 50 18 40 41 29 22 45
40 41 25 44 36 19 19 43
33 14 9 34 28 26 14 36
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 130 spots
Based on a median spot size of 5 by 4 pixels in X and Y, the measurement box
parameters have been set to 17 15 9 5 5
The overall size of the box has been fixed.
To prevent this use keywords PROFILE NOFIXBOX.
***** WARNING ***** Lattice type not specified, so assumed primitive
Based on a median spot size of 5 by 4 pixels in X and Y, the spot separation
parameters (in X and Y) have been set to 0.57 0.48mm.
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-ntest2_1.spt, Filename: ref-ntest2_1.spt
1101 spots written for image 2
A total of 1101 spots were written to file
FORMATTED OLD file opened on unit 10
Logical name: ref-ntest2_1.spt, Filename: ref-ntest2_1.spt
DPS Indexing at Two-theta = 0.00 with 948 reflections (minimum spot separation = 0.33mm. 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 180.31 129.29 127.64 89.8 90.2 89.7 I23,I213,I432,I4132
43 514 cP 127.42 128.07 128.26 119.4 90.3 120.1 P23,P213,P432,P4232,P4332,P4132
42 510 tP 127.42 127.64 128.26 119.9 89.7 119.7 P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
41 509 tP 128.07 128.26 127.42 90.3 120.1 119.4 P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
40 507 oP 127.42 128.07 128.26 119.4 90.3 120.1 P222,P2221,P21212,P212121
39 504 hR 220.48 181.29 128.07 89.7 106.5 113.6 H3,H32 (hexagonal settings of R3 and R32)
38 494 tI 129.29 180.31 127.64 89.8 89.8 90.3 I4,I41,I422,I4122
37 488 oF 127.64 221.33 222.41 71.3 90.0 90.3 F222
36 264 hP 128.07 127.42 128.26 90.3 119.4 120.1 P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
35 260 hR 221.33 181.29 128.17 90.8 106.0 114.2 H3,H32 (hexagonal settings of R3 and R32)
34 260 oC 128.07 220.57 128.26 73.1 119.4 90.1 C222,C2221
33 260 oC 127.64 222.41 127.42 106.2 119.7 90.0 C222,C2221
32 259 hP 128.26 128.17 127.42 119.2 90.3 120.3 P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
31 259 oC 128.07 220.57 128.26 73.1 119.4 90.1 C222,C2221
30 258 oC 127.64 222.41 127.42 73.8 119.7 90.0 C222,C2221
29 256 mP 127.42 128.26 128.07 119.4 120.1 90.3 P2,P21
28 255 mP 127.42 128.26 128.07 119.4 120.1 90.3 P2,P21
27 255 oC 127.64 222.41 127.42 106.2 119.7 90.0 C222,C2221
26 254 mP 128.26 127.42 128.17 119.2 120.3 90.3 P2,P21
25 247 mC 127.64 221.33 128.17 74.0 119.8 89.7 C2
24 245 mC 127.64 222.41 127.42 73.8 119.7 90.0 C2
23 244 mC 127.64 222.41 127.42 73.8 119.7 90.0 C2
22 22 tI 129.29 127.64 180.31 90.2 89.7 89.8 I4,I41,I422,I4122
21 21 tI 127.42 128.26 182.07 89.4 90.5 90.3 I4,I41,I422,I4122
20 19 cF 180.31 181.29 182.07 90.7 90.0 90.4 F23,F432,F4132
19 18 oI 127.42 128.26 182.07 90.6 90.5 89.7 I222,I212121
18 17 tI 129.29 127.64 180.31 90.2 89.7 89.8 I4,I41,I422,I4122
17 16 oF 180.31 181.29 182.07 90.7 90.0 89.6 F222
16 16 mC 180.31 181.29 128.07 89.7 134.7 89.6 C2
15 15 mC 180.31 181.29 128.07 89.7 134.7 89.6 C2
14 15 hR 127.42 128.07 316.00 89.4 90.5 120.1 H3,H32 (hexagonal settings of R3 and R32)
13 13 mC 221.32 128.26 127.42 90.3 124.7 90.3 C2
12 13 mI 127.42 182.07 128.26 89.4 90.3 90.5 C2
11 13 hR 128.07 129.29 311.91 90.4 89.7 120.2 H3,H32 (hexagonal settings of R3 and R32)
10 13 oI 127.64 129.29 180.31 89.7 90.2 89.8 I222,I212121
9 12 oI 127.64 180.31 129.29 89.7 89.8 90.2 I222,I212121
8 11 mC 221.70 127.42 128.26 90.3 124.8 90.2 C2
7 10 mC 221.70 127.42 128.26 90.3 124.8 90.2 C2
6 10 mC 221.33 127.64 180.31 90.2 144.3 89.7 C2
5 8 mC 221.33 127.64 129.29 90.2 125.4 89.7 C2
4 7 mC 221.32 128.26 127.42 90.3 124.7 90.3 C2
3 7 mC 220.57 128.07 128.17 89.4 124.7 90.1 C2
2 4 aP 127.42 128.07 128.26 119.4 90.3 120.1 P1
1 0 aP 127.42 127.64 128.17 60.2 60.8 60.3 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 #20 with F23 (number 196) symmetry imposed
Initial cell (before refinement) is 181.2205 181.2205 181.2205 90.000 90.000 90.000
Using 928 indexed reflections (out of 948 spots found, {delta(XY) <= 2.5 sigma}),
final sd in spot positions is 0.08mm and in phi 0.23 degrees
Refined cell parameters 180.93 180.93 180.93 90.00 90.00 90.00
Beam coordinates of 93.58 92.24 have been refined to 93.60 92.00
This is a shift of 0.24mm or 0.189 times the minimum spot separation of ca 1.29mm.
Final cell (after refinement) is 180.9307 180.9307 180.9307 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 9440.518 9200.215
****** 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-ntest2_1.gen Filename: ref-ntest2_1.gen
Title for MTZ and GENERATE Files (TITLE):
.
Crystal identifier (IDENT): ref-ntest2_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= 65
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 0 185 187 198 192 195 163 196 183 179 206 186 170 172 193 164 176 187 188
No gained 189 178
Total intensity 94819 97549 98310 98703 99054 99283 99396 99540 99612 99681 99735 99780 99837 99873 99893 99917 99935 99952 99976
Total intensity 99988 99998
SD of intensity 182 184 184 185 185 185 185 187 187 187 187 188 188 188 188 188 190 190 190
SD of intensity 190 192
The mosaicity has been estimated as ---> 0.27 <--- 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-ntest2_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-ntest2_1_001.img Filename: /scisoft/pxsoft/data/dna_040402/ref-ntest2_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-ntest2_1_001.img
(Q)QOPEN: file opened on unit 1 Status: READONLY
Logical Name: /scisoft/pxsoft/data/dna_040402/ref-ntest2_1_001.img Filename: /scisoft/pxsoft/data/dna_040402/ref-ntest2_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 116 spots
Threshold set to 4.5
sorting 118 spots
Threshold set to 4.5
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 357 349 345 338 331 322 317 310 303 295 290 284
SIGMA 18 18 18 18 18 17 17 17 17 17 17 16
NREJ 19 16 10 10 8 9 3 2 2 4 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 276 273 265 259 252 248 244 240 235 229 225 220
SIGMA 16 16 16 16 15 15 15 15 15 15 14 14
NREJ 1 0 1 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 217 214 209 206 202 198 194 191 189 186 182 180
SIGMA 14 14 14 14 14 14 13 13 13 13 13 13
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 177 176 173 169 167 165 165 162 157 156 152 151
SIGMA 13 13 13 13 12 12 12 12 12 12 12 12
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 149 146 142 141 141 140 136 134 133 132 130 127
SIGMA 12 12 11 11 11 11 11 11 11 11 11 11
NREJ 0 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 127 125 123 123 122 121 122 120 116 115 113 112
SIGMA 11 11 11 11 11 10 11 10 10 10 10 10
NREJ 0 0 0 0 0 1 6 4 4 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 110 109 108 107 106 104 104 101 100 99 97 98
SIGMA 10 10 10 10 10 10 10 10 10 9 9 9
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 98 96 95 95 93 92 93 92 90 88 88 87
SIGMA 9 9 9 9 9 9 9 9 9 9 9 9
NREJ 1 0 0 0 0 0 2 6 7 2 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 88 86 86 85 84 84 83 82 82 81 81 80
SIGMA 9 9 9 9 9 9 9 9 9 9 9 8
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 79 79 79 78 77 78 79 80 79 76 75 75
SIGMA 8 8 8 8 8 8 8 8 8 8 8 8
NREJ 1 0 0 0 0 0 5 8 8 5 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 75 74 75 75 74 74 73 72 73 72 72 71
SIGMA 8 8 8 8 8 8 8 8 8 8 8 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 72 71 70 69 68 69 69 70 69 68 67 67
SIGMA 8 8 8 8 8 8 8 8 8 8 8 8
NREJ 0 2 0 0 0 0 0 2 4 2 1 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 68 67 68 67 68 66 67 66 67 68 67 68
SIGMA 8 8 8 8 8 8 8 8 8 8 8 8
NREJ 0 0 4 2 2 0 0 0 0 0 7 7
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 67 68 66 66 66 65 66 65 66 65 67 66
SIGMA 8 8 8 8 8 8 8 8 8 8 8 8
NREJ 5 0 0 0 0 0 0 0 0 0 0 0
RADIUS 64.2 64.5 64.9 65.2 65.5 65.9 66.2 66.5 66.8 67.2 67.5 67.8
BACKG 66 65 65 66 66 66 66 65 64 65 65 65
SIGMA 8 8 8 8 8 8 8 8 8 8 8 8
NREJ 0 0 0 0 2 2 0 0 0 0 0 2
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 65 65 63 63 63 63 63 63 61 62 62 62
SIGMA 8 8 7 7 7 7 7 7 7 7 7 7
NREJ 0 1 0 0 1 0 3 0 0 0 0 2
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 61 61 60 59 59 58 58 59 60 58 57 57
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 4 4 2 0 0 0 0 2 1 3 0 0
RADIUS 76.0 76.3 76.6 76.9 77.3 77.6 77.9 78.3 78.6 78.9 79.2 79.6
BACKG 56 56 55 55 55 54 54 54 54 53 53 53
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 79.9 80.2 80.5 80.9 81.2 81.5 81.8 82.2 82.5 82.8 83.2 83.5
BACKG 53 52 51 50 50 49 50 50 50 50 49 49
SIGMA 7 7 7 7 7 7 7 7 7 7 7 6
NREJ 0 0 1 1 0 0 0 1 0 3 4 3
RADIUS 83.8 84.1 84.5
BACKG 49 48 24
SIGMA 7 6 3
NREJ 0 0 0
Starting spot search...
sorting 957 spots
Median spot size is 4 x 4 pixels
Total number of spots found: 957
Number rejected as too small on X: 0
Number rejected as too small on Y: 0
Number rejected as too big on X: 7
Number rejected as too big on Y: 2
Number too close (SEPARATION keyword): 0
Number stored as OK: 948
Number of spots found in each bin
21 14 7 22 24 8 9 17
36 19 13 29 34 17 19 33
38 27 21 39 42 19 20 37
35 20 20 31 38 16 20 36
21 21 14 35 21 20 14 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 118 spots
Based on a median spot size of 4 by 4 pixels in X and Y, the measurement box
parameters have been set to 15 15 9 5 5
The overall size of the box has been fixed.
To prevent this use keywords PROFILE NOFIXBOX.
***** WARNING ***** Lattice type not specified, so assumed primitive
Based on a median spot size of 4 by 4 pixels in X and Y, the spot separation
parameters (in X and Y) have been set to 0.48 0.48mm.
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-ntest2_1_002.img
(Q)QOPEN: file opened on unit 1 Status: READONLY
Logical Name: /scisoft/pxsoft/data/dna_040402/ref-ntest2_1_002.img Filename: /scisoft/pxsoft/data/dna_040402/ref-ntest2_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 354 349 342 339 329 321 314 306 301 290 286 281
SIGMA 18 18 18 18 18 17 17 17 17 17 16 16
NREJ 19 13 13 4 7 3 6 3 1 6 3 1
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 275 269 263 256 253 247 240 235 231 227 224 219
SIGMA 16 16 16 16 15 15 15 15 15 15 14 14
NREJ 0 0 0 2 0 0 1 0 0 0 1 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 213 208 206 203 202 198 194 189 188 184 181 178
SIGMA 14 14 14 14 14 14 13 13 13 13 13 13
NREJ 2 0 0 0 3 7 3 0 0 0 2 8
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 175 173 170 168 164 162 160 158 154 152 150 149
SIGMA 13 13 13 12 12 12 12 12 12 12 12 12
NREJ 10 4 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 146 145 143 141 140 136 134 133 130 130 128 127
SIGMA 12 12 11 11 11 11 11 11 11 11 11 11
NREJ 0 0 0 0 2 0 0 0 0 0 0 3
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 124 122 121 120 119 117 116 115 114 114 111 111
SIGMA 11 11 11 10 10 10 10 10 10 10 10 10
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 108 107 107 105 104 103 101 100 99 98 98 97
SIGMA 10 10 10 10 10 10 10 10 9 9 9 9
NREJ 0 0 0 2 2 0 0 0 0 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 95 94 95 91 91 91 91 89 88 86 87 87
SIGMA 9 9 9 9 9 9 9 9 9 9 9 9
NREJ 0 0 0 0 0 2 1 0 0 0 0 0
RADIUS 40.7 41.0 41.4 41.7 42.0 42.4 42.7 43.0 43.3 43.7 44.0 44.3
BACKG 85 84 83 83 83 82 81 80 80 80 80 80
SIGMA 9 9 9 9 9 9 9 8 8 8 8 8
NREJ 0 0 0 2 4 0 0 0 0 0 4 7
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 79 77 76 76 75 75 74 74 74 74 73 73
SIGMA 8 8 8 8 8 8 8 8 8 8 8 8
NREJ 1 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 72 72 73 73 74 72 71 70 70 70 70 69
SIGMA 8 8 8 8 8 8 8 8 8 8 8 8
NREJ 0 0 0 4 8 5 0 0 0 0 0 3
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 69 69 68 68 67 68 66 66 67 68 66 66
SIGMA 8 8 8 8 8 8 8 8 8 8 8 8
NREJ 2 0 0 0 0 0 0 0 0 1 5 2
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 66 66 66 65 66 67 66 66 65 64 65 65
SIGMA 8 8 8 8 8 8 8 8 8 8 8 8
NREJ 0 0 0 0 0 5 2 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 65 65 65 64 65 66 64 65 65 63 64 64
SIGMA 8 8 8 7 8 8 8 8 8 7 8 7
NREJ 0 0 0 0 0 1 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 63 63 63 62 62 62 61 62 62 61 63 63
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 4
RADIUS 68.1 68.5 68.8 69.1 69.4 69.8 70.1 70.4 70.7 71.1 71.4 71.7
BACKG 61 60 60 61 61 60 61 60 59 58 58 59
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 2 0 0 0 0 3 6 2 0 0 2 2
RADIUS 72.1 72.4 72.7 73.0 73.4 73.7 74.0 74.3 74.7 75.0 75.3 75.6
BACKG 58 57 56 56 56 56 56 56 54 55 54 54
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 0 0 0 0 0 5 3 1 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 53 53 52 51 52 52 52 50 50 50 50 49
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 0 0 0 0 2 2 0 0 0 0 0
RADIUS 79.9 80.2 80.5 80.9 81.2 81.5 81.8 82.2 82.5 82.8 83.2 83.5
BACKG 51 49 49 48 48 49 47 48 48 47 47 47
SIGMA 7 7 7 6 6 6 6 6 6 6 6 6
NREJ 0 1 0 0 0 0 2 1 0 0 0 0
RADIUS 83.8 84.1 84.5
BACKG 48 47 24
SIGMA 6 6 3
NREJ 1 6 1
Starting spot search...
sorting 1149 spots
Median spot size is 5 x 4 pixels
Total number of spots found:1149
Number rejected as too small on X: 16
Number rejected as too small on Y: 0
Number rejected as too big on X: 4
Number rejected as too big on Y: 17
Number too close (SEPARATION keyword): 2
Number stored as OK:1110
Number of spots found in each bin
25 13 11 18 22 11 13 21
36 23 17 40 33 22 19 32
44 48 18 43 42 28 22 44
41 40 26 45 38 20 19 43
33 15 9 34 30 22 15 37
FORMATTED UNKNOWN file opened on unit 10
Logical name: ref-ntest2_1.spt, Filename: ref-ntest2_1.spt
948 spots written for image 1
1110 spots written for image 2
A total of 2058 spots were written to file
FORMATTED OLD file opened on unit 10
Logical name: ref-ntest2_1.spt, Filename: ref-ntest2_1.spt
DPS Indexing at Two-theta = 0.00 with 1775 reflections (minimum spot separation = 0.33mm. Maximum expected cell edge 297.43, 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 127.83 180.65 128.22 90.0 90.1 90.0 I23,I213,I432,I4132
43 505 cP 127.78 127.90 127.93 120.0 119.8 90.1 P23,P213,P432,P4232,P4332,P4132
42 504 tP 127.90 127.93 127.78 119.8 90.1 120.0 P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
41 504 tP 127.93 127.93 127.78 119.8 120.0 90.2 P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
40 503 oP 127.78 127.90 127.93 120.0 119.8 90.1 P222,P2221,P21212,P212121
39 501 hR 221.38 181.18 127.78 89.9 106.7 114.1 H3,H32 (hexagonal settings of R3 and R32)
38 500 tI 128.22 180.65 127.83 90.0 89.9 90.0 I4,I41,I422,I4122
37 499 oF 127.83 221.46 221.60 70.7 90.0 90.1 F222
36 253 oC 127.83 221.60 127.78 73.4 119.9 90.0 C222,C2221
35 253 oC 127.93 221.44 127.78 73.2 119.8 90.0 C222,C2221
34 253 hP 127.93 127.90 127.78 90.1 119.8 120.0 P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
33 253 oC 127.93 221.44 127.78 73.2 119.8 90.0 C222,C2221
32 252 hP 127.93 127.90 127.78 90.1 119.8 120.0 P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
31 252 mP 127.78 127.93 127.93 90.2 120.0 119.8 P2,P21
30 252 mP 127.78 127.93 127.93 90.2 120.0 119.8 P2,P21
29 252 oC 127.93 221.44 127.78 73.2 119.8 90.0 C222,C2221
28 252 hR 181.18 221.46 127.90 73.3 89.9 114.2 H3,H32 (hexagonal settings of R3 and R32)
27 252 oC 127.83 221.60 127.78 106.6 119.9 90.0 C222,C2221
26 251 mP 127.90 127.78 127.93 119.8 120.0 90.1 P2,P21
25 250 mC 127.83 221.46 127.93 73.4 120.0 89.9 C2
24 250 mC 127.83 221.60 127.78 106.6 119.9 90.0 C2
23 249 mC 127.83 221.60 127.78 106.6 119.9 90.0 C2
22 5 cF 180.65 180.93 181.18 90.2 90.0 90.1 F23,F432,F4132
21 4 tI 127.78 127.90 181.18 89.9 89.9 89.9 I4,I41,I422,I4122
20 4 tI 127.83 128.22 180.65 90.0 90.0 90.1 I4,I41,I422,I4122
19 4 tI 127.83 128.22 180.65 90.0 90.0 89.9 I4,I41,I422,I4122
18 4 hR 127.78 127.93 313.78 89.8 90.1 120.0 H3,H32 (hexagonal settings of R3 and R32)
17 4 oF 180.65 181.18 180.93 90.2 90.1 90.0 F222
16 4 oI 127.78 127.90 181.18 90.1 90.1 89.9 I222,I212121
15 4 hR 127.93 128.22 312.95 90.1 89.9 120.1 H3,H32 (hexagonal settings of R3 and R32)
14 3 mC 180.65 181.18 127.78 89.9 134.9 90.0 C2
13 3 mC 221.55 127.78 127.90 89.9 125.1 90.0 C2
12 3 oI 127.83 180.65 128.22 90.0 89.9 90.0 I222,I212121
11 3 mC 221.55 127.78 127.90 89.9 125.1 90.0 C2
10 2 mI 127.78 181.18 127.90 90.1 90.1 89.9 C2
9 2 mC 221.48 127.90 127.78 90.1 125.1 90.0 C2
8 2 oI 180.65 128.22 127.83 89.9 90.0 90.0 I222,I212121
7 2 mC 180.93 180.65 127.83 90.0 134.9 90.1 C2
6 2 mC 221.48 127.90 127.78 90.1 125.1 90.0 C2
5 2 mC 221.46 127.83 180.65 90.0 144.6 89.9 C2
4 2 mC 180.93 180.65 128.22 90.0 135.0 89.9 C2
3 2 mC 180.65 181.18 127.78 90.1 134.9 90.0 C2
2 1 aP 127.78 127.90 127.93 120.0 119.8 90.1 P1
1 0 aP 127.78 127.83 127.90 60.0 89.9 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 #22 with F23 (number 196) symmetry imposed
Initial cell (before refinement) is 180.9202 180.9202 180.9202 90.000 90.000 90.000
Using 1689 indexed reflections (out of 1775 spots found, {delta(XY) <= 2.5 sigma}),
final sd in spot positions is 0.10mm and in phi 0.27 degrees
Refined cell parameters 180.95 180.95 180.95 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 0.27mm or 0.212 times the minimum spot separation of ca 1.29mm.
Final cell (after refinement) is 180.9525 180.9525 180.9525 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 9440.746 9197.264
****** 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-ntest2_1.gen Filename: ref-ntest2_1.gen
Title for MTZ and GENERATE Files (TITLE):
.
Crystal identifier (IDENT): ref-ntest2_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= 72
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 179 398 420 386 396 368 378 379 360 365 350 50 39 43 37 40 53 33 40
No gained 50 25
Total intensity 59689 67680 76955 83601 93942 98447 99746 99894 99943 99981 99998 99955 99908 99849 99783 99751 99695 99652 99349
Total intensity 99130 99064
SD of intensity 245 265 292 303 345 350 352 352 354 354 354 354 354 354 354 354 354 354 354
SD of intensity 354 354
The mosaicity has been estimated as ---> 0.42 <--- 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