Index results for ntest1_1
Symmetry and refined cell parameters
Image |
Symmetry |
a |
b |
c |
alpha |
beta |
gamma |
1 |
P222 |
54.775 |
58.060 |
67.294 |
90.000 |
90.000 |
90.000 |
2 |
P4 |
54.837 |
54.837 |
67.286 |
90.000 |
90.000 |
90.000 |
1+2 |
P222 |
54.787 |
58.068 |
67.200 |
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 |
236 |
37 |
0.157 |
0.090 |
0.015 |
-0.265 |
2 |
218 |
25 |
0.115 |
0.100 |
0.025 |
-0.195 |
1+2 |
454 |
62 |
0.137 |
0.100 |
0.005 |
-0.285 |
Image 1: /scisoft/pxsoft/data/dna_040402/ref-ntest1_1_001.img
Image 2: /scisoft/pxsoft/data/dna_040402/ref-ntest1_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-ntest1_1_###.img
===> directory /scisoft/pxsoft/data/dna_040402
===> detector adsc
===> beam 93.630000 95.185000
===> autoindex threshold 10 dps image 1
Using DPS code for background indexing
===> mosaic estimate
===> go
(Q)QOPEN: file opened on unit 1 Status: READONLY
Logical Name: /scisoft/pxsoft/data/dna_040402/ref-ntest1_1_001.img Filename: /scisoft/pxsoft/data/dna_040402/ref-ntest1_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
***** WARNING *****
***** WARNING *****
***** WARNING *****
***** WARNING *****
Input beam coordinates 93.63mm 95.18mm DO NOT agree with
those calculated from the image header ( 93.58mm 92.24mm)
Autoindexing image 1
=======================
image FILENAME: /scisoft/pxsoft/data/dna_040402/ref-ntest1_1_001.img
(Q)QOPEN: file opened on unit 1 Status: READONLY
Logical Name: /scisoft/pxsoft/data/dna_040402/ref-ntest1_1_001.img Filename: /scisoft/pxsoft/data/dna_040402/ref-ntest1_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 214 spots
Threshold set to 4.2
sorting 267 spots
Threshold set to 4.2
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 318 312 309 306 299 293 293 287 281 277 274 271
SIGMA 17 17 17 17 17 17 17 16 16 16 16 16
NREJ 23 22 18 15 15 16 10 10 10 8 3 2
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 266 261 252 249 246 242 237 234 228 225 223 218
SIGMA 16 16 15 15 15 15 15 15 15 15 14 14
NREJ 3 5 8 5 2 1 2 1 2 1 0 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 215 211 208 204 200 199 193 192 188 185 182 180
SIGMA 14 14 14 14 14 14 13 13 13 13 13 13
NREJ 0 0 0 0 0 0 1 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 177 175 175 172 169 165 163 161 159 156 154 153
SIGMA 13 13 13 13 13 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 149 148 145 143 141 140 137 136 134 131 130 128
SIGMA 12 12 12 11 11 11 11 11 11 11 11 11
NREJ 0 0 0 0 0 0 0 0 1 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 127 126 124 124 122 121 119 118 117 117 114 113
SIGMA 11 11 11 11 11 11 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 112 110 109 108 107 105 105 103 103 102 100 98
SIGMA 10 10 10 10 10 10 10 10 10 10 10 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 97 96 95 93 93 92 91 91 89 88 87
SIGMA 9 9 9 9 9 9 9 9 9 9 9 9
NREJ 0 0 0 0 0 0 0 0 0 0 0 0
RADIUS 40.7 41.0 41.4 41.7 42.0 42.4 42.7 43.0 43.3 43.7 44.0 44.3
BACKG 86 86 85 84 84 83 83 81 82 80 79 78
SIGMA 9 9 9 9 9 9 9 9 9 8 8 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 78 79 79 77 77 76 75 74 73 73 73 73
SIGMA 8 8 8 8 8 8 8 8 8 8 8 8
NREJ 0 0 4 10 7 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 73 72 71 70 70 70 70 70 69 68 68 67
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 66 67 66 66 65 64 65 64 65 64 64 64
SIGMA 8 8 8 8 8 8 8 8 8 8 8 7
NREJ 0 0 0 0 0 0 0 0 0 0 0 0
RADIUS 56.4 56.7 57.0 57.4 57.7 58.0 58.3 58.7 59.0 59.3 59.6 60.0
BACKG 63 63 63 63 63 63 63 63 63 62 61 61
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 0 0 0 0 0 7 9 2 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 61 61 62 61 62 62 61 62 63 62 61 61
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 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 61 61 60 61 60 60 60 58 59 57 58 58
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 0 0 0 0 0 0 0 0 0 0 0
RADIUS 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 57 58 57 57 56 57 57 55 56 55 55 55
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 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 54 53 54 54 53 53 53 52 52 51 50 50
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 0 0 0 0 0 0 0 0 0 0 0
RADIUS 76.0 76.3 76.6 76.9 77.3 77.6 77.9 78.3 78.6 78.9 79.2 79.6
BACKG 50 50 51 50 51 49 48 47 46 46 47 46
SIGMA 7 7 7 7 7 7 6 6 6 6 6 6
NREJ 0 0 5 7 0 1 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 46 46 45 45 45 45 45 44 44 43 42 42
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 0 0 0 0 1 0 0 0 0 0 0 0
RADIUS 83.8 84.1 84.5
BACKG 43 42 21
SIGMA 6 6 3
NREJ 0 0 0
Starting spot search...
sorting 479 spots
Median spot size is 8 x 7 pixels
Total number of spots found: 479
Number rejected as too small on X: 55
Number rejected as too small on Y: 43
Number rejected as too big on X: 15
Number rejected as too big on Y: 33
Number too close (SEPARATION keyword): 0
Number stored as OK: 333
Number of spots found in each bin
41 36 30 28 11 2 0 5
4 4 4 7 7 1 5 5
5 5 3 9 9 4 5 11
8 6 2 6 6 4 2 9
8 2 4 10 7 5 6 7
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 269 spots
Based on a median spot size of 9 by 8 pixels in X and Y, the measurement box
parameters have been set to 23 21 12 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 9 by 8 pixels in X and Y, the spot separation
parameters (in X and Y) have been set to 0.89 0.81mm.
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-ntest1_1.spt, Filename: ref-ntest1_1.spt
333 spots written for image 1
A total of 333 spots were written to file
FORMATTED OLD file opened on unit 10
Logical name: ref-ntest1_1.spt, Filename: ref-ntest1_1.spt
DPS Indexing at Two-theta = 0.00 with 193 reflections (minimum spot separation = 0.65mm. Maximum expected cell edge 267.90, Beam position is 93.63 95.18
Generating direct lattice vectors (This may take some time):
|-----------------|
..................
Refining 30 direct space vectors:
|----------------------------|
..............................
selected 1
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 hR 208.63 163.76 58.03 90.2 74.5 90.7 H3,H32 (hexagonal settings of R3 and R32)
43 964 tI 144.16 139.52 104.22 83.1 66.7 43.3 I4,I41,I422,I4122
42 903 tI 139.52 104.22 144.16 66.7 43.3 83.1 I4,I41,I422,I4122
41 901 oI 104.22 139.52 144.16 43.3 66.7 83.1 I222,I212121
40 896 cI 139.52 104.22 144.16 66.7 43.3 83.1 I23,I213,I432,I4132
39 872 cF 156.07 154.73 173.51 116.3 78.8 136.1 F23,F432,F4132
38 790 tI 144.16 173.51 58.03 70.7 89.3 110.1 I4,I41,I422,I4122
37 696 hR 104.82 139.52 173.98 126.4 72.0 109.3 H3,H32 (hexagonal settings of R3 and R32)
36 692 hR 104.82 140.56 154.73 121.6 80.2 97.7 H3,H32 (hexagonal settings of R3 and R32)
35 673 oI 58.03 144.16 173.51 69.9 70.7 90.7 I222,I212121
34 635 cP 58.03 86.93 127.45 97.8 90.6 90.4 P23,P213,P432,P4232,P4332,P4132
33 584 hP 86.93 127.45 58.03 90.6 90.4 97.8 P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
32 492 hR 58.03 104.82 384.14 89.8 98.0 124.0 H3,H32 (hexagonal settings of R3 and R32)
31 460 oF 104.82 104.22 263.64 106.3 92.7 67.5 F222
30 451 tP 86.93 127.45 58.03 90.6 90.4 97.8 P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
29 410 oF 58.03 183.63 260.87 78.8 102.3 108.8 F222
28 398 mI 58.03 263.64 86.93 78.7 89.6 102.0 C2
27 397 hP 58.03 86.93 127.45 97.8 90.6 90.4 P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
26 386 mC 163.76 144.16 58.03 89.3 90.2 111.6 C2
25 385 oC 144.16 163.76 58.03 90.2 90.7 68.4 C222,C2221
24 384 mC 104.22 104.82 127.45 96.2 96.8 67.5 C2
23 382 mC 144.16 163.76 58.03 90.2 90.7 68.4 C2
22 341 oI 58.03 86.93 263.64 101.3 102.0 90.4 I222,I212121
21 341 tI 58.03 86.93 263.64 78.7 78.0 90.4 I4,I41,I422,I4122
20 293 mC 183.63 58.03 144.16 90.7 117.4 71.2 C2
19 281 mC 58.03 183.63 127.45 82.8 90.6 71.2 C2
18 276 mC 58.03 260.87 86.93 82.3 89.6 77.7 C2
17 254 tP 58.03 86.93 127.45 97.8 90.6 90.4 P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
16 253 oC 104.22 104.82 127.45 96.2 96.8 67.5 C222,C2221
15 248 mC 104.22 104.82 127.45 83.8 96.8 112.5 C2
14 246 mC 104.22 104.82 127.45 96.2 96.8 67.5 C2
13 214 oC 58.03 182.94 127.45 82.4 90.6 108.1 C222,C2221
12 209 oC 58.03 260.87 86.93 82.3 90.4 102.3 C222,C2221
11 208 mC 86.93 257.86 58.03 89.3 89.6 78.3 C2
10 203 oC 86.93 257.86 58.03 89.3 90.4 101.7 C222,C2221
9 200 mC 257.86 86.93 58.03 90.4 90.7 78.3 C2
8 148 mC 182.94 58.03 127.45 90.6 97.6 71.9 C2
7 143 mC 260.87 58.03 86.93 90.4 97.7 77.7 C2
6 71 oP 58.03 86.93 127.45 97.8 90.6 90.4 P222,P2221,P21212,P212121
5 69 mP 58.03 127.45 86.93 97.8 90.4 90.6 P2,P21
4 67 mP 58.03 86.93 127.45 97.8 90.6 90.4 P2,P21
3 5 mP 86.93 58.03 127.45 90.6 97.8 90.4 P2,P21
2 1 aP 58.03 86.93 127.45 82.2 89.4 90.4 P1
1 0 aP 58.03 86.93 127.45 97.8 90.6 90.4 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 # 3 with P2 (number 3) symmetry imposed
Initial cell (before refinement) is 86.9275 58.0342 127.4495 90.000 97.829 90.000
Using 190 indexed reflections (out of 193 spots found, {delta(XY) <= 2.5 sigma}),
final sd in spot positions is 0.16mm and in phi 0.26 degrees
Refined cell parameters 86.92 58.07 126.29 90.00 98.03 90.00
Beam coordinates of 93.63 95.18 have been refined to 93.41 95.01
This is a shift of 0.28mm or 0.104 times the minimum spot separation of ca 2.71mm.
Final cell (after refinement) is 86.9196 58.0652 126.2925 90.000 98.031 90.000
FORMATTED UNKNOWN file opened on unit 12
Logical name: autoindex.mat, Filename: autoindex.mat
Updating the stored central beam position from 9363.000 9518.500 to 9459.473 9500.791
****** 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-ntest1_1.gen Filename: ref-ntest1_1.gen
Title for MTZ and GENERATE Files (TITLE):
.
Crystal identifier (IDENT): ref-ntest1_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= 35
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 87 173 173 147 196 152 174 175 165 168 167 3 5 2 0 3 1 1 2
No gained 0 2
Total intensity 86512 94835 96112 96465 96576 99779 99978 99983 99990 99998 99990 99989 99983 99983 99983 99981 99983 99981 99985
Total intensity 99985 99985
SD of intensity 126 131 132 132 133 138 138 139 140 140 141 141 141 141 141 141 141 141 141
SD of intensity 141 141
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: P2 number 3
*********** 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-ntest1_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-ntest1_1_001.img Filename: /scisoft/pxsoft/data/dna_040402/ref-ntest1_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-ntest1_1_001.img
(Q)QOPEN: file opened on unit 1 Status: READONLY
Logical Name: /scisoft/pxsoft/data/dna_040402/ref-ntest1_1_001.img Filename: /scisoft/pxsoft/data/dna_040402/ref-ntest1_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 30 spots
Threshold set to 4.4
sorting 29 spots
Threshold set to 4.3
Finding spots on image 1 (Midpoint of phi 0.500 degrees)
Calculating radial background.....
The background is radial along the X (slow) direction
The average of 51 pixels, excluding outliers, is used
The scan is offset by 4.7mm from the image centre in Y to avoid any
backstop shadow
Radial Background calculation complete
RADIUS 9.4 9.7 10.0 10.4 10.7 11.0 11.3 11.7 12.0 12.3 12.6 13.0
BACKG 382 372 373 357 356 346 334 333 324 316 309 301
SIGMA 19 19 19 18 18 18 18 18 17 17 17 17
NREJ 19 21 7 16 7 7 7 2 4 4 2 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 296 289 284 276 269 264 260 253 248 245 239 235
SIGMA 17 17 16 16 16 16 16 15 15 15 15 15
NREJ 1 0 0 0 0 0 0 0 0 0 0 0
RADIUS 17.2 17.5 17.9 18.2 18.5 18.8 19.2 19.5 19.8 20.2 20.5 20.8
BACKG 228 224 222 216 213 211 206 204 200 196 192 189
SIGMA 15 14 14 14 14 14 14 14 14 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 185 184 180 179 176 172 171 168 164 163 160 158
SIGMA 13 13 13 13 13 13 13 12 12 12 12 12
NREJ 0 0 0 0 0 0 0 0 0 0 0 1
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 155 153 150 148 146 144 142 141 139 136 133 132
SIGMA 12 12 12 12 12 12 11 11 11 11 11 11
NREJ 0 0 0 0 0 0 0 0 1 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 133 130 127 127 124 123 122 120 119 118 116 115
SIGMA 11 11 11 11 11 11 11 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 115 112 112 109 109 108 107 105 105 104 102 100
SIGMA 10 10 10 10 10 10 10 10 10 10 10 10
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 101 99 97 96 95 95 93 92 92 89 90 89
SIGMA 10 9 9 9 9 9 9 9 9 9 9 9
NREJ 0 0 0 0 0 0 0 0 0 0 0 0
RADIUS 40.7 41.0 41.4 41.7 42.0 42.4 42.7 43.0 43.3 43.7 44.0 44.3
BACKG 87 88 86 85 84 84 82 83 81 81 80 79
SIGMA 9 9 9 9 9 9 9 9 9 9 8 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 78 77 77 77 76 75 75 74 74 73 73
SIGMA 8 8 8 8 8 8 8 8 8 8 8 8
NREJ 0 0 0 0 0 0 0 0 0 0 1 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 73 73 74 72 72 72 71 70 69 68 68 68
SIGMA 8 8 8 8 8 8 8 8 8 8 8 8
NREJ 0 0 5 11 9 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 67 67 66 66 66 65 65 65 65 64 65 63
SIGMA 8 8 8 8 8 8 8 8 8 8 8 7
NREJ 0 0 0 0 0 0 0 0 0 0 0 0
RADIUS 56.4 56.7 57.0 57.4 57.7 58.0 58.3 58.7 59.0 59.3 59.6 60.0
BACKG 63 64 64 63 63 63 63 64 63 62 61 62
SIGMA 7 8 8 7 7 7 7 7 7 7 7 7
NREJ 0 0 0 0 0 1 7 7 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 61 61 61 61 61 62 61 62 62 61 60 60
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 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 61 61 61 61 60 59 59 59 59 58 58 58
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 0 0 0 0 0 0 0 0 0 0 0
RADIUS 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 59 58 57 57 56 57 57 56 56 56 57 56
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 0 0 0 0 0 0 0 0 0 6 11
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 55 55 54 53 54 53 52 52 52 52 51 50
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 8 0 0 0 0 0 0 0 0 0 0 0
RADIUS 76.0 76.3 76.6 76.9 77.3 77.6 77.9 78.3 78.6 78.9 79.2 79.6
BACKG 51 51 50 48 48 49 48 47 47 47 47 46
SIGMA 7 7 7 6 6 6 6 6 6 6 6 6
NREJ 0 0 0 0 0 0 0 0 0 0 0 0
RADIUS 79.9 80.2 80.5 80.9 81.2 81.5 81.8 82.2 82.5 82.8 83.2 83.5
BACKG 46 46 46 45 45 45 45 44 43 43 43 42
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 0 0 1 4 1 0 0 1 0 0 0 0
RADIUS 83.8 84.1 84.5
BACKG 43 42 21
SIGMA 6 6 3
NREJ 0 0 0
Starting spot search...
sorting 236 spots
Median spot size is 7 x 7 pixels
Total number of spots found: 236
Number rejected as too small on X: 27
Number rejected as too small on Y: 8
Number rejected as too big on X: 2
Number rejected as too big on Y: 0
Number too close (SEPARATION keyword): 0
Number stored as OK: 199
Number of spots found in each bin
10 1 0 3 3 2 1 4
3 1 6 8 6 2 3 6
7 3 3 9 8 3 6 10
7 6 3 5 8 4 3 9
9 2 1 9 7 4 5 9
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 31 spots
Based on a median spot size of 7 by 7 pixels in X and Y, the measurement box
parameters have been set to 21 21 12 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 7 pixels in X and Y, the spot separation
parameters (in X and Y) have been set to 0.73 0.73mm.
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-ntest1_1.spt, Filename: ref-ntest1_1.spt
199 spots written for image 1
A total of 199 spots were written to file
FORMATTED OLD file opened on unit 10
Logical name: ref-ntest1_1.spt, Filename: ref-ntest1_1.spt
DPS Indexing at Two-theta = 0.00 with 189 reflections (minimum spot separation = 0.57mm. 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 24
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 hR 143.64 89.18 54.58 90.2 68.2 100.4 H3,H32 (hexagonal settings of R3 and R32)
43 791 cF 104.20 103.19 104.42 112.0 100.0 116.5 F23,F432,F4132
42 776 cI 86.06 79.44 88.17 62.1 54.6 65.1 I23,I213,I432,I4132
41 754 tI 88.17 104.42 54.58 58.6 89.4 96.7 I4,I41,I422,I4122
40 719 mI 54.58 154.83 58.05 68.7 90.3 70.0 C2
39 705 hR 54.58 79.93 215.13 91.2 104.1 133.4 H3,H32 (hexagonal settings of R3 and R32)
38 668 oF 54.58 128.60 144.29 80.3 111.7 115.5 F222
37 587 tI 88.17 86.06 79.44 65.1 62.1 54.6 I4,I41,I422,I4122
36 587 tI 86.06 79.44 88.17 62.1 54.6 65.1 I4,I41,I422,I4122
35 586 oI 79.44 86.06 88.17 54.6 62.1 65.1 I222,I212121
34 536 oI 54.58 89.18 103.19 83.1 58.7 90.2 I222,I212121
33 501 oF 79.44 79.93 154.83 91.7 120.0 86.5 F222
32 500 mC 79.93 79.44 86.06 65.1 116.0 86.5 C2
31 475 tI 54.58 58.05 154.83 68.7 70.0 90.3 I4,I41,I422,I4122
30 475 oI 54.58 58.05 154.83 111.3 110.0 90.3 I222,I212121
29 450 mC 128.00 54.58 89.18 90.2 126.8 65.1 C2
28 340 hP 58.05 67.03 54.58 90.5 90.3 90.7 P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
27 260 hP 54.58 58.05 67.03 90.7 90.5 90.3 P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
26 259 mC 58.05 145.48 54.58 89.4 89.7 67.1 C2
25 255 oC 58.05 145.48 54.58 89.4 90.3 112.9 C222,C2221
24 252 mC 145.48 58.05 54.58 90.3 90.6 67.1 C2
23 236 mC 54.58 128.60 67.03 89.6 90.5 64.5 C2
22 232 mC 54.58 144.29 58.05 89.3 89.7 68.3 C2
21 231 oC 54.58 128.00 67.03 89.2 90.5 114.9 C222,C2221
20 227 mC 128.00 54.58 67.03 90.5 90.8 65.1 C2
19 227 oC 54.58 144.29 58.05 89.3 90.3 111.7 C222,C2221
18 224 mC 144.29 54.58 58.05 90.3 90.7 68.3 C2
17 123 hR 79.93 86.06 104.69 100.1 87.2 116.0 H3,H32 (hexagonal settings of R3 and R32)
16 123 cP 54.58 58.05 67.03 90.7 90.5 90.3 P23,P213,P432,P4232,P4332,P4132
15 118 hR 79.93 86.82 103.19 99.6 87.4 115.5 H3,H32 (hexagonal settings of R3 and R32)
14 93 tP 58.05 67.03 54.58 90.5 90.3 90.7 P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
13 90 oC 88.17 89.18 54.58 90.2 90.6 81.8 C222,C2221
12 90 mC 88.17 89.18 54.58 89.8 90.6 98.2 C2
11 87 mC 88.17 89.18 54.58 90.2 90.6 81.8 C2
10 37 tP 54.58 58.05 67.03 90.7 90.5 90.3 P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
9 36 oC 79.44 79.93 67.03 90.1 90.8 86.5 C222,C2221
8 32 mC 79.44 79.93 67.03 89.9 90.8 93.5 C2
7 31 mC 79.44 79.93 67.03 90.1 90.8 86.5 C2
6 7 oP 54.58 58.05 67.03 90.7 90.5 90.3 P222,P2221,P21212,P212121
5 6 mP 54.58 67.03 58.05 90.7 90.3 90.5 P2,P21
4 5 mP 54.58 58.05 67.03 90.7 90.5 90.3 P2,P21
3 4 mP 58.05 54.58 67.03 90.5 90.7 90.3 P2,P21
2 1 aP 54.58 58.05 67.03 89.3 89.5 90.3 P1
1 0 aP 54.58 58.05 67.03 90.7 90.5 90.3 P1
No PENALTY SDCELL FRACN LATT a b c alpha beta gamma Possible spacegroups
The solution and direct beam position will now be refined; reflections which deviate by more
than the sigma cutoff from their calculated position will be excluded from the refinement.
Refining solution # 6 with P222 (number 16) symmetry imposed
Initial cell (before refinement) is 54.5823 58.0540 67.0293 90.000 90.000 90.000
Using 181 indexed reflections (out of 189 spots found, {delta(XY) <= 2.5 sigma}),
final sd in spot positions is 0.09mm and in phi 0.24 degrees
Refined cell parameters 54.77 58.06 67.29 90.00 90.00 90.00
Beam coordinates of 93.58 92.24 have been refined to 93.60 91.98
This is a shift of 0.26mm or 0.076 times the minimum spot separation of ca 3.47mm.
Final cell (after refinement) is 54.7749 58.0600 67.2939 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 9440.455 9198.185
****** 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-ntest1_1.gen Filename: ref-ntest1_1.gen
Title for MTZ and GENERATE Files (TITLE):
.
Crystal identifier (IDENT): ref-ntest1_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= 26
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 27 28 37 28 32 27 26 24 22 26 32 28 28 27 28 30 35 33
No gained 25 33
Total intensity 98729 99431 99737 99800 99838 99861 99884 99904 99922 99942 99953 99958 99967 99977 99987 99987 99991 99993 99994
Total intensity 99994 99998
SD of intensity 178 178 178 178 178 178 179 179 179 179 179 179 179 179 179 179 179 179 179
SD of intensity 179 179
The mosaicity has been estimated as ---> 0.20 <--- for this image only;
This value can be used cautiously as an initial estimate.
Storing space group from DPS autoindexing: P222 number 16
*********** 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-ntest1_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-ntest1_1_002.img Filename: /scisoft/pxsoft/data/dna_040402/ref-ntest1_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-ntest1_1_002.img
(Q)QOPEN: file opened on unit 1 Status: READONLY
Logical Name: /scisoft/pxsoft/data/dna_040402/ref-ntest1_1_002.img Filename: /scisoft/pxsoft/data/dna_040402/ref-ntest1_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 30 spots
Threshold set to 4.1
sorting 33 spots
Threshold set to 4.1
Finding spots on image 2 (Midpoint of phi 90.500 degrees)
Calculating radial background.....
The background is radial along the X (slow) direction
The average of 51 pixels, excluding outliers, is used
The scan is offset by 4.7mm from the image centre in Y to avoid any
backstop shadow
Radial Background calculation complete
RADIUS 9.4 9.7 10.0 10.4 10.7 11.0 11.3 11.7 12.0 12.3 12.6 13.0
BACKG 29 30 30 30 30 30 30 29 29 29 29 29
SIGMA 5 5 5 5 5 5 5 5 5 5 5 5
NREJ 0 1 0 0 0 0 0 1 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 29 29 29 29 29 28 29 29 29 29 29 29
SIGMA 5 5 5 5 5 5 5 5 5 5 5 5
NREJ 0 0 0 0 0 0 0 0 0 0 0 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 29 28 29 29 29 29 28 29 29 29 29 28
SIGMA 5 5 5 5 5 5 5 5 5 5 5 5
NREJ 1 0 0 0 0 0 0 0 0 0 0 0
RADIUS 21.1 21.5 21.8 22.1 22.4 22.8 23.1 23.4 23.7 24.1 24.4 24.7
BACKG 28 28 29 29 28 28 28 29 28 28 28 28
SIGMA 5 5 5 5 5 5 5 5 5 5 5 5
NREJ 0 0 1 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 28 28 28 28 28 28 28 28 28 28 27 28
SIGMA 5 5 5 5 5 5 5 5 5 5 5 5
NREJ 0 0 0 1 0 0 0 0 1 1 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 28 28 28 28 27 28 28 28 28 28 27 27
SIGMA 5 5 5 5 5 5 5 5 5 5 5 5
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 27 27 28 28 28 27 27 28 28 28 27 28
SIGMA 5 5 5 5 5 5 5 5 5 5 5 5
NREJ 1 1 1 0 0 1 2 0 0 0 0 1
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 27 28 28 27 28 28 28 27 27 28 28 29
SIGMA 5 5 5 5 5 5 5 5 5 5 5 5
NREJ 1 2 1 0 0 0 0 0 0 1 8 13
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 28 28 27 27 27 27 27 28 27 27 27 27
SIGMA 5 5 5 5 5 5 5 5 5 5 5 5
NREJ 13 4 1 0 0 0 0 0 1 1 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 27 27 27 27 27 27 27 27 28 27 27 27
SIGMA 5 5 5 5 5 5 5 5 5 5 5 5
NREJ 0 1 0 0 0 0 1 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 26 27 27 27 27 27 27 27 27 27 27 27
SIGMA 5 5 5 5 5 5 5 5 5 5 5 5
NREJ 0 0 0 0 0 0 0 0 1 0 0 0
RADIUS 52.5 52.8 53.1 53.4 53.8 54.1 54.4 54.8 55.1 55.4 55.7 56.1
BACKG 27 27 27 27 27 27 27 27 28 28 28 28
SIGMA 5 5 5 5 5 5 5 5 5 5 5 5
NREJ 0 0 0 0 0 0 0 0 0 0 0 1
RADIUS 56.4 56.7 57.0 57.4 57.7 58.0 58.3 58.7 59.0 59.3 59.6 60.0
BACKG 28 28 28 29 28 29 29 29 29 29 28 29
SIGMA 5 5 5 5 5 5 5 5 5 5 5 5
NREJ 0 0 0 0 1 0 0 0 0 0 1 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 30 30 30 31 31 31 31 31 31 31 32 32
SIGMA 5 5 5 5 5 5 5 5 5 5 5 5
NREJ 0 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 32 32 33 33 33 32 32 32 32 32 32 32
SIGMA 5 5 5 5 5 5 5 5 5 5 5 5
NREJ 0 0 0 0 0 0 0 0 0 0 0 1
RADIUS 68.1 68.5 68.8 69.1 69.4 69.8 70.1 70.4 70.7 71.1 71.4 71.7
BACKG 32 32 31 32 32 32 31 31 31 31 31 30
SIGMA 5 5 5 5 5 5 5 5 5 5 5 5
NREJ 0 0 0 0 0 0 0 0 0 0 1 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 31 30 31 31 31 30 30 31 31 30 29 30
SIGMA 5 5 5 5 5 5 5 5 5 5 5 5
NREJ 0 0 0 0 3 10 12 5 0 0 0 0
RADIUS 76.0 76.3 76.6 76.9 77.3 77.6 77.9 78.3 78.6 78.9 79.2 79.6
BACKG 29 30 29 28 28 28 28 28 28 28 27 27
SIGMA 5 5 5 5 5 5 5 5 5 5 5 5
NREJ 0 0 0 1 1 0 0 0 0 0 0 1
RADIUS 79.9 80.2 80.5 80.9 81.2 81.5 81.8 82.2 82.5 82.8 83.2 83.5
BACKG 27 27 27 27 27 27 27 26 27 26 26 26
SIGMA 5 5 5 5 5 5 5 5 5 5 5 5
NREJ 0 0 0 2 0 0 0 1 0 0 0 0
RADIUS 83.8 84.1 84.5
BACKG 27 26 13
SIGMA 5 5 2
NREJ 0 0 0
Starting spot search...
sorting 218 spots
Median spot size is 8 x 7 pixels
Total number of spots found: 218
Number rejected as too small on X: 13
Number rejected as too small on Y: 7
Number rejected as too big on X: 3
Number rejected as too big on Y: 2
Number too close (SEPARATION keyword): 0
Number stored as OK: 193
Number of spots found in each bin
1 2 2 5 1 1 2 7
10 1 4 6 9 0 4 0
6 3 8 6 7 6 0 11
7 5 1 8 7 2 7 8
5 3 2 9 5 7 0 15
Determining average spot size for spots in centre of image.
==========================================================
Finding spot size around direct beam position
Default parameters may be reset with SPOTS keyword.
Minimum radius 9.4mm, maximum radius 37.60mm, minimum number of spots 10
sorting 33 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-ntest1_1.spt, Filename: ref-ntest1_1.spt
193 spots written for image 2
A total of 193 spots were written to file
FORMATTED OLD file opened on unit 10
Logical name: ref-ntest1_1.spt, Filename: ref-ntest1_1.spt
DPS Indexing at Two-theta = 0.00 with 192 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 23
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 hR 140.24 88.96 54.89 89.3 67.7 98.8 H3,H32 (hexagonal settings of R3 and R32)
43 775 cF 102.06 102.85 103.93 113.8 98.6 115.2 F23,F432,F4132
42 768 cI 86.85 78.11 86.51 63.2 54.5 65.0 I23,I213,I432,I4132
41 745 tI 86.51 103.93 54.89 58.9 90.5 98.7 I4,I41,I422,I4122
40 675 hR 54.89 78.11 214.87 89.6 104.9 133.7 H3,H32 (hexagonal settings of R3 and R32)
39 672 mI 54.89 154.10 56.48 70.4 91.0 69.3 C2
38 645 oF 54.89 124.78 144.92 79.4 112.1 115.1 F222
37 573 tI 86.51 86.85 78.11 65.0 63.2 54.5 I4,I41,I422,I4122
36 568 tI 86.85 78.11 86.51 63.2 54.5 65.0 I4,I41,I422,I4122
35 564 oI 78.11 86.85 86.51 54.5 63.2 65.0 I222,I212121
34 549 oI 54.89 86.51 103.93 81.3 58.9 89.5 I222,I212121
33 472 oF 78.11 79.42 154.10 89.7 119.4 88.4 F222
32 463 mC 79.42 78.11 86.85 65.0 117.5 88.4 C2
31 461 tI 54.89 56.48 154.48 69.7 69.0 89.0 I4,I41,I422,I4122
30 461 oI 54.89 56.48 154.48 110.3 111.0 89.0 I222,I212121
29 449 mC 124.78 54.89 86.51 89.5 124.6 64.9 C2
28 332 hP 56.48 67.14 54.89 89.8 91.0 91.6 P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
27 245 hP 54.89 56.48 67.14 91.6 89.8 91.0 P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
26 243 oC 54.89 144.92 56.48 88.9 89.0 112.1 C222,C2221
25 240 mC 54.89 144.92 56.48 88.9 91.0 67.9 C2
24 237 mC 54.89 124.78 67.14 88.6 90.2 64.9 C2
23 235 mC 144.92 54.89 56.48 89.0 91.1 67.9 C2
22 232 oC 56.48 144.20 54.89 89.8 91.0 111.4 C222,C2221
21 231 oC 54.89 124.78 67.14 88.6 89.8 115.1 C222,C2221
20 231 mC 144.20 56.48 54.89 91.0 90.2 68.6 C2
19 228 mC 56.48 144.20 54.89 90.2 91.0 68.6 C2
18 223 mC 124.78 54.89 67.14 89.8 91.4 64.9 C2
17 128 hR 79.42 86.60 102.06 99.4 89.6 115.4 H3,H32 (hexagonal settings of R3 and R32)
16 127 cP 54.89 56.48 67.14 91.6 89.8 91.0 P23,P213,P432,P4232,P4332,P4132
15 125 hR 78.11 86.60 105.13 99.8 88.1 116.9 H3,H32 (hexagonal settings of R3 and R32)
14 114 tP 56.48 67.14 54.89 89.8 91.0 91.6 P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
13 106 oC 86.51 88.96 54.89 89.3 90.5 80.1 C222,C2221
12 106 mC 86.51 88.96 54.89 89.3 90.5 80.1 C2
11 103 mC 88.96 86.51 54.89 90.5 90.7 99.9 C2
10 27 tP 54.89 56.48 67.14 91.6 89.8 91.0 P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
9 23 oC 78.11 79.42 67.14 91.3 91.1 88.4 C222,C2221
8 23 mC 78.11 79.42 67.14 91.3 91.1 88.4 C2
7 21 mC 79.42 78.11 67.14 88.9 91.3 91.6 C2
6 14 oP 54.89 56.48 67.14 91.6 89.8 91.0 P222,P2221,P21212,P212121
5 13 mP 54.89 56.48 67.14 91.6 89.8 91.0 P2,P21
4 10 mP 54.89 67.14 56.48 91.6 91.0 89.8 P2,P21
3 6 mP 56.48 54.89 67.14 89.8 91.6 91.0 P2,P21
2 1 aP 54.89 56.48 67.14 91.6 89.8 91.0 P1
1 0 aP 54.89 56.48 67.14 88.4 89.8 89.0 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 #10 with P4 (number 75) symmetry imposed
Initial cell (before refinement) is 55.6889 55.6889 67.1423 90.000 90.000 90.000
Using 181 indexed reflections (out of 192 spots found, {delta(XY) <= 2.5 sigma}),
final sd in spot positions is 0.10mm and in phi 0.48 degrees
Refined cell parameters 54.84 54.84 67.29 90.00 90.00 90.00
Beam coordinates of 93.58 92.24 have been refined to 93.61 92.05
This is a shift of 0.20mm or 0.057 times the minimum spot separation of ca 3.47mm.
Final cell (after refinement) is 54.8368 54.8368 67.2860 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 9439.480 9204.795
****** 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-ntest1_1.gen Filename: ref-ntest1_1.gen
Title for MTZ and GENERATE Files (TITLE):
.
Crystal identifier (IDENT): ref-ntest1_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= 17
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 35 61 70 52 49 57 59 49 38 40 57 1 0 2 0 1 1 0 1
No gained 0 0
Total intensity 50645 60776 65227 69833 75081 80829 88001 92189 95846 97459 99997 99998 99998 99998 99998 99998 99997 99997 99993
Total intensity 99993 99993
SD of intensity 116 135 139 142 148 151 162 164 167 167 169 169 169 169 169 169 169 169 169
SD of intensity 169 169
The mosaicity has been estimated as ---> 0.74 <--- for this image only;
This value can be used cautiously as an initial estimate.
Storing space group from DPS autoindexing: P4 number 75
*********** END OF PROCESSING *****************
************ Version 6.2.3 (beta test 1.6) for Image plate and CCD data 4th November 2002 ***********
A.G.W. Leslie, MRC Laboratory Of Molecular Biology, HILLS ROAD, CAMBRIDGE CB2 2QH, UK
E-mail andrew@mrc-lmb.cam.ac.uk
New auto-indexing using DPS due to Ingo Steller Robert Bolotovsky and Michael Rossmann
(1998) J. Appl. Cryst. 30, 1036-1040
Original auto-indexing using REFIX due to Wolfgang Kabsch (Kabsch,W. (1993),
J.Appl.Cryst. 24,795-800.)
X-windows interface using xdl_view due to John Campbell (Daresbury Laboratory, UK.)
(Campbell,J.W. (1995) J. Appl. Cryst. 28, 236-242.
===> newmat autoindex.mat
===> template ref-ntest1_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-ntest1_1_001.img Filename: /scisoft/pxsoft/data/dna_040402/ref-ntest1_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-ntest1_1_001.img
(Q)QOPEN: file opened on unit 1 Status: READONLY
Logical Name: /scisoft/pxsoft/data/dna_040402/ref-ntest1_1_001.img Filename: /scisoft/pxsoft/data/dna_040402/ref-ntest1_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 30 spots
Threshold set to 4.4
sorting 29 spots
Threshold set to 4.3
Finding spots on image 1 (Midpoint of phi 0.500 degrees)
Calculating radial background.....
The background is radial along the X (slow) direction
The average of 51 pixels, excluding outliers, is used
The scan is offset by 4.7mm from the image centre in Y to avoid any
backstop shadow
Radial Background calculation complete
RADIUS 9.4 9.7 10.0 10.4 10.7 11.0 11.3 11.7 12.0 12.3 12.6 13.0
BACKG 382 372 373 357 356 346 334 333 324 316 309 301
SIGMA 19 19 19 18 18 18 18 18 17 17 17 17
NREJ 19 21 7 16 7 7 7 2 4 4 2 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 296 289 284 276 269 264 260 253 248 245 239 235
SIGMA 17 17 16 16 16 16 16 15 15 15 15 15
NREJ 1 0 0 0 0 0 0 0 0 0 0 0
RADIUS 17.2 17.5 17.9 18.2 18.5 18.8 19.2 19.5 19.8 20.2 20.5 20.8
BACKG 228 224 222 216 213 211 206 204 200 196 192 189
SIGMA 15 14 14 14 14 14 14 14 14 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 185 184 180 179 176 172 171 168 164 163 160 158
SIGMA 13 13 13 13 13 13 13 12 12 12 12 12
NREJ 0 0 0 0 0 0 0 0 0 0 0 1
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 155 153 150 148 146 144 142 141 139 136 133 132
SIGMA 12 12 12 12 12 12 11 11 11 11 11 11
NREJ 0 0 0 0 0 0 0 0 1 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 133 130 127 127 124 123 122 120 119 118 116 115
SIGMA 11 11 11 11 11 11 11 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 115 112 112 109 109 108 107 105 105 104 102 100
SIGMA 10 10 10 10 10 10 10 10 10 10 10 10
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 101 99 97 96 95 95 93 92 92 89 90 89
SIGMA 10 9 9 9 9 9 9 9 9 9 9 9
NREJ 0 0 0 0 0 0 0 0 0 0 0 0
RADIUS 40.7 41.0 41.4 41.7 42.0 42.4 42.7 43.0 43.3 43.7 44.0 44.3
BACKG 87 88 86 85 84 84 82 83 81 81 80 79
SIGMA 9 9 9 9 9 9 9 9 9 9 8 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 78 77 77 77 76 75 75 74 74 73 73
SIGMA 8 8 8 8 8 8 8 8 8 8 8 8
NREJ 0 0 0 0 0 0 0 0 0 0 1 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 73 73 74 72 72 72 71 70 69 68 68 68
SIGMA 8 8 8 8 8 8 8 8 8 8 8 8
NREJ 0 0 5 11 9 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 67 67 66 66 66 65 65 65 65 64 65 63
SIGMA 8 8 8 8 8 8 8 8 8 8 8 7
NREJ 0 0 0 0 0 0 0 0 0 0 0 0
RADIUS 56.4 56.7 57.0 57.4 57.7 58.0 58.3 58.7 59.0 59.3 59.6 60.0
BACKG 63 64 64 63 63 63 63 64 63 62 61 62
SIGMA 7 8 8 7 7 7 7 7 7 7 7 7
NREJ 0 0 0 0 0 1 7 7 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 61 61 61 61 61 62 61 62 62 61 60 60
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 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 61 61 61 61 60 59 59 59 59 58 58 58
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 0 0 0 0 0 0 0 0 0 0 0
RADIUS 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 59 58 57 57 56 57 57 56 56 56 57 56
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 0 0 0 0 0 0 0 0 0 6 11
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 55 55 54 53 54 53 52 52 52 52 51 50
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 8 0 0 0 0 0 0 0 0 0 0 0
RADIUS 76.0 76.3 76.6 76.9 77.3 77.6 77.9 78.3 78.6 78.9 79.2 79.6
BACKG 51 51 50 48 48 49 48 47 47 47 47 46
SIGMA 7 7 7 6 6 6 6 6 6 6 6 6
NREJ 0 0 0 0 0 0 0 0 0 0 0 0
RADIUS 79.9 80.2 80.5 80.9 81.2 81.5 81.8 82.2 82.5 82.8 83.2 83.5
BACKG 46 46 46 45 45 45 45 44 43 43 43 42
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 0 0 1 4 1 0 0 1 0 0 0 0
RADIUS 83.8 84.1 84.5
BACKG 43 42 21
SIGMA 6 6 3
NREJ 0 0 0
Starting spot search...
sorting 236 spots
Median spot size is 7 x 7 pixels
Total number of spots found: 236
Number rejected as too small on X: 27
Number rejected as too small on Y: 8
Number rejected as too big on X: 2
Number rejected as too big on Y: 0
Number too close (SEPARATION keyword): 0
Number stored as OK: 199
Number of spots found in each bin
10 1 0 3 3 2 1 4
3 1 6 8 6 2 3 6
7 3 3 9 8 3 6 10
7 6 3 5 8 4 3 9
9 2 1 9 7 4 5 9
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 31 spots
Based on a median spot size of 7 by 7 pixels in X and Y, the measurement box
parameters have been set to 21 21 12 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 7 pixels in X and Y, the spot separation
parameters (in X and Y) have been set to 0.73 0.73mm.
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-ntest1_1_002.img
(Q)QOPEN: file opened on unit 1 Status: READONLY
Logical Name: /scisoft/pxsoft/data/dna_040402/ref-ntest1_1_002.img Filename: /scisoft/pxsoft/data/dna_040402/ref-ntest1_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 29 30 30 30 30 30 30 29 29 29 29 29
SIGMA 5 5 5 5 5 5 5 5 5 5 5 5
NREJ 0 1 0 0 0 0 0 1 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 29 29 29 29 29 28 29 29 29 29 29 29
SIGMA 5 5 5 5 5 5 5 5 5 5 5 5
NREJ 0 0 0 0 0 0 0 0 0 0 0 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 29 28 29 29 29 29 28 29 29 29 29 28
SIGMA 5 5 5 5 5 5 5 5 5 5 5 5
NREJ 1 0 0 0 0 0 0 0 0 0 0 0
RADIUS 21.1 21.5 21.8 22.1 22.4 22.8 23.1 23.4 23.7 24.1 24.4 24.7
BACKG 28 28 29 29 28 28 28 29 28 28 28 28
SIGMA 5 5 5 5 5 5 5 5 5 5 5 5
NREJ 0 0 1 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 28 28 28 28 28 28 28 28 28 28 27 28
SIGMA 5 5 5 5 5 5 5 5 5 5 5 5
NREJ 0 0 0 1 0 0 0 0 1 1 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 28 28 28 28 27 28 28 28 28 28 27 27
SIGMA 5 5 5 5 5 5 5 5 5 5 5 5
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 27 27 28 28 28 27 27 28 28 28 27 28
SIGMA 5 5 5 5 5 5 5 5 5 5 5 5
NREJ 1 1 1 0 0 1 2 0 0 0 0 1
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 27 28 28 27 28 28 28 27 27 28 28 29
SIGMA 5 5 5 5 5 5 5 5 5 5 5 5
NREJ 1 2 1 0 0 0 0 0 0 1 8 13
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 28 28 27 27 27 27 27 28 27 27 27 27
SIGMA 5 5 5 5 5 5 5 5 5 5 5 5
NREJ 13 4 1 0 0 0 0 0 1 1 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 27 27 27 27 27 27 27 27 28 27 27 27
SIGMA 5 5 5 5 5 5 5 5 5 5 5 5
NREJ 0 1 0 0 0 0 1 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 26 27 27 27 27 27 27 27 27 27 27 27
SIGMA 5 5 5 5 5 5 5 5 5 5 5 5
NREJ 0 0 0 0 0 0 0 0 1 0 0 0
RADIUS 52.5 52.8 53.1 53.4 53.8 54.1 54.4 54.8 55.1 55.4 55.7 56.1
BACKG 27 27 27 27 27 27 27 27 28 28 28 28
SIGMA 5 5 5 5 5 5 5 5 5 5 5 5
NREJ 0 0 0 0 0 0 0 0 0 0 0 1
RADIUS 56.4 56.7 57.0 57.4 57.7 58.0 58.3 58.7 59.0 59.3 59.6 60.0
BACKG 28 28 28 29 28 29 29 29 29 29 28 29
SIGMA 5 5 5 5 5 5 5 5 5 5 5 5
NREJ 0 0 0 0 1 0 0 0 0 0 1 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 30 30 30 31 31 31 31 31 31 31 32 32
SIGMA 5 5 5 5 5 5 5 5 5 5 5 5
NREJ 0 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 32 32 33 33 33 32 32 32 32 32 32 32
SIGMA 5 5 5 5 5 5 5 5 5 5 5 5
NREJ 0 0 0 0 0 0 0 0 0 0 0 1
RADIUS 68.1 68.5 68.8 69.1 69.4 69.8 70.1 70.4 70.7 71.1 71.4 71.7
BACKG 32 32 31 32 32 32 31 31 31 31 31 30
SIGMA 5 5 5 5 5 5 5 5 5 5 5 5
NREJ 0 0 0 0 0 0 0 0 0 0 1 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 31 30 31 31 31 30 30 31 31 30 29 30
SIGMA 5 5 5 5 5 5 5 5 5 5 5 5
NREJ 0 0 0 0 3 10 12 5 0 0 0 0
RADIUS 76.0 76.3 76.6 76.9 77.3 77.6 77.9 78.3 78.6 78.9 79.2 79.6
BACKG 29 30 29 28 28 28 28 28 28 28 27 27
SIGMA 5 5 5 5 5 5 5 5 5 5 5 5
NREJ 0 0 0 1 1 0 0 0 0 0 0 1
RADIUS 79.9 80.2 80.5 80.9 81.2 81.5 81.8 82.2 82.5 82.8 83.2 83.5
BACKG 27 27 27 27 27 27 27 26 27 26 26 26
SIGMA 5 5 5 5 5 5 5 5 5 5 5 5
NREJ 0 0 0 2 0 0 0 1 0 0 0 0
RADIUS 83.8 84.1 84.5
BACKG 27 26 13
SIGMA 5 5 2
NREJ 0 0 0
Starting spot search...
sorting 218 spots
Median spot size is 8 x 7 pixels
Total number of spots found: 218
Number rejected as too small on X: 14
Number rejected as too small on Y: 7
Number rejected as too big on X: 3
Number rejected as too big on Y: 1
Number too close (SEPARATION keyword): 4
Number stored as OK: 193
Number of spots found in each bin
1 2 2 5 1 1 2 8
10 1 4 6 9 0 4 0
6 3 8 6 7 6 0 11
7 5 0 8 7 2 7 8
5 3 2 9 5 7 0 15
FORMATTED UNKNOWN file opened on unit 10
Logical name: ref-ntest1_1.spt, Filename: ref-ntest1_1.spt
199 spots written for image 1
193 spots written for image 2
A total of 392 spots were written to file
FORMATTED OLD file opened on unit 10
Logical name: ref-ntest1_1.spt, Filename: ref-ntest1_1.spt
DPS Indexing at Two-theta = 0.00 with 382 reflections (minimum spot separation = 0.57mm. 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 1
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 hR 144.79 88.64 54.79 90.0 67.9 100.0 H3,H32 (hexagonal settings of R3 and R32)
43 777 cI 86.69 79.72 88.64 61.6 54.2 64.3 I23,I213,I432,I4132
42 776 cF 104.19 104.23 104.23 112.4 99.8 116.6 F23,F432,F4132
41 748 tI 88.64 104.23 54.79 58.4 90.0 97.1 I4,I41,I422,I4122
40 719 mI 54.79 156.34 58.02 68.1 89.9 69.4 C2
39 692 hR 54.79 79.72 216.47 91.2 104.6 133.3 H3,H32 (hexagonal settings of R3 and R32)
38 664 oF 54.79 128.22 144.92 80.7 112.1 115.2 F222
37 582 oI 79.88 86.69 88.79 54.0 61.5 64.2 I222,I212121
36 582 tI 86.69 79.88 88.79 61.5 54.0 64.2 I4,I41,I422,I4122
35 582 tI 88.79 86.69 79.88 64.2 61.5 54.0 I4,I41,I422,I4122
34 528 oI 54.79 88.64 104.23 82.9 58.4 90.0 I222,I212121
33 498 oF 79.88 79.72 156.34 91.7 120.8 86.7 F222
32 498 mC 79.72 79.88 86.69 64.2 115.7 86.7 C2
31 471 tI 54.79 58.02 156.07 68.2 69.5 89.9 I4,I41,I422,I4122
30 471 oI 54.79 58.02 156.07 111.8 110.5 89.9 I222,I212121
29 443 mC 128.22 54.79 88.64 90.0 126.2 64.8 C2
28 334 hP 58.02 67.12 54.79 89.9 90.1 90.1 P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
27 250 hP 54.79 58.02 67.12 90.1 89.9 90.1 P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
26 250 oC 58.02 146.15 54.79 90.0 90.1 113.3 C222,C2221
25 249 mC 58.02 146.15 54.79 90.0 90.1 66.7 C2
24 249 mC 146.15 58.02 54.79 90.1 90.0 66.7 C2
23 223 mC 144.92 54.79 58.02 89.9 90.0 67.9 C2
22 223 oC 54.79 128.22 67.12 89.9 89.9 115.2 C222,C2221
21 223 oC 54.79 144.92 58.02 90.0 89.9 112.1 C222,C2221
20 222 mC 128.22 54.79 67.12 89.9 90.1 64.8 C2
19 222 mC 54.79 144.92 58.02 90.0 90.1 67.9 C2
18 222 mC 54.79 128.22 67.12 89.9 90.1 64.8 C2
17 113 cP 54.79 58.02 67.12 90.1 89.9 90.1 P23,P213,P432,P4232,P4332,P4132
16 112 hR 79.72 86.59 104.43 99.6 87.5 115.7 H3,H32 (hexagonal settings of R3 and R32)
15 112 hR 79.88 86.59 104.19 99.6 87.6 115.7 H3,H32 (hexagonal settings of R3 and R32)
14 86 tP 58.02 67.12 54.79 89.9 90.1 90.1 P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
13 85 mC 88.79 88.64 54.79 90.0 90.1 98.3 C2
12 85 oC 88.64 88.79 54.79 89.9 90.0 81.7 C222,C2221
11 85 mC 88.79 88.64 54.79 90.0 90.1 81.7 C2
10 29 tP 54.79 58.02 67.12 90.1 89.9 90.1 P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
9 28 oC 79.72 79.88 67.12 90.1 90.0 86.7 C222,C2221
8 28 mC 79.88 79.72 67.12 90.0 90.1 86.7 C2
7 27 mC 79.88 79.72 67.12 90.0 90.1 93.3 C2
6 2 oP 54.79 58.02 67.12 90.1 89.9 90.1 P222,P2221,P21212,P212121
5 1 mP 54.79 58.02 67.12 90.1 89.9 90.1 P2,P21
4 1 mP 54.79 67.12 58.02 90.1 90.1 89.9 P2,P21
3 1 mP 58.02 54.79 67.12 89.9 90.1 90.1 P2,P21
2 0 aP 54.79 58.02 67.12 89.9 89.9 89.9 P1
1 0 aP 54.79 58.02 67.12 90.1 89.9 90.1 P1
No PENALTY SDCELL FRACN LATT a b c alpha beta gamma Possible spacegroups
The solution and direct beam position will now be refined; reflections which deviate by more
than the sigma cutoff from their calculated position will be excluded from the refinement.
Refining solution # 6 with P222 (number 16) symmetry imposed
Initial cell (before refinement) is 54.7895 58.0195 67.1157 90.000 90.000 90.000
Using 375 indexed reflections (out of 382 spots found, {delta(XY) <= 2.5 sigma}),
final sd in spot positions is 0.10mm and in phi 0.29 degrees
Refined cell parameters 54.79 58.07 67.20 90.00 90.00 90.00
Beam coordinates of 93.58 92.24 have been refined to 93.59 91.96
This is a shift of 0.29mm or 0.083 times the minimum spot separation of ca 3.47mm.
Final cell (after refinement) is 54.7869 58.0682 67.2004 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 9441.932 9195.560
****** 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-ntest1_1.gen Filename: ref-ntest1_1.gen
Title for MTZ and GENERATE Files (TITLE):
.
Crystal identifier (IDENT): ref-ntest1_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= 19
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 25 53 46 51 69 56 66 57 46 65 54 1 0 2 0 0 0 0 0
No gained 1 0
Total intensity 74557 80652 83769 88345 94098 96848 99914 99942 99950 99977 99998 99998 99998 99996 99996 99996 99996 99996 99996
Total intensity 99995 99995
SD of intensity 122 125 128 132 138 140 145 145 145 145 146 146 146 146 146 146 146 146 146
SD of intensity 146 146
The mosaicity has been estimated as ---> 0.50 <--- for this image only;
This value can be used cautiously as an initial estimate.
Storing space group from DPS autoindexing: P222 number 16
Storing space group from DPS autoindexing: P222 number 16
*********** END OF PROCESSING *****************
/n