Index results for dntr_1
Symmetry and refined cell parameters
Image |
Symmetry |
a |
b |
c |
alpha |
beta |
gamma |
1 |
P3 |
107.093 |
107.093 |
296.616 |
90.000 |
90.000 |
120.000 |
2 |
H3 |
107.267 |
107.267 |
894.683 |
90.000 |
90.000 |
120.000 |
1+2 |
P3 |
107.092 |
107.092 |
296.674 |
90.000 |
90.000 |
120.000 |
Spots found, rejected, RMS spot deviation, beamcentre shift
Image |
Spots found |
Spots rejected |
Fraction |
RMS spot deviation |
Beam shift x |
Beam shift y |
1 |
274 |
1 |
0.004 |
0.040 |
0.080 |
-0.065 |
2 |
173 |
0 |
0.000 |
0.650 |
0.110 |
0.035 |
1+2 |
447 |
1 |
0.002 |
0.050 |
0.080 |
-0.065 |
Image 1: /scisoft/pxsoft/data/dna_061202/ref-dntr_1_001.img
Image 2: /scisoft/pxsoft/data/dna_061202/ref-dntr_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-dntr_1_###.img
===> directory /scisoft/pxsoft/data/dna_061202
===> detector adsc
===> beam 93.630000 95.185000
===> autoindex threshold 10 dps image 1
Using DPS code for background indexing
===> mosaic estimate
===> go
(Q)QOPEN: file opened on unit 1 Status: READONLY
Logical Name: /scisoft/pxsoft/data/dna_061202/ref-dntr_1_001.img Filename: /scisoft/pxsoft/data/dna_061202/ref-dntr_1_001.img
Crystal to detector distance of 249.99mm taken from image header
Wavelength of 0.93400A taken from image header
Pixel size of 0.0816mm taken from image header.
IBEAM = 2 it should be 2
Input beam coordinates 93.63mm 95.18mm will be used
Autoindexing image 1
=======================
image FILENAME: /scisoft/pxsoft/data/dna_061202/ref-dntr_1_001.img
(Q)QOPEN: file opened on unit 1 Status: READONLY
Logical Name: /scisoft/pxsoft/data/dna_061202/ref-dntr_1_001.img Filename: /scisoft/pxsoft/data/dna_061202/ref-dntr_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 82 spots
Threshold set to 4.3
sorting 87 spots
Threshold set to 4.2
Finding spots on image 1 (Midpoint of phi 0.250 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 163 163 163 163 164 163 164 163 163 166 166 166
SIGMA 12 12 12 12 12 12 12 12 12 12 12 12
NREJ 0 0 0 0 0 0 0 0 0 0 0 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 167 165 164 164 166 163 164 165 165 166 165 166
SIGMA 12 12 12 12 12 12 12 12 12 12 12 12
NREJ 2 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 164 166 167 166 166 166 166 166 164 162 163 163
SIGMA 12 12 12 12 12 12 12 12 12 12 12 12
NREJ 0 0 0 0 0 0 0 0 1 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 162 163 164 163 161 162 159 158 158 159 157 157
SIGMA 12 12 12 12 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 156 156 156 156 153 154 154 153 153 151 154 150
SIGMA 12 12 12 12 12 12 12 12 12 12 12 12
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 149 151 151 148 148 148 148 147 147 148 146 144
SIGMA 12 12 12 12 12 12 12 12 12 12 12 12
NREJ 0 0 1 0 0 0 0 0 0 0 0 0
RADIUS 32.9 33.2 33.5 33.9 34.2 34.5 34.8 35.2 35.5 35.8 36.1 36.5
BACKG 145 146 144 144 144 142 143 143 142 141 143 144
SIGMA 12 12 12 12 12 11 11 11 11 11 11 11
NREJ 0 0 0 1 0 0 0 0 0 0 1 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 142 141 140 142 141 141 140 139 140 140 139 139
SIGMA 11 11 11 11 11 11 11 11 11 11 11 11
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 138 139 139 139 139 138 139 139 137 137 139 140
SIGMA 11 11 11 11 11 11 11 11 11 11 11 11
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 139 140 139 141 138 139 140 139 141 141 140 141
SIGMA 11 11 11 11 11 11 11 11 11 11 11 11
NREJ 0 0 0 0 1 0 0 1 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 143 143 144 143 144 145 145 147 149 149 150 151
SIGMA 11 11 12 11 11 12 12 12 12 12 12 12
NREJ 0 0 0 1 0 0 1 0 0 0 1 0
RADIUS 52.5 52.8 53.1 53.4 53.8 54.1 54.4 54.8 55.1 55.4 55.7 56.1
BACKG 152 152 155 158 158 160 160 159 159 158 158 159
SIGMA 12 12 12 12 12 12 12 12 12 12 12 12
NREJ 0 0 0 0 0 0 1 1 0 2 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 158 158 157 158 158 158 159 158 161 158 158 158
SIGMA 12 12 12 12 12 12 12 12 12 12 12 12
NREJ 0 0 0 1 0 2 0 0 0 0 0 0
RADIUS 60.3 60.6 61.0 61.3 61.6 61.9 62.3 62.6 62.9 63.2 63.6 63.9
BACKG 160 163 163 161 164 164 167 165 166 166 166 168
SIGMA 12 12 12 12 12 12 12 12 12 12 12 12
NREJ 0 1 4 2 1 1 0 0 2 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 168 166 167 166 165 164 162 163 161 158 158 157
SIGMA 12 12 12 12 12 12 12 12 12 12 12 12
NREJ 0 0 0 0 0 0 2 0 1 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 158 156 152 152 151 152 150 149 147 145 147 146
SIGMA 12 12 12 12 12 12 12 12 12 12 12 12
NREJ 0 0 0 0 0 0 0 0 0 1 0 0
RADIUS 72.1 72.4 72.7 73.0 73.4 73.7 74.0 74.3 74.7 75.0 75.3 75.6
BACKG 143 144 142 144 141 142 141 139 139 136 135 135
SIGMA 11 12 11 11 11 11 11 11 11 11 11 11
NREJ 0 0 1 0 0 0 0 0 0 2 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 137 134 134 134 131 131 130 129 129 127 128 126
SIGMA 11 11 11 11 11 11 11 11 11 11 11 11
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 127 126 125 125 126 124 123 123 122 121 119 119
SIGMA 11 11 11 11 11 11 11 11 11 11 10 10
NREJ 0 1 0 0 0 0 0 0 0 0 0 0
RADIUS 83.8 84.1 84.5
BACKG 119 118 58
SIGMA 10 10 5
NREJ 0 0 0
Starting spot search...
sorting 274 spots
Median spot size is 3 x 3 pixels
Total number of spots found: 274
Number rejected as too small on X: 0
Number rejected as too small on Y: 0
Number rejected as too big on X: 1
Number rejected as too big on Y: 0
Number too close (SEPARATION keyword): 0
Number stored as OK: 273
Number of spots found in each bin
14 8 6 8 10 7 7 17
13 8 8 9 14 3 6 12
12 5 12 12 12 14 7 9
5 4 7 3 4 3 4 4
0 0 3 0 0 0 2 1
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 88 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-dntr_1.spt, Filename: ref-dntr_1.spt
273 spots written for image 1
A total of 273 spots were written to file
FORMATTED OLD file opened on unit 10
Logical name: ref-dntr_1.spt, Filename: ref-dntr_1.spt
DPS Indexing at Two-theta = 0.00 with 225 reflections (minimum spot separation = 0.33mm. Maximum expected cell edge 306.54, Beam position is 93.63 95.18
Generating direct lattice vectors (This may take some time):
|-----------------|
..................
Refining 30 direct space vectors:
|----------------------------|
..............................
selected 11
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 314.72 107.89 315.88 80.2 34.3 80.3 I23,I213,I432,I4132
43 995 hR 350.74 315.04 107.27 80.6 90.2 50.4 H3,H32 (hexagonal settings of R3 and R32)
42 940 cF 315.73 349.03 315.35 142.6 40.0 142.8 F23,F432,F4132
41 937 tI 315.04 315.35 107.27 80.5 99.4 145.5 I4,I41,I422,I4122
40 890 tI 314.72 107.89 315.88 80.2 34.3 80.3 I4,I41,I422,I4122
39 890 hP 107.27 296.53 107.64 89.8 119.7 90.3 P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
38 841 tI 315.88 314.72 107.89 80.3 80.2 34.3 I4,I41,I422,I4122
37 837 oI 107.89 314.72 315.88 34.3 80.2 80.3 I222,I212121
36 832 oI 107.27 315.04 315.35 34.5 80.5 80.6 I222,I212121
35 785 tP 107.64 296.53 107.27 90.3 119.7 89.8 P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
34 785 cP 107.27 107.64 296.53 89.8 90.3 119.7 P23,P213,P432,P4232,P4332,P4132
33 785 hR 185.86 314.72 315.73 145.6 90.2 106.8 H3,H32 (hexagonal settings of R3 and R32)
32 783 oC 315.88 315.04 107.27 80.6 100.1 39.9 C222,C2221
31 780 hR 107.89 314.72 350.88 129.9 90.0 99.7 H3,H32 (hexagonal settings of R3 and R32)
30 780 mC 315.88 315.04 107.27 80.6 100.1 39.9 C2
29 779 mC 315.88 315.04 107.27 99.4 100.1 140.1 C2
28 214 hR 107.27 107.89 907.72 90.2 99.9 120.0 H3,H32 (hexagonal settings of R3 and R32)
27 211 oF 107.27 186.93 602.04 89.9 99.9 90.2 F222
26 176 tI 107.27 107.64 602.98 94.9 95.5 119.7 I4,I41,I422,I4122
25 175 oI 107.27 107.64 602.59 84.6 85.2 119.7 I222,I212121
24 163 mI 107.64 602.59 107.27 85.2 119.7 84.6 C2
23 163 oC 107.27 602.04 107.64 85.2 119.7 99.9 C222,C2221
22 163 oC 107.27 602.04 107.64 85.2 119.7 99.9 C222,C2221
21 162 mC 602.04 107.27 107.64 119.7 94.8 80.1 C2
20 161 mC 602.04 107.27 107.64 119.7 94.8 80.1 C2
19 158 mC 107.64 602.30 107.27 94.7 119.7 79.9 C2
18 158 mC 107.27 602.04 107.64 94.8 119.7 80.1 C2
17 115 oF 107.89 185.86 602.59 90.4 100.2 89.8 F222
16 112 mC 185.86 107.89 314.72 80.3 106.8 89.8 C2
15 63 mC 186.30 107.64 349.47 90.4 122.0 89.6 C2
14 60 tP 107.27 107.64 296.53 89.8 90.3 119.7 P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
13 59 oP 107.27 107.64 296.53 89.8 90.3 119.7 P222,P2221,P21212,P212121
12 58 mP 107.64 107.27 296.53 90.3 89.8 119.7 P2,P21
11 57 mP 107.27 107.64 296.53 89.8 90.3 119.7 P2,P21
10 6 hP 107.27 107.64 296.53 89.8 90.3 119.7 P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
9 5 oC 107.89 185.86 296.53 89.7 90.1 89.8 C222,C2221
8 5 mC 107.89 185.86 296.53 89.7 90.1 89.8 C2
7 5 oC 107.27 186.93 296.53 90.1 90.3 90.2 C222,C2221
6 4 mC 186.93 107.27 296.53 90.3 89.9 89.8 C2
5 4 mP 107.27 296.53 107.64 89.8 119.7 90.3 P2,P21
4 1 mC 107.27 186.93 296.53 89.9 90.3 89.8 C2
3 1 mC 185.86 107.89 296.53 90.1 90.3 90.2 C2
2 1 aP 107.27 107.64 296.53 89.8 90.3 119.7 P1
1 0 aP 107.27 107.64 296.53 89.8 89.7 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 #10 with P3 (number 143) symmetry imposed
Initial cell (before refinement) is 107.4513 107.4513 296.5257 90.000 90.000 120.000
Using 218 indexed reflections (out of 225 spots found, {delta(XY) <= 2.5 sigma}),
final sd in spot positions is 0.04mm and in phi 0.11 degrees
Refined cell parameters 107.09 107.09 296.62 90.00 90.00 120.00
Beam coordinates of 93.63 95.18 have been refined to 93.71 95.12
This is a shift of 0.10mm or 0.129 times the minimum spot separation of ca 0.79mm.
Final cell (after refinement) is 107.0925 107.0925 296.6158 90.000 90.000 120.000
FORMATTED UNKNOWN file opened on unit 12
Logical name: autoindex.mat, Filename: autoindex.mat
Updating the stored central beam position from 9363.000 9518.500 to 9430.001 9511.762
****** INFORMATION *****
****** INFORMATION *****
****** INFORMATION *****
The cell derived from autoindexing will override that given on the CELL keyword.
To force the program to use the input cell, add the keyword KEEP. eg:
CELL KEEP 74.2 74.2 35.1 90 90 90
**** WARNING ****
Because input wavelength ( 0.9340) is not CuKa (1.5418) or Mo (0.7107),
source is assumed to be a synchrotron and synchrotron defaults for polarisation and beam divergence
will be used if these have not been defined explicitly (SYNCH POLAR and DIVH/DIVV keywords.
(Q)QOPEN: file opened on unit 1 Status: UNKNOWN
Logical Name: ref-dntr_1.gen Filename: ref-dntr_1.gen
Title for MTZ and GENERATE Files (TITLE):
.
Crystal identifier (IDENT): ref-dntr_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= 81
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 0 400 393 421 376 394 395 402 396 387 375 392 400 394 420 399 370 377 382
No gained 366 386
Total intensity 82400 89521 93788 96642 97399 97863 98418 98680 98851 99184 99497 99467 99507 99638 99608 99769 99860 99910 99991
Total intensity 99951 99789
SD of intensity 464 484 504 525 545 555 575 585 605 615 625 646 656 666 686 696 706 716 726
SD of intensity 736 746
The mosaicity has been estimated as ---> 0.24 <--- for this image only;
This value can be used cautiously as an initial estimate.
Storing space group from DPS autoindexing: P3 number 143
*********** 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-dntr_1_###.img
===> directory /scisoft/pxsoft/data/dna_061202
===> detector adsc
===> beam 93.630000 95.185000
===> autoindex threshold 10 dps image 2
Using DPS code for background indexing
===> mosaic estimate
===> go
(Q)QOPEN: file opened on unit 1 Status: READONLY
Logical Name: /scisoft/pxsoft/data/dna_061202/ref-dntr_1_002.img Filename: /scisoft/pxsoft/data/dna_061202/ref-dntr_1_002.img
Crystal to detector distance of 249.99mm taken from image header
Wavelength of 0.93400A taken from image header
Pixel size of 0.0816mm taken from image header.
IBEAM = 2 it should be 2
Input beam coordinates 93.63mm 95.18mm will be used
Autoindexing image 2
=======================
image FILENAME: /scisoft/pxsoft/data/dna_061202/ref-dntr_1_002.img
(Q)QOPEN: file opened on unit 1 Status: READONLY
Logical Name: /scisoft/pxsoft/data/dna_061202/ref-dntr_1_002.img Filename: /scisoft/pxsoft/data/dna_061202/ref-dntr_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 74 spots
Threshold set to 4.2
sorting 85 spots
Threshold set to 4.1
Finding spots on image 2 (Midpoint of phi 89.750 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 161 161 161 164 163 163 162 161 163 163 163 163
SIGMA 12 12 12 12 12 12 12 12 12 12 12 12
NREJ 0 0 0 0 0 0 0 0 0 0 0 0
RADIUS 13.3 13.6 14.0 14.3 14.6 14.9 15.3 15.6 15.9 16.2 16.6 16.9
BACKG 163 162 163 165 165 165 163 163 163 167 164 164
SIGMA 12 12 12 12 12 12 12 12 12 12 12 12
NREJ 0 0 0 0 4 0 0 0 0 0 0 0
RADIUS 17.2 17.5 17.9 18.2 18.5 18.8 19.2 19.5 19.8 20.2 20.5 20.8
BACKG 165 164 164 164 163 166 165 163 164 162 164 163
SIGMA 12 12 12 12 12 12 12 12 12 12 12 12
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 163 161 161 161 159 159 158 157 157 158 159 156
SIGMA 12 12 12 12 12 12 12 12 12 12 12 12
NREJ 0 0 0 0 0 1 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 155 156 155 152 153 152 153 151 151 151 150 148
SIGMA 12 12 12 12 12 12 12 12 12 12 12 12
NREJ 0 2 2 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 149 148 148 148 148 147 148 147 145 146 144 145
SIGMA 12 12 12 12 12 12 12 12 12 12 12 12
NREJ 0 0 0 0 0 0 1 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 145 143 144 144 143 142 143 142 142 141 141 140
SIGMA 12 11 12 11 11 11 11 11 11 11 11 11
NREJ 0 0 0 0 0 0 0 0 0 1 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 141 142 141 140 141 141 140 140 138 137 139 140
SIGMA 11 11 11 11 11 11 11 11 11 11 11 11
NREJ 0 0 0 1 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 139 137 140 138 138 140 139 140 138 138 139 140
SIGMA 11 11 11 11 11 11 11 11 11 11 11 11
NREJ 0 0 0 0 2 0 0 0 0 1 1 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 140 141 140 140 140 143 143 141 141 142 144 144
SIGMA 11 11 11 11 11 11 11 11 11 11 11 12
NREJ 2 2 0 0 0 0 2 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 146 145 147 145 147 150 152 152 154 156 161 162
SIGMA 12 12 12 12 12 12 12 12 12 12 12 12
NREJ 0 0 0 0 0 0 0 1 0 0 0 1
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 164 169 173 179 180 178 178 180 178 175 174 171
SIGMA 12 13 13 13 13 13 13 13 13 13 13 13
NREJ 0 0 0 0 0 0 1 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 172 168 167 167 167 168 167 166 168 169 167 168
SIGMA 13 12 12 12 12 12 12 12 12 12 12 12
NREJ 0 0 0 0 0 0 0 0 0 0 0 0
RADIUS 60.3 60.6 61.0 61.3 61.6 61.9 62.3 62.6 62.9 63.2 63.6 63.9
BACKG 170 171 174 175 175 177 181 182 183 184 185 185
SIGMA 13 13 13 13 13 13 13 13 13 13 13 13
NREJ 0 0 2 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 184 183 183 184 181 179 177 174 170 170 168 167
SIGMA 13 13 13 13 13 13 13 13 13 13 12 12
NREJ 0 1 1 0 0 2 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 162 162 161 159 157 153 153 153 150 150 149 148
SIGMA 12 12 12 12 12 12 12 12 12 12 12 12
NREJ 0 0 1 0 0 1 0 1 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 147 145 144 143 143 142 141 140 138 137 138 137
SIGMA 12 12 12 11 11 11 11 11 11 11 11 11
NREJ 0 1 0 0 0 1 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 135 134 134 134 132 132 130 131 131 129 127 127
SIGMA 11 11 11 11 11 11 11 11 11 11 11 11
NREJ 0 0 0 0 1 0 0 0 0 0 1 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 127 126 126 125 124 124 121 122 121 119 119 120
SIGMA 11 11 11 11 11 11 11 11 10 10 10 10
NREJ 0 0 0 0 0 0 0 1 0 0 0 0
RADIUS 83.8 84.1 84.5
BACKG 118 116 59
SIGMA 10 10 5
NREJ 0 0 0
Starting spot search...
sorting 173 spots
Median spot size is 4 x 3 pixels
Total number of spots found: 173
Number rejected as too small on X: 0
Number rejected as too small on Y: 0
Number rejected as too big on X: 0
Number rejected as too big on Y: 0
Number too close (SEPARATION keyword): 0
Number stored as OK: 173
Number of spots found in each bin
12 10 5 8 10 2 6 15
5 4 5 2 4 5 8 6
4 8 6 4 5 4 6 4
2 0 3 2 4 3 4 2
0 2 1 0 1 0 0 1
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 85 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-dntr_1.spt, Filename: ref-dntr_1.spt
173 spots written for image 2
A total of 173 spots were written to file
FORMATTED OLD file opened on unit 10
Logical name: ref-dntr_1.spt, Filename: ref-dntr_1.spt
DPS Indexing at Two-theta = 0.00 with 140 reflections (minimum spot separation = 0.33mm. Maximum expected cell edge 267.65, Beam position is 93.63 95.18
Generating direct lattice vectors (This may take some time):
|-----------------|
..................
Refining 30 direct space vectors:
|----------------------------|
..............................
selected 15
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 316.57 106.93 313.44 80.3 33.6 80.4 I23,I213,I432,I4132
43 987 hR 350.68 313.60 105.67 81.5 90.4 49.7 H3,H32 (hexagonal settings of R3 and R32)
42 930 cF 315.35 345.49 315.69 143.1 39.6 143.1 F23,F432,F4132
41 920 tI 313.44 315.69 105.64 81.0 98.6 145.9 I4,I41,I422,I4122
40 893 tI 313.44 106.93 316.57 80.4 33.6 80.3 I4,I41,I422,I4122
39 891 hP 105.67 296.85 105.64 89.1 119.2 91.0 P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
38 856 tI 313.44 316.57 106.93 80.4 80.3 33.6 I4,I41,I422,I4122
37 846 oI 106.93 316.57 313.44 33.6 80.3 80.4 I222,I212121
36 833 oI 105.67 313.60 315.35 34.1 81.0 81.5 I222,I212121
35 800 tP 105.67 296.85 105.64 89.1 119.2 91.0 P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
34 800 cP 105.64 105.67 296.85 91.0 89.1 119.2 P23,P213,P432,P4232,P4332,P4132
33 795 oC 313.44 316.75 105.64 79.8 98.6 39.2 C222,C2221
32 795 hR 182.27 313.60 315.35 145.9 91.0 105.9 H3,H32 (hexagonal settings of R3 and R32)
31 785 mC 316.57 313.60 105.67 81.5 100.3 39.2 C2
30 781 mC 316.57 313.60 105.67 98.5 100.3 140.8 C2
29 781 hR 106.93 313.60 351.18 130.9 89.9 99.9 H3,H32 (hexagonal settings of R3 and R32)
28 197 hR 105.64 106.93 905.74 89.9 99.1 120.4 H3,H32 (hexagonal settings of R3 and R32)
27 187 oF 105.64 184.50 601.47 89.3 99.3 90.8 F222
26 169 tI 105.64 106.93 601.30 95.0 94.1 120.4 I4,I41,I422,I4122
25 166 oI 105.64 106.93 601.30 85.0 85.9 120.4 I222,I212121
24 157 mI 105.64 603.08 105.67 85.8 119.2 84.0 C2
23 157 oC 105.67 601.30 105.64 85.9 119.2 99.2 C222,C2221
22 157 oC 105.67 601.30 105.64 85.9 119.2 99.2 C222,C2221
21 153 mC 601.30 105.67 105.64 119.2 94.1 80.8 C2
20 153 mC 601.30 105.67 105.64 119.2 94.1 80.8 C2
19 140 mC 105.67 601.30 105.64 94.1 119.2 80.8 C2
18 139 mC 105.64 601.47 105.67 94.0 119.2 80.7 C2
17 122 oF 106.93 182.27 603.08 89.0 100.1 90.0 F222
16 113 mC 182.27 106.93 316.57 80.4 107.8 90.0 C2
15 66 oP 105.64 105.67 296.85 91.0 89.1 119.2 P222,P2221,P21212,P212121
14 66 tP 105.64 105.67 296.85 91.0 89.1 119.2 P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
13 61 mP 105.67 105.64 296.85 89.1 91.0 119.2 P2,P21
12 61 mP 105.67 105.64 296.85 89.1 91.0 119.2 P2,P21
11 51 mC 182.27 106.93 345.49 89.9 120.8 90.0 C2
10 17 hP 105.64 105.67 296.85 91.0 89.1 119.2 P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
9 16 oC 105.64 184.50 296.85 89.4 89.1 90.8 C222,C2221
8 14 oC 106.93 182.27 296.85 91.0 90.1 90.0 C222,C2221
7 14 mC 106.93 182.27 296.85 91.0 90.1 90.0 C2
6 14 mP 105.64 296.85 105.67 91.0 119.2 89.1 P2,P21
5 11 mC 184.50 105.64 296.85 89.1 90.6 89.2 C2
4 7 mC 105.67 184.45 296.85 89.6 91.0 89.2 C2
3 4 aP 105.64 105.67 296.85 91.0 89.1 119.2 P1
2 1 mC 182.27 106.93 296.85 89.9 91.0 90.0 C2
1 0 aP 105.64 105.67 296.85 89.0 89.1 60.8 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 #28 with H3 (number 146) symmetry imposed
Initial cell (before refinement) is 106.2866 106.2866 905.7405 90.000 90.000 120.000
Using 140 indexed reflections (out of 140 spots found, {delta(XY) <= 2.5 sigma}),
final sd in spot positions is 0.65mm and in phi 0.96 degrees
Refined cell parameters 107.27 107.27 894.68 90.00 90.00 120.00
Beam coordinates of 93.63 95.18 have been refined to 93.74 95.22
***** WARNING ***** WARNING ***** WARNING ***** WARNING ***** WARNING ***** WARNING
This is a shift of 0.12mm or 0.452 times the minimum spot separation of ca 0.26mm.
Final cell (after refinement) is 107.2668 107.2668 894.6829 90.000 90.000 120.000
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 9426.329 9521.846
****** INFORMATION *****
****** INFORMATION *****
****** INFORMATION *****
The cell derived from autoindexing will override that given on the CELL keyword.
To force the program to use the input cell, add the keyword KEEP. eg:
CELL KEEP 74.2 74.2 35.1 90 90 90
**** WARNING ****
Because input wavelength ( 0.9340) is not CuKa (1.5418) or Mo (0.7107),
source is assumed to be a synchrotron and synchrotron defaults for polarisation and beam divergence
will be used if these have not been defined explicitly (SYNCH POLAR and DIVH/DIVV keywords.
(Q)QOPEN: file opened on unit 1 Status: UNKNOWN
Logical Name: ref-dntr_1.gen Filename: ref-dntr_1.gen
Title for MTZ and GENERATE Files (TITLE):
.
Crystal identifier (IDENT): ref-dntr_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= 80
Beam divergence refinement
Beam divergence refinement
Beam divergence refinement
More than 1000 Reflections LOST/GAINED per STEP
RERUN with smaller STEP SIZE
************ 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-dntr_1_###.img
===> directory /scisoft/pxsoft/data/dna_061202
===> detector adsc
===> beam 93.630000 95.185000
===> autoindex threshold 10 dps image 1
Using DPS code for background indexing
===> autoindex threshold 10 dps image 2
Using DPS code for background indexing
===> mosaic estimate
===> go
(Q)QOPEN: file opened on unit 1 Status: READONLY
Logical Name: /scisoft/pxsoft/data/dna_061202/ref-dntr_1_001.img Filename: /scisoft/pxsoft/data/dna_061202/ref-dntr_1_001.img
Crystal to detector distance of 249.99mm taken from image header
Wavelength of 0.93400A taken from image header
Pixel size of 0.0816mm taken from image header.
IBEAM = 2 it should be 2
Input beam coordinates 93.63mm 95.18mm will be used
Autoindexing using 2 images
Image numbers: 1 2
image FILENAME: /scisoft/pxsoft/data/dna_061202/ref-dntr_1_001.img
(Q)QOPEN: file opened on unit 1 Status: READONLY
Logical Name: /scisoft/pxsoft/data/dna_061202/ref-dntr_1_001.img Filename: /scisoft/pxsoft/data/dna_061202/ref-dntr_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 82 spots
Threshold set to 4.3
sorting 87 spots
Threshold set to 4.2
Finding spots on image 1 (Midpoint of phi 0.250 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 163 163 163 163 164 163 164 163 163 166 166 166
SIGMA 12 12 12 12 12 12 12 12 12 12 12 12
NREJ 0 0 0 0 0 0 0 0 0 0 0 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 167 165 164 164 166 163 164 165 165 166 165 166
SIGMA 12 12 12 12 12 12 12 12 12 12 12 12
NREJ 2 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 164 166 167 166 166 166 166 166 164 162 163 163
SIGMA 12 12 12 12 12 12 12 12 12 12 12 12
NREJ 0 0 0 0 0 0 0 0 1 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 162 163 164 163 161 162 159 158 158 159 157 157
SIGMA 12 12 12 12 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 156 156 156 156 153 154 154 153 153 151 154 150
SIGMA 12 12 12 12 12 12 12 12 12 12 12 12
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 149 151 151 148 148 148 148 147 147 148 146 144
SIGMA 12 12 12 12 12 12 12 12 12 12 12 12
NREJ 0 0 1 0 0 0 0 0 0 0 0 0
RADIUS 32.9 33.2 33.5 33.9 34.2 34.5 34.8 35.2 35.5 35.8 36.1 36.5
BACKG 145 146 144 144 144 142 143 143 142 141 143 144
SIGMA 12 12 12 12 12 11 11 11 11 11 11 11
NREJ 0 0 0 1 0 0 0 0 0 0 1 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 142 141 140 142 141 141 140 139 140 140 139 139
SIGMA 11 11 11 11 11 11 11 11 11 11 11 11
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 138 139 139 139 139 138 139 139 137 137 139 140
SIGMA 11 11 11 11 11 11 11 11 11 11 11 11
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 139 140 139 141 138 139 140 139 141 141 140 141
SIGMA 11 11 11 11 11 11 11 11 11 11 11 11
NREJ 0 0 0 0 1 0 0 1 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 143 143 144 143 144 145 145 147 149 149 150 151
SIGMA 11 11 12 11 11 12 12 12 12 12 12 12
NREJ 0 0 0 1 0 0 1 0 0 0 1 0
RADIUS 52.5 52.8 53.1 53.4 53.8 54.1 54.4 54.8 55.1 55.4 55.7 56.1
BACKG 152 152 155 158 158 160 160 159 159 158 158 159
SIGMA 12 12 12 12 12 12 12 12 12 12 12 12
NREJ 0 0 0 0 0 0 1 1 0 2 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 158 158 157 158 158 158 159 158 161 158 158 158
SIGMA 12 12 12 12 12 12 12 12 12 12 12 12
NREJ 0 0 0 1 0 2 0 0 0 0 0 0
RADIUS 60.3 60.6 61.0 61.3 61.6 61.9 62.3 62.6 62.9 63.2 63.6 63.9
BACKG 160 163 163 161 164 164 167 165 166 166 166 168
SIGMA 12 12 12 12 12 12 12 12 12 12 12 12
NREJ 0 1 4 2 1 1 0 0 2 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 168 166 167 166 165 164 162 163 161 158 158 157
SIGMA 12 12 12 12 12 12 12 12 12 12 12 12
NREJ 0 0 0 0 0 0 2 0 1 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 158 156 152 152 151 152 150 149 147 145 147 146
SIGMA 12 12 12 12 12 12 12 12 12 12 12 12
NREJ 0 0 0 0 0 0 0 0 0 1 0 0
RADIUS 72.1 72.4 72.7 73.0 73.4 73.7 74.0 74.3 74.7 75.0 75.3 75.6
BACKG 143 144 142 144 141 142 141 139 139 136 135 135
SIGMA 11 12 11 11 11 11 11 11 11 11 11 11
NREJ 0 0 1 0 0 0 0 0 0 2 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 137 134 134 134 131 131 130 129 129 127 128 126
SIGMA 11 11 11 11 11 11 11 11 11 11 11 11
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 127 126 125 125 126 124 123 123 122 121 119 119
SIGMA 11 11 11 11 11 11 11 11 11 11 10 10
NREJ 0 1 0 0 0 0 0 0 0 0 0 0
RADIUS 83.8 84.1 84.5
BACKG 119 118 58
SIGMA 10 10 5
NREJ 0 0 0
Starting spot search...
sorting 274 spots
Median spot size is 3 x 3 pixels
Total number of spots found: 274
Number rejected as too small on X: 0
Number rejected as too small on Y: 0
Number rejected as too big on X: 1
Number rejected as too big on Y: 0
Number too close (SEPARATION keyword): 0
Number stored as OK: 273
Number of spots found in each bin
14 8 6 8 10 7 7 17
13 8 8 9 14 3 6 12
12 5 12 12 12 14 7 9
5 4 7 3 4 3 4 4
0 0 3 0 0 0 2 1
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 88 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_061202/ref-dntr_1_002.img
(Q)QOPEN: file opened on unit 1 Status: READONLY
Logical Name: /scisoft/pxsoft/data/dna_061202/ref-dntr_1_002.img Filename: /scisoft/pxsoft/data/dna_061202/ref-dntr_1_002.img
Finding spots on image 2 (Midpoint of phi 89.750 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 161 161 161 164 163 163 162 161 163 163 163 163
SIGMA 12 12 12 12 12 12 12 12 12 12 12 12
NREJ 0 0 0 0 0 0 0 0 0 0 0 0
RADIUS 13.3 13.6 14.0 14.3 14.6 14.9 15.3 15.6 15.9 16.2 16.6 16.9
BACKG 163 162 163 165 165 165 163 163 163 167 164 164
SIGMA 12 12 12 12 12 12 12 12 12 12 12 12
NREJ 0 0 0 0 4 0 0 0 0 0 0 0
RADIUS 17.2 17.5 17.9 18.2 18.5 18.8 19.2 19.5 19.8 20.2 20.5 20.8
BACKG 165 164 164 164 163 166 165 163 164 162 164 163
SIGMA 12 12 12 12 12 12 12 12 12 12 12 12
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 163 161 161 161 159 159 158 157 157 158 159 156
SIGMA 12 12 12 12 12 12 12 12 12 12 12 12
NREJ 0 0 0 0 0 1 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 155 156 155 152 153 152 153 151 151 151 150 148
SIGMA 12 12 12 12 12 12 12 12 12 12 12 12
NREJ 0 2 2 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 149 148 148 148 148 147 148 147 145 146 144 145
SIGMA 12 12 12 12 12 12 12 12 12 12 12 12
NREJ 0 0 0 0 0 0 1 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 145 143 144 144 143 142 143 142 142 141 141 140
SIGMA 12 11 12 11 11 11 11 11 11 11 11 11
NREJ 0 0 0 0 0 0 0 0 0 1 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 141 142 141 140 141 141 140 140 138 137 139 140
SIGMA 11 11 11 11 11 11 11 11 11 11 11 11
NREJ 0 0 0 1 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 139 137 140 138 138 140 139 140 138 138 139 140
SIGMA 11 11 11 11 11 11 11 11 11 11 11 11
NREJ 0 0 0 0 2 0 0 0 0 1 1 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 140 141 140 140 140 143 143 141 141 142 144 144
SIGMA 11 11 11 11 11 11 11 11 11 11 11 12
NREJ 2 2 0 0 0 0 2 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 146 145 147 145 147 150 152 152 154 156 161 162
SIGMA 12 12 12 12 12 12 12 12 12 12 12 12
NREJ 0 0 0 0 0 0 0 1 0 0 0 1
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 164 169 173 179 180 178 178 180 178 175 174 171
SIGMA 12 13 13 13 13 13 13 13 13 13 13 13
NREJ 0 0 0 0 0 0 1 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 172 168 167 167 167 168 167 166 168 169 167 168
SIGMA 13 12 12 12 12 12 12 12 12 12 12 12
NREJ 0 0 0 0 0 0 0 0 0 0 0 0
RADIUS 60.3 60.6 61.0 61.3 61.6 61.9 62.3 62.6 62.9 63.2 63.6 63.9
BACKG 170 171 174 175 175 177 181 182 183 184 185 185
SIGMA 13 13 13 13 13 13 13 13 13 13 13 13
NREJ 0 0 2 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 184 183 183 184 181 179 177 174 170 170 168 167
SIGMA 13 13 13 13 13 13 13 13 13 13 12 12
NREJ 0 1 1 0 0 2 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 162 162 161 159 157 153 153 153 150 150 149 148
SIGMA 12 12 12 12 12 12 12 12 12 12 12 12
NREJ 0 0 1 0 0 1 0 1 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 147 145 144 143 143 142 141 140 138 137 138 137
SIGMA 12 12 12 11 11 11 11 11 11 11 11 11
NREJ 0 1 0 0 0 1 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 135 134 134 134 132 132 130 131 131 129 127 127
SIGMA 11 11 11 11 11 11 11 11 11 11 11 11
NREJ 0 0 0 0 1 0 0 0 0 0 1 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 127 126 126 125 124 124 121 122 121 119 119 120
SIGMA 11 11 11 11 11 11 11 11 10 10 10 10
NREJ 0 0 0 0 0 0 0 1 0 0 0 0
RADIUS 83.8 84.1 84.5
BACKG 118 116 59
SIGMA 10 10 5
NREJ 0 0 0
Starting spot search...
sorting 173 spots
Median spot size is 4 x 3 pixels
Total number of spots found: 173
Number rejected as too small on X: 0
Number rejected as too small on Y: 0
Number rejected as too big on X: 0
Number rejected as too big on Y: 0
Number too close (SEPARATION keyword): 0
Number stored as OK: 173
Number of spots found in each bin
12 10 5 8 10 2 6 15
5 4 5 2 4 5 8 6
4 8 6 4 5 4 6 4
2 0 3 2 4 3 4 2
0 2 1 0 1 0 0 1
FORMATTED UNKNOWN file opened on unit 10
Logical name: ref-dntr_1.spt, Filename: ref-dntr_1.spt
273 spots written for image 1
173 spots written for image 2
A total of 446 spots were written to file
FORMATTED OLD file opened on unit 10
Logical name: ref-dntr_1.spt, Filename: ref-dntr_1.spt
DPS Indexing at Two-theta = 0.00 with 364 reflections (minimum spot separation = 0.24mm. Maximum expected cell edge 306.54, Beam position is 93.63 95.18
Generating direct lattice vectors (This may take some time):
|-----------------|
..................
Refining 30 direct space vectors:
|----------------------------|
..............................
selected 0
List of possible Laue groups, sorted on penalty index.
The lower the PENALTY, the better
No PENALTY LATT a b c alpha beta gamma Possible spacegroups
44 999 cI 315.17 107.32 315.42 80.2 34.1 80.4 I23,I213,I432,I4132
43 999 hR 350.03 315.55 106.71 80.4 90.0 50.2 H3,H32 (hexagonal settings of R3 and R32)
42 945 cF 315.42 349.46 315.55 142.8 39.7 143.0 F23,F432,F4132
41 943 tI 315.31 315.55 106.71 80.4 99.7 145.7 I4,I41,I422,I4122
40 892 tI 315.17 107.32 315.42 80.2 34.1 80.4 I4,I41,I422,I4122
39 892 hP 107.32 296.70 106.71 89.9 119.9 90.1 P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
38 839 tI 315.42 315.17 107.32 80.4 80.2 34.1 I4,I41,I422,I4122
37 838 oI 106.71 315.55 315.31 34.3 80.3 80.4 I222,I212121
36 837 oI 106.71 315.31 315.55 34.3 80.4 80.3 I222,I212121
35 785 cP 106.71 107.25 296.70 90.0 90.1 119.8 P23,P213,P432,P4232,P4332,P4132
34 784 tP 107.25 296.70 106.71 90.1 119.8 90.0 P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
33 784 hR 107.25 315.17 350.07 130.1 89.8 99.7 H3,H32 (hexagonal settings of R3 and R32)
32 784 hR 185.10 315.44 315.31 145.8 89.9 107.0 H3,H32 (hexagonal settings of R3 and R32)
31 783 mC 315.71 315.31 106.71 99.7 99.8 140.2 C2
30 783 oC 315.42 315.55 106.71 80.4 99.8 39.7 C222,C2221
29 783 mC 315.42 315.55 106.71 80.4 99.8 39.7 C2
28 216 hR 106.71 107.25 908.81 90.0 100.1 119.8 H3,H32 (hexagonal settings of R3 and R32)
27 214 oF 106.71 186.16 602.77 89.9 100.1 90.0 F222
26 167 tI 106.71 107.25 602.81 95.1 95.0 119.8 I4,I41,I422,I4122
25 165 oI 106.71 107.25 602.81 84.9 85.0 119.8 I222,I212121
24 163 mC 602.77 106.71 107.25 119.8 95.1 79.9 C2
23 163 oC 106.71 602.77 107.25 84.9 119.8 100.1 C222,C2221
22 162 mC 106.71 602.77 107.32 94.9 119.9 79.9 C2
21 162 mI 107.25 602.77 107.32 85.1 120.4 84.9 C2
20 162 oC 106.71 602.77 107.25 84.9 119.8 100.1 C222,C2221
19 162 mC 602.77 106.71 107.25 119.8 95.1 79.9 C2
18 161 mC 106.71 602.77 107.32 94.9 119.9 79.9 C2
17 110 oF 107.32 185.10 602.81 90.1 100.1 89.7 F222
16 109 mC 186.16 106.71 315.31 80.3 107.1 90.0 C2
15 56 tP 106.71 107.25 296.70 90.0 90.1 119.8 P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
14 56 mC 186.16 106.71 350.03 90.0 122.0 90.0 C2
13 55 oP 106.71 107.25 296.70 90.0 90.1 119.8 P222,P2221,P21212,P212121
12 55 mP 107.25 106.71 296.70 90.1 90.0 119.8 P2,P21
11 54 mP 106.71 107.25 296.70 90.0 90.1 119.8 P2,P21
10 2 oC 107.32 185.10 296.70 90.0 90.1 89.7 C222,C2221
9 2 hP 106.71 107.25 296.70 90.0 90.1 119.8 P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
8 2 mC 185.22 107.25 296.70 90.0 90.1 90.4 C2
7 1 mC 107.32 185.10 296.70 90.0 90.1 89.7 C2
6 1 mP 106.71 296.70 107.25 90.0 119.8 90.1 P2,P21
5 1 mC 106.71 186.16 296.70 89.9 90.1 90.0 C2
4 1 mC 186.16 106.71 296.70 90.1 90.1 90.0 C2
3 1 oC 106.71 186.16 296.70 89.9 90.1 90.0 C222,C2221
2 0 aP 106.71 107.32 296.70 89.9 89.9 60.1 P1
1 0 aP 106.71 107.25 296.70 90.0 90.1 119.8 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 # 9 with P3 (number 143) symmetry imposed
Initial cell (before refinement) is 106.9813 106.9813 296.6982 90.000 90.000 120.000
Using 341 indexed reflections (out of 364 spots found, {delta(XY) <= 2.5 sigma}),
final sd in spot positions is 0.05mm and in phi 0.13 degrees
Refined cell parameters 107.09 107.09 296.67 90.00 90.00 120.00
Beam coordinates of 93.63 95.18 have been refined to 93.71 95.12
This is a shift of 0.11mm or 0.136 times the minimum spot separation of ca 0.79mm.
Final cell (after refinement) is 107.0922 107.0922 296.6736 90.000 90.000 120.000
FORMATTED UNKNOWN file opened on unit 12
Logical name: autoindex.mat, Filename: autoindex.mat
Updating the stored central beam position from 9363.000 9518.500 to 9429.460 9511.583
****** INFORMATION *****
****** INFORMATION *****
****** INFORMATION *****
The cell derived from autoindexing will override that given on the CELL keyword.
To force the program to use the input cell, add the keyword KEEP. eg:
CELL KEEP 74.2 74.2 35.1 90 90 90
**** WARNING ****
Because input wavelength ( 0.9340) is not CuKa (1.5418) or Mo (0.7107),
source is assumed to be a synchrotron and synchrotron defaults for polarisation and beam divergence
will be used if these have not been defined explicitly (SYNCH POLAR and DIVH/DIVV keywords.
(Q)QOPEN: file opened on unit 1 Status: UNKNOWN
Logical Name: ref-dntr_1.gen Filename: ref-dntr_1.gen
Title for MTZ and GENERATE Files (TITLE):
.
Crystal identifier (IDENT): ref-dntr_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= 81
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 0 406 387 361 412 395 428 365 399 426 417 390 394 398 402 394 355 406 428
No gained 370 400
Total intensity 74330 82904 88849 94556 96417 97689 99018 99732 99997 99704 99760 99676 99396 99746 99788 99774 99592 99368 99368
Total intensity 99368 99200
SD of intensity 587 629 657 685 713 727 755 769 797 811 839 853 881 895 909 937 951 965 979
SD of intensity 993 1021
The mosaicity has been estimated as ---> 0.21 <--- for this image only;
This value can be used cautiously as an initial estimate.
Storing space group from DPS autoindexing: P3 number 143
Storing space group from DPS autoindexing: P3 number 143
*********** END OF PROCESSING *****************
/n