Index results for ferritin_1
Symmetry and refined cell parameters
Image |
Symmetry |
a |
b |
c |
alpha |
beta |
gamma |
1 |
F23 |
181.139 |
181.139 |
181.139 |
90.000 |
90.000 |
90.000 |
2 |
C2 |
222.549 |
128.091 |
181.958 |
90.000 |
144.919 |
90.000 |
1+2 |
F23 |
181.123 |
181.123 |
181.123 |
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 |
558 |
27 |
0.048 |
0.040 |
0.070 |
-0.085 |
2 |
536 |
23 |
0.043 |
0.040 |
0.060 |
-0.095 |
1+2 |
1093 |
50 |
0.046 |
0.050 |
0.070 |
-0.085 |
Image 1: /scisoft/pxsoft/data/dna_061202/ref-ferritin_1_001.img
Image 2: /scisoft/pxsoft/data/dna_061202/ref-ferritin_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-ferritin_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-ferritin_1_001.img Filename: /scisoft/pxsoft/data/dna_061202/ref-ferritin_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-ferritin_1_001.img
(Q)QOPEN: file opened on unit 1 Status: READONLY
Logical Name: /scisoft/pxsoft/data/dna_061202/ref-ferritin_1_001.img Filename: /scisoft/pxsoft/data/dna_061202/ref-ferritin_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 141 spots
Threshold set to 4.1
sorting 156 spots
Threshold set to 4.1
Finding spots on image 1 (Midpoint of phi 0.500 degrees)
Calculating radial background.....
The background is radial along the X (slow) direction
The average of 51 pixels, excluding outliers, is used
The scan is offset by 4.7mm from the image centre in Y to avoid any
backstop shadow
Radial Background calculation complete
RADIUS 9.4 9.7 10.0 10.4 10.7 11.0 11.3 11.7 12.0 12.3 12.6 13.0
BACKG 56 55 55 55 54 53 52 53 52 51 50 50
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 0 0 0 5 12 11 3 0 0 0 0
RADIUS 13.3 13.6 14.0 14.3 14.6 14.9 15.3 15.6 15.9 16.2 16.6 16.9
BACKG 50 49 48 48 48 49 48 48 49 47 47 48
SIGMA 7 6 6 6 6 7 6 6 7 6 6 6
NREJ 0 0 0 0 0 0 0 0 0 0 0 0
RADIUS 17.2 17.5 17.9 18.2 18.5 18.8 19.2 19.5 19.8 20.2 20.5 20.8
BACKG 48 48 49 48 48 48 49 48 47 47 47 46
SIGMA 6 6 7 6 6 6 7 6 6 6 6 6
NREJ 5 7 4 10 6 0 0 2 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 46 46 46 46 45 46 45 45 46 45 46 45
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 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 48 47 46 46 46 46 46 45 46 45 46 44
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 4 4 11 10 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 45 45 44 44 45 45 45 45 44 45 45 45
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 0 0 1 0 0 0 0 0 0 0 1 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 45 45 45 45 44 45 44 45 44 44 44 44
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 0 5 9 3 4 1 0 0 1 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 45 45 43 45 44 43 44 44 43 44 43 44
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 0 0 0 0 0 0 0 0 0 0 0 0
RADIUS 40.7 41.0 41.4 41.7 42.0 42.4 42.7 43.0 43.3 43.7 44.0 44.3
BACKG 44 44 44 43 44 44 44 45 46 45 44 45
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 0 0 0 0 0 0 0 0 2 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 45 45 45 46 46 45 45 45 46 45 47 46
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 0 0 0 0 0 0 0 2 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 46 47 46 47 47 47 48 47 49 50 48 47
SIGMA 6 6 6 6 6 6 6 6 6 7 6 6
NREJ 0 0 1 0 1 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 48 48 48 49 48 48 48 49 49 50 50 51
SIGMA 6 6 6 6 6 6 6 7 7 7 7 7
NREJ 0 0 0 0 0 0 0 0 1 8 7 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 51 50 50 50 50 49 49 50 51 51 51 50
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 3 1 0 0 0 0 0 0 0 0 2 9
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 51 51 50 48 49 50 51 50 49 50 50 50
SIGMA 7 7 7 6 7 7 7 7 7 7 7 7
NREJ 3 0 0 0 0 0 3 0 1 1 6 4
RADIUS 64.2 64.5 64.9 65.2 65.5 65.9 66.2 66.5 66.8 67.2 67.5 67.8
BACKG 49 49 48 49 50 50 49 49 50 50 49 48
SIGMA 7 7 6 7 7 7 6 7 7 7 7 6
NREJ 0 0 0 0 0 2 0 0 0 2 1 0
RADIUS 68.1 68.5 68.8 69.1 69.4 69.8 70.1 70.4 70.7 71.1 71.4 71.7
BACKG 47 47 48 47 47 47 47 47 47 46 47 47
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 0 0 0 0 0 0 0 0 0 0 0 0
RADIUS 72.1 72.4 72.7 73.0 73.4 73.7 74.0 74.3 74.7 75.0 75.3 75.6
BACKG 47 47 47 46 45 46 46 45 45 44 44 44
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 0 0 0 0 0 0 0 0 0 0 0 0
RADIUS 76.0 76.3 76.6 76.9 77.3 77.6 77.9 78.3 78.6 78.9 79.2 79.6
BACKG 45 44 45 44 44 43 44 43 44 43 44 43
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 0 0 0 0 0 0 0 0 0 0 0 0
RADIUS 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 43 43 42 42 42 42 42 42 42 42 41 41
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 1 0 0 0 1 0 0 0 0 0 0 0
RADIUS 83.8 84.1 84.5
BACKG 41 41 20
SIGMA 6 6 3
NREJ 0 0 0
Starting spot search...
sorting 558 spots
Median spot size is 5 x 5 pixels
Total number of spots found: 558
Number rejected as too small on X: 14
Number rejected as too small on Y: 11
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: 531
Number of spots found in each bin
22 15 17 22 27 10 15 27
22 21 15 22 19 13 23 23
27 23 19 20 29 18 12 13
10 16 8 4 5 4 2 0
2 1 1 0 1 1 0 2
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 156 spots
Based on a median spot size of 5 by 5 pixels in X and Y, the measurement box
parameters have been set to 17 17 10 5 5
The overall size of the box has been fixed.
To prevent this use keywords PROFILE NOFIXBOX.
***** WARNING ***** Lattice type not specified, so assumed primitive
Based on a median spot size of 5 by 5 pixels in X and Y, the spot separation
parameters (in X and Y) have been set to 0.57 0.57mm.
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-ferritin_1.spt, Filename: ref-ferritin_1.spt
531 spots written for image 1
A total of 531 spots were written to file
FORMATTED OLD file opened on unit 10
Logical name: ref-ferritin_1.spt, Filename: ref-ferritin_1.spt
DPS Indexing at Two-theta = 0.00 with 263 reflections (minimum spot separation = 0.41mm. 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 8
List of possible Laue groups, sorted on penalty index.
The lower the PENALTY, the better
No PENALTY LATT a b c alpha beta gamma Possible spacegroups
44 999 cI 128.09 180.84 128.28 90.0 90.0 89.8 I23,I213,I432,I4132
43 505 cP 127.84 127.91 128.15 90.1 120.0 119.8 P23,P213,P432,P4232,P4332,P4132
42 504 tP 127.91 128.15 127.84 120.0 119.8 90.1 P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
41 503 tP 127.84 127.91 128.15 90.1 120.0 119.8 P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
40 503 oP 127.84 127.91 128.15 90.1 120.0 119.8 P222,P2221,P21212,P212121
39 502 tI 128.28 180.84 128.09 89.8 90.0 90.0 I4,I41,I422,I4122
38 501 hR 221.79 181.30 127.84 90.1 106.6 114.1 H3,H32 (hexagonal settings of R3 and R32)
37 501 oF 128.09 221.64 221.79 70.7 90.1 90.2 F222
36 256 hP 128.15 128.20 127.84 90.1 120.0 119.9 P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
35 255 hP 127.84 128.15 127.91 90.1 119.8 120.0 P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
34 255 hR 181.30 221.64 128.20 73.3 90.0 114.3 H3,H32 (hexagonal settings of R3 and R32)
33 254 oC 128.09 221.79 127.84 73.4 119.9 89.9 C222,C2221
32 254 oC 128.28 221.25 128.15 73.3 120.0 90.0 C222,C2221
31 254 oC 127.84 222.07 127.91 73.2 119.8 90.0 C222,C2221
30 253 oC 127.84 222.07 127.91 73.2 119.8 90.0 C222,C2221
29 253 mC 128.09 221.79 127.84 73.4 119.9 89.9 C2
28 253 mC 128.09 221.79 127.84 73.4 119.9 89.9 C2
27 253 mP 127.84 128.15 127.91 90.1 119.8 120.0 P2,P21
26 252 mC 128.09 221.79 127.84 73.4 119.9 89.9 C2
25 252 oC 127.84 222.07 127.91 73.2 119.8 90.0 C222,C2221
24 252 mP 127.84 127.91 128.15 90.1 120.0 119.8 P2,P21
23 251 mP 127.84 127.91 128.15 90.1 120.0 119.8 P2,P21
22 9 tI 128.28 128.09 180.84 90.2 90.0 90.0 I4,I41,I422,I4122
21 9 tI 128.09 128.28 180.84 90.0 89.8 90.0 I4,I41,I422,I4122
20 8 oF 180.84 181.26 181.30 90.1 89.9 89.8 F222
19 6 mC 180.84 181.30 128.20 90.0 135.0 89.9 C2
18 6 cF 181.26 180.84 181.30 90.1 90.1 90.2 F23,F432,F4132
17 5 oI 127.84 128.20 181.30 90.0 89.9 90.1 I222,I212121
16 5 oI 127.84 128.20 181.30 90.0 89.9 90.1 I222,I212121
15 5 tI 128.09 128.28 180.84 90.0 89.8 90.0 I4,I41,I422,I4122
14 4 mI 127.84 181.30 128.20 90.0 90.1 89.9 C2
13 4 mC 221.25 128.28 128.09 90.0 125.2 90.0 C2
12 4 mC 221.25 128.28 128.09 90.0 125.2 90.0 C2
11 4 hR 127.84 128.28 314.06 90.0 90.0 120.1 H3,H32 (hexagonal settings of R3 and R32)
10 4 mC 180.84 181.30 127.84 90.1 134.9 89.9 C2
9 4 mC 221.25 128.28 128.09 90.0 125.2 90.0 C2
8 3 oI 128.28 128.09 180.84 89.8 90.0 90.0 I222,I212121
7 3 hR 128.28 128.15 313.07 90.2 90.0 120.0 H3,H32 (hexagonal settings of R3 and R32)
6 3 mC 222.02 127.84 128.20 90.1 125.3 89.8 C2
5 3 mC 221.59 128.20 127.84 89.9 125.1 90.1 C2
4 2 mC 221.25 128.28 128.09 90.0 125.2 90.0 C2
3 1 mC 221.25 128.28 128.09 90.0 125.2 90.0 C2
2 1 aP 127.84 127.91 128.15 90.1 120.0 119.8 P1
1 0 aP 127.84 127.91 128.09 60.1 60.1 60.2 P1
No PENALTY SDCELL FRACN LATT a b c alpha beta gamma Possible spacegroups
The solution and direct beam position will now be refined; reflections which deviate by more
than the sigma cutoff from their calculated position will be excluded from the refinement.
Refining solution #18 with F23 (number 196) symmetry imposed
Initial cell (before refinement) is 181.1299 181.1299 181.1299 90.000 90.000 90.000
Using 251 indexed reflections (out of 263 spots found, {delta(XY) <= 2.5 sigma}),
final sd in spot positions is 0.04mm and in phi 0.26 degrees
Refined cell parameters 181.14 181.14 181.14 90.00 90.00 90.00
Beam coordinates of 93.63 95.18 have been refined to 93.70 95.10
This is a shift of 0.11mm or 0.085 times the minimum spot separation of ca 1.29mm.
Final cell (after refinement) is 181.1395 181.1395 181.1395 90.000 90.000 90.000
FORMATTED UNKNOWN file opened on unit 12
Logical name: autoindex.mat, Filename: autoindex.mat
Updating the stored central beam position from 9363.000 9518.500 to 9431.107 9509.664
****** 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-ferritin_1.gen Filename: ref-ferritin_1.gen
Title for MTZ and GENERATE Files (TITLE):
.
Crystal identifier (IDENT): ref-ferritin_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= 63
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 194 421 408 399 416 399 430 414 360 410 394 8 7 9 16 15 22 28 30
No gained 39 38
Total intensity 71369 78694 85766 89788 95256 96559 97974 98767 99327 99727 99991 99991 99997 99930 99942 99936 99911 99905 99886
Total intensity 99868 99874
SD of intensity 240 252 264 277 289 301 307 314 326 332 338 338 338 338 338 338 338 338 332
SD of intensity 332 332
The mosaicity has been estimated as ---> 0.49 <--- for this image only;
This value can be used cautiously as an initial estimate.
Storing space group from DPS autoindexing: F23 number 196
*********** END OF PROCESSING *****************
************ Version 6.2.3 (beta test 1.6) for Image plate and CCD data 4th November 2002 ***********
A.G.W. Leslie, MRC Laboratory Of Molecular Biology, HILLS ROAD, CAMBRIDGE CB2 2QH, UK
E-mail andrew@mrc-lmb.cam.ac.uk
New auto-indexing using DPS due to Ingo Steller Robert Bolotovsky and Michael Rossmann
(1998) J. Appl. Cryst. 30, 1036-1040
Original auto-indexing using REFIX due to Wolfgang Kabsch (Kabsch,W. (1993),
J.Appl.Cryst. 24,795-800.)
X-windows interface using xdl_view due to John Campbell (Daresbury Laboratory, UK.)
(Campbell,J.W. (1995) J. Appl. Cryst. 28, 236-242.
===> newmat autoindex.mat
===> template ref-ferritin_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-ferritin_1_002.img Filename: /scisoft/pxsoft/data/dna_061202/ref-ferritin_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-ferritin_1_002.img
(Q)QOPEN: file opened on unit 1 Status: READONLY
Logical Name: /scisoft/pxsoft/data/dna_061202/ref-ferritin_1_002.img Filename: /scisoft/pxsoft/data/dna_061202/ref-ferritin_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 140 spots
Threshold set to 4.1
sorting 148 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 62 61 61 59 59 57 57 56 55 54 54 53
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 6 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 54 53 52 52 52 53 51 51 51 51 52 51
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 0 0 0 0 0 0 0 0 0 1 5
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 51 50 52 51 51 51 50 50 50 50 50 50
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 1 0 0 0 0 0 0 0 0 0 0 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 50 49 50 50 50 50 51 49 51 50 51 52
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 0 0 5 4 0 0 0 0 9 7 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 50 51 50 50 50 49 49 49 49 50 50 49
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 0 0 1 2 0 0 0 0 2 1 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 50 50 50 48 50 49 49 49 50 50 50 49
SIGMA 7 7 7 6 7 7 7 7 7 7 7 6
NREJ 0 0 3 10 5 0 0 0 3 7 3 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 50 49 50 50 50 50 50 49 49 49 49 49
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 0 1 5 2 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 49 50 50 49 49 49 50 50 50 49 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 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 51 51 52 52 51 52 52 53 53 52 51 51
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 0 8 3 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 53 53 53 53 54 54 54 56 56 56 56 56
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 5 3 0 0 0 0 3 6 1 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 57 58 58 58 56 58 58 59 58 59 59 59
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 7 8 0 0 0 0 0 2 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 60 61 60 60 60 61 61 62 63 60 62 62
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 1 0 0 0 0 0 3 3 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 63 63 64 63 62 62 64 65 64 63 63 63
SIGMA 7 7 8 7 7 7 8 8 8 7 7 7
NREJ 1 7 2 0 1 0 0 1 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 63 63 63 62 63 63 63 62 62 63 62 63
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 4 6 0 0 1 1 0 4 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 64 64 63 63 63 61 64 62 61 60 61 61
SIGMA 7 8 7 7 7 7 8 7 7 7 7 7
NREJ 3 3 4 0 0 0 2 5 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 61 62 61 60 59 59 60 59 59 58 58 58
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 4 2 0 0 0 0 0 2 2 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 58 59 59 58 58 57 59 58 57 57 55 54
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 2 7 1 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 56 55 56 54 54 54 55 55 55 54 53 51
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 1 0 0 0 0 0 3 4 0 0 0
RADIUS 79.9 80.2 80.5 80.9 81.2 81.5 81.8 82.2 82.5 82.8 83.2 83.5
BACKG 53 54 54 52 52 52 52 54 52 52 50 51
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 0 0 1 0 0 0 0 0 0 0 0
RADIUS 83.8 84.1 84.5
BACKG 50 51 25
SIGMA 7 7 3
NREJ 0 0 0
Starting spot search...
sorting 536 spots
Median spot size is 5 x 6 pixels
Total number of spots found: 536
Number rejected as too small on X: 6
Number rejected as too small on Y: 9
Number rejected as too big on X: 8
Number rejected as too big on Y: 0
Number too close (SEPARATION keyword): 0
Number stored as OK: 513
Number of spots found in each bin
24 19 3 19 21 17 17 25
20 20 25 22 25 15 15 28
19 18 11 17 19 24 13 24
8 8 2 3 4 5 8 7
1 5 1 0 0 0 1 0
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 148 spots
Based on a median spot size of 5 by 5 pixels in X and Y, the measurement box
parameters have been set to 17 17 10 5 5
The overall size of the box has been fixed.
To prevent this use keywords PROFILE NOFIXBOX.
***** WARNING ***** Lattice type not specified, so assumed primitive
Based on a median spot size of 5 by 5 pixels in X and Y, the spot separation
parameters (in X and Y) have been set to 0.57 0.57mm.
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-ferritin_1.spt, Filename: ref-ferritin_1.spt
513 spots written for image 2
A total of 513 spots were written to file
FORMATTED OLD file opened on unit 10
Logical name: ref-ferritin_1.spt, Filename: ref-ferritin_1.spt
DPS Indexing at Two-theta = 0.00 with 277 reflections (minimum spot separation = 0.41mm. 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 16
List of possible Laue groups, sorted on penalty index.
The lower the PENALTY, the better
No PENALTY LATT a b c alpha beta gamma Possible spacegroups
44 999 cI 127.92 177.09 128.09 89.9 90.1 89.2 I23,I213,I432,I4132
43 541 cP 125.93 126.10 127.22 119.3 91.2 118.9 P23,P213,P432,P4232,P4332,P4132
42 539 tP 126.10 127.22 125.93 91.2 118.9 119.3 P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
41 531 tP 125.93 126.10 127.22 119.3 91.2 118.9 P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
40 530 oP 125.93 126.10 127.22 119.3 91.2 118.9 P222,P2221,P21212,P212121
39 517 tI 128.09 177.09 127.92 89.2 90.1 89.9 I4,I41,I422,I4122
38 516 oF 127.92 218.65 218.46 71.8 90.7 90.6 F222
37 505 hR 218.65 181.15 125.93 90.4 105.5 114.1 H3,H32 (hexagonal settings of R3 and R32)
36 291 hP 127.22 127.22 125.93 119.3 91.2 119.5 P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
35 284 oC 125.93 221.90 126.10 72.5 118.9 90.4 C222,C2221
34 283 hP 126.10 127.22 125.93 91.2 118.9 119.3 P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
33 277 oC 127.92 218.65 125.93 74.5 119.9 89.4 C222,C2221
32 275 oC 128.09 217.06 127.22 105.8 120.2 89.9 C222,C2221
31 275 mC 128.09 219.85 125.93 74.3 120.5 90.0 C2
30 274 mP 125.93 127.22 126.10 119.3 118.9 91.2 P2,P21
29 274 oC 125.93 221.90 126.10 72.5 118.9 90.4 C222,C2221
28 274 oC 126.10 221.80 125.93 72.6 118.9 90.4 C222,C2221
27 269 mC 128.09 219.85 126.10 74.3 120.6 90.0 C2
26 269 mC 128.09 219.85 126.10 74.3 120.6 90.0 C2
25 268 mP 126.10 125.93 127.22 91.2 119.3 118.9 P2,P21
24 268 hR 217.06 180.90 127.22 90.4 105.7 114.1 H3,H32 (hexagonal settings of R3 and R32)
23 268 mP 125.93 126.10 127.22 91.3 119.3 118.9 P2,P21
22 59 cF 180.90 177.09 181.15 90.5 90.1 90.6 F23,F432,F4132
21 44 hR 126.10 128.09 313.10 90.0 89.2 120.6 H3,H32 (hexagonal settings of R3 and R32)
20 42 hR 128.09 127.22 309.20 91.3 89.9 120.2 H3,H32 (hexagonal settings of R3 and R32)
19 34 tI 128.09 127.92 177.09 90.8 89.9 89.9 I4,I41,I422,I4122
18 34 oF 177.09 180.90 181.15 90.1 89.5 89.4 F222
17 31 tI 127.92 128.09 177.09 89.9 89.2 90.1 I4,I41,I422,I4122
16 31 oI 127.92 128.09 177.09 89.9 90.8 89.9 I222,I212121
15 29 oI 128.09 127.92 177.09 89.2 90.1 89.9 I222,I212121
14 27 mC 221.90 125.93 127.22 91.2 125.3 89.6 C2
13 24 mC 177.09 181.15 127.22 90.3 134.7 89.5 C2
12 23 mI 125.93 181.15 127.22 89.7 91.2 89.6 C2
11 20 mC 217.06 128.09 127.92 90.1 125.3 89.9 C2
10 20 mC 217.06 128.09 127.92 90.1 125.3 89.9 C2
9 20 mC 217.06 128.09 127.92 89.9 125.3 90.1 C2
8 19 mC 217.06 128.09 127.92 90.1 125.3 89.9 C2
7 16 tI 127.92 128.09 177.09 89.9 89.2 90.1 I4,I41,I422,I4122
6 15 mC 177.09 181.15 125.93 90.4 134.1 89.5 C2
5 14 mC 217.06 128.09 127.92 89.9 125.3 90.1 C2
4 11 oI 128.09 177.09 127.92 89.2 89.9 90.1 I222,I212121
3 11 aP 125.93 126.10 127.22 60.7 91.2 61.1 P1
2 1 mC 217.06 128.09 177.09 90.1 143.9 89.9 C2
1 0 aP 125.93 126.10 127.22 119.3 91.2 118.9 P1
No PENALTY SDCELL FRACN LATT a b c alpha beta gamma Possible spacegroups
The solution and direct beam position will now be refined; reflections which deviate by more
than the sigma cutoff from their calculated position will be excluded from the refinement.
Refining solution # 2 with C2 (number 5) symmetry imposed
Initial cell (before refinement) is 217.0640 128.0856 177.0887 90.000 143.894 90.000
Using 259 indexed reflections (out of 277 spots found, {delta(XY) <= 2.5 sigma}),
final sd in spot positions is 0.04mm and in phi 0.25 degrees
Refined cell parameters 222.55 128.09 181.96 90.00 144.92 90.00
Beam coordinates of 93.63 95.18 have been refined to 93.69 95.09
This is a shift of 0.11mm or 0.062 times the minimum spot separation of ca 1.82mm.
Final cell (after refinement) is 222.5495 128.0914 181.9577 90.000 144.919 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 9431.500 9509.074
****** 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-ferritin_1.gen Filename: ref-ferritin_1.gen
Title for MTZ and GENERATE Files (TITLE):
.
Crystal identifier (IDENT): ref-ferritin_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= 62
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 214 374 403 385 416 376 394 406 396 402 418 7 6 6 8 5 2 7 4
No gained 5 3
Total intensity 78668 83547 88339 92026 93979 95542 97671 98627 99074 99583 99995 99974 99923 99928 99923 99918 99897 99871 99871
Total intensity 99871 99820
SD of intensity 267 278 283 293 298 308 314 319 329 334 339 339 339 339 339 339 339 339 339
SD of intensity 339 339
The mosaicity has been estimated as ---> 0.58 <--- for this image only;
This value can be used cautiously as an initial estimate.
Storing space group from DPS autoindexing: C2 number 5
*********** 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-ferritin_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-ferritin_1_001.img Filename: /scisoft/pxsoft/data/dna_061202/ref-ferritin_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-ferritin_1_001.img
(Q)QOPEN: file opened on unit 1 Status: READONLY
Logical Name: /scisoft/pxsoft/data/dna_061202/ref-ferritin_1_001.img Filename: /scisoft/pxsoft/data/dna_061202/ref-ferritin_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 141 spots
Threshold set to 4.1
sorting 156 spots
Threshold set to 4.1
Finding spots on image 1 (Midpoint of phi 0.500 degrees)
Calculating radial background.....
The background is radial along the X (slow) direction
The average of 51 pixels, excluding outliers, is used
The scan is offset by 4.7mm from the image centre in Y to avoid any
backstop shadow
Radial Background calculation complete
RADIUS 9.4 9.7 10.0 10.4 10.7 11.0 11.3 11.7 12.0 12.3 12.6 13.0
BACKG 56 55 55 55 54 53 52 53 52 51 50 50
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 0 0 0 5 12 11 3 0 0 0 0
RADIUS 13.3 13.6 14.0 14.3 14.6 14.9 15.3 15.6 15.9 16.2 16.6 16.9
BACKG 50 49 48 48 48 49 48 48 49 47 47 48
SIGMA 7 6 6 6 6 7 6 6 7 6 6 6
NREJ 0 0 0 0 0 0 0 0 0 0 0 0
RADIUS 17.2 17.5 17.9 18.2 18.5 18.8 19.2 19.5 19.8 20.2 20.5 20.8
BACKG 48 48 49 48 48 48 49 48 47 47 47 46
SIGMA 6 6 7 6 6 6 7 6 6 6 6 6
NREJ 5 7 4 10 6 0 0 2 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 46 46 46 46 45 46 45 45 46 45 46 45
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 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 48 47 46 46 46 46 46 45 46 45 46 44
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 4 4 11 10 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 45 45 44 44 45 45 45 45 44 45 45 45
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 0 0 1 0 0 0 0 0 0 0 1 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 45 45 45 45 44 45 44 45 44 44 44 44
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 0 5 9 3 4 1 0 0 1 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 45 45 43 45 44 43 44 44 43 44 43 44
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 0 0 0 0 0 0 0 0 0 0 0 0
RADIUS 40.7 41.0 41.4 41.7 42.0 42.4 42.7 43.0 43.3 43.7 44.0 44.3
BACKG 44 44 44 43 44 44 44 45 46 45 44 45
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 0 0 0 0 0 0 0 0 2 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 45 45 45 46 46 45 45 45 46 45 47 46
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 0 0 0 0 0 0 0 2 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 46 47 46 47 47 47 48 47 49 50 48 47
SIGMA 6 6 6 6 6 6 6 6 6 7 6 6
NREJ 0 0 1 0 1 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 48 48 48 49 48 48 48 49 49 50 50 51
SIGMA 6 6 6 6 6 6 6 7 7 7 7 7
NREJ 0 0 0 0 0 0 0 0 1 8 7 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 51 50 50 50 50 49 49 50 51 51 51 50
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 3 1 0 0 0 0 0 0 0 0 2 9
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 51 51 50 48 49 50 51 50 49 50 50 50
SIGMA 7 7 7 6 7 7 7 7 7 7 7 7
NREJ 3 0 0 0 0 0 3 0 1 1 6 4
RADIUS 64.2 64.5 64.9 65.2 65.5 65.9 66.2 66.5 66.8 67.2 67.5 67.8
BACKG 49 49 48 49 50 50 49 49 50 50 49 48
SIGMA 7 7 6 7 7 7 6 7 7 7 7 6
NREJ 0 0 0 0 0 2 0 0 0 2 1 0
RADIUS 68.1 68.5 68.8 69.1 69.4 69.8 70.1 70.4 70.7 71.1 71.4 71.7
BACKG 47 47 48 47 47 47 47 47 47 46 47 47
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 0 0 0 0 0 0 0 0 0 0 0 0
RADIUS 72.1 72.4 72.7 73.0 73.4 73.7 74.0 74.3 74.7 75.0 75.3 75.6
BACKG 47 47 47 46 45 46 46 45 45 44 44 44
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 0 0 0 0 0 0 0 0 0 0 0 0
RADIUS 76.0 76.3 76.6 76.9 77.3 77.6 77.9 78.3 78.6 78.9 79.2 79.6
BACKG 45 44 45 44 44 43 44 43 44 43 44 43
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 0 0 0 0 0 0 0 0 0 0 0 0
RADIUS 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 43 43 42 42 42 42 42 42 42 42 41 41
SIGMA 6 6 6 6 6 6 6 6 6 6 6 6
NREJ 1 0 0 0 1 0 0 0 0 0 0 0
RADIUS 83.8 84.1 84.5
BACKG 41 41 20
SIGMA 6 6 3
NREJ 0 0 0
Starting spot search...
sorting 558 spots
Median spot size is 5 x 5 pixels
Total number of spots found: 558
Number rejected as too small on X: 14
Number rejected as too small on Y: 11
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: 531
Number of spots found in each bin
22 15 17 22 27 10 15 27
22 21 15 22 19 13 23 23
27 23 19 20 29 18 12 13
10 16 8 4 5 4 2 0
2 1 1 0 1 1 0 2
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 156 spots
Based on a median spot size of 5 by 5 pixels in X and Y, the measurement box
parameters have been set to 17 17 10 5 5
The overall size of the box has been fixed.
To prevent this use keywords PROFILE NOFIXBOX.
***** WARNING ***** Lattice type not specified, so assumed primitive
Based on a median spot size of 5 by 5 pixels in X and Y, the spot separation
parameters (in X and Y) have been set to 0.57 0.57mm.
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-ferritin_1_002.img
(Q)QOPEN: file opened on unit 1 Status: READONLY
Logical Name: /scisoft/pxsoft/data/dna_061202/ref-ferritin_1_002.img Filename: /scisoft/pxsoft/data/dna_061202/ref-ferritin_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 62 61 61 59 59 57 57 56 55 54 54 53
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 6 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 54 53 52 52 52 53 51 51 51 51 52 51
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 0 0 0 0 0 0 0 0 0 1 5
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 51 50 52 51 51 51 50 50 50 50 50 50
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 1 0 0 0 0 0 0 0 0 0 0 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 50 49 50 50 50 50 51 49 51 50 51 52
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 0 0 5 4 0 0 0 0 9 7 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 50 51 50 50 50 49 49 49 49 50 50 49
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 0 0 1 2 0 0 0 0 2 1 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 50 50 50 48 50 49 49 49 50 50 50 49
SIGMA 7 7 7 6 7 7 7 7 7 7 7 6
NREJ 0 0 3 10 5 0 0 0 3 7 3 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 50 49 50 50 50 50 50 49 49 49 49 49
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 0 1 5 2 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 49 50 50 49 49 49 50 50 50 49 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 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 51 51 52 52 51 52 52 53 53 52 51 51
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 0 8 3 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 53 53 53 53 54 54 54 56 56 56 56 56
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 5 3 0 0 0 0 3 6 1 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 57 58 58 58 56 58 58 59 58 59 59 59
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 7 8 0 0 0 0 0 2 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 60 61 60 60 60 61 61 62 63 60 62 62
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 1 0 0 0 0 0 3 3 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 63 63 64 63 62 62 64 65 64 63 63 63
SIGMA 7 7 8 7 7 7 8 8 8 7 7 7
NREJ 1 7 2 0 1 0 0 1 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 63 63 63 62 63 63 63 62 62 63 62 63
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 4 6 0 0 1 1 0 4 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 64 64 63 63 63 61 64 62 61 60 61 61
SIGMA 7 8 7 7 7 7 8 7 7 7 7 7
NREJ 3 3 4 0 0 0 2 5 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 61 62 61 60 59 59 60 59 59 58 58 58
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 4 2 0 0 0 0 0 2 2 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 58 59 59 58 58 57 59 58 57 57 55 54
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 2 7 1 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 56 55 56 54 54 54 55 55 55 54 53 51
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 1 0 0 0 0 0 3 4 0 0 0
RADIUS 79.9 80.2 80.5 80.9 81.2 81.5 81.8 82.2 82.5 82.8 83.2 83.5
BACKG 53 54 54 52 52 52 52 54 52 52 50 51
SIGMA 7 7 7 7 7 7 7 7 7 7 7 7
NREJ 0 0 0 1 0 0 0 0 0 0 0 0
RADIUS 83.8 84.1 84.5
BACKG 50 51 25
SIGMA 7 7 3
NREJ 0 0 0
Starting spot search...
sorting 535 spots
Median spot size is 5 x 6 pixels
Total number of spots found: 535
Number rejected as too small on X: 6
Number rejected as too small on Y: 9
Number rejected as too big on X: 8
Number rejected as too big on Y: 0
Number too close (SEPARATION keyword): 0
Number stored as OK: 512
Number of spots found in each bin
24 19 3 19 21 17 17 25
20 20 25 22 25 15 15 28
19 18 11 17 19 24 13 24
8 8 2 3 4 5 8 7
1 5 1 0 0 0 0 0
FORMATTED UNKNOWN file opened on unit 10
Logical name: ref-ferritin_1.spt, Filename: ref-ferritin_1.spt
531 spots written for image 1
512 spots written for image 2
A total of 1043 spots were written to file
FORMATTED OLD file opened on unit 10
Logical name: ref-ferritin_1.spt, Filename: ref-ferritin_1.spt
DPS Indexing at Two-theta = 0.00 with 540 reflections (minimum spot separation = 0.41mm. 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 2
List of possible Laue groups, sorted on penalty index.
The lower the PENALTY, the better
No PENALTY LATT a b c alpha beta gamma Possible spacegroups
44 999 cI 128.10 180.97 128.33 89.9 89.8 89.9 I23,I213,I432,I4132
43 501 cP 127.96 127.99 128.02 119.8 119.9 90.0 P23,P213,P432,P4232,P4332,P4132
42 501 tP 127.96 127.99 128.02 119.8 119.9 90.0 P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
41 501 tI 128.33 180.97 128.10 89.9 90.2 90.1 I4,I41,I422,I4122
40 501 oF 128.10 221.62 222.07 70.7 90.2 90.0 F222
39 500 hR 221.90 181.01 128.02 89.9 106.6 114.0 H3,H32 (hexagonal settings of R3 and R32)
38 500 oP 127.96 127.99 128.02 119.8 119.9 90.0 P222,P2221,P21212,P212121
37 500 tP 127.99 128.02 127.96 119.9 90.0 119.8 P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212 P4322,P43212
36 251 mC 128.10 221.62 127.99 73.3 119.8 90.0 C2
35 251 mC 128.10 221.62 127.99 106.7 119.8 90.0 C2
34 251 hP 127.96 128.02 127.99 119.8 90.0 119.9 P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
33 251 hP 127.96 128.02 127.99 119.8 90.0 119.9 P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221
P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322
32 251 oC 127.96 221.85 127.99 55.0 90.0 90.0 C222,C2221
31 251 oC 127.96 221.85 127.99 55.0 90.0 90.0 C222,C2221
30 251 hR 181.01 221.62 128.38 73.4 89.9 114.1 H3,H32 (hexagonal settings of R3 and R32)
29 251 mC 128.10 221.62 127.99 106.7 119.8 90.0 C2
28 250 oC 128.10 221.62 127.99 106.7 119.8 90.0 C222,C2221
27 250 mP 127.96 127.99 128.02 119.8 119.9 90.0 P2,P21
26 250 mP 127.96 127.99 128.02 119.8 119.9 90.0 P2,P21
25 250 mP 127.96 127.99 128.02 119.8 119.9 90.0 P2,P21
24 250 oC 127.96 221.85 127.99 55.0 90.0 90.0 C222,C2221
23 250 oC 128.10 221.62 127.99 106.7 119.8 90.0 C222,C2221
22 8 cF 181.01 180.97 181.63 90.2 90.1 90.0 F23,F432,F4132
21 7 hR 127.99 128.33 313.93 89.8 90.1 120.1 H3,H32 (hexagonal settings of R3 and R32)
20 5 tI 128.33 128.10 180.97 89.9 89.9 89.8 I4,I41,I422,I4122
19 4 tI 128.33 128.10 180.97 89.9 89.9 89.8 I4,I41,I422,I4122
18 4 hR 127.96 128.38 313.39 89.9 90.0 119.9 H3,H32 (hexagonal settings of R3 and R32)
17 4 oF 180.97 181.01 181.63 90.1 90.2 90.0 F222
16 4 oI 128.02 181.01 128.38 90.1 89.8 90.1 I222,I212121
15 3 mC 180.97 181.01 128.02 89.9 134.8 90.0 C2
14 3 tI 127.96 127.99 181.63 89.8 90.0 90.0 I4,I41,I422,I4122
13 3 mC 221.85 127.96 181.63 90.0 144.8 90.0 C2
12 3 mI 127.99 181.63 127.96 90.0 90.0 89.8 C2
11 3 oI 127.96 127.99 181.63 90.2 90.0 90.0 I222,I212121
10 3 oI 180.97 128.10 128.33 89.8 89.9 89.9 I222,I212121
9 2 mC 180.97 181.01 128.02 89.9 134.8 90.0 C2
8 1 mC 221.85 127.96 127.99 90.0 125.0 90.0 C2
7 1 mC 180.97 181.01 128.02 89.9 134.8 90.0 C2
6 1 mC 180.97 181.01 128.02 90.1 134.8 90.0 C2
5 1 mC 221.85 127.96 127.99 90.0 125.0 90.0 C2
4 1 mC 221.85 127.96 127.99 90.0 125.0 90.0 C2
3 1 mC 180.97 181.01 128.02 89.9 134.8 90.0 C2
2 0 aP 127.96 127.99 128.02 60.2 60.1 90.0 P1
1 0 aP 127.96 127.99 128.02 119.8 119.9 90.0 P1
No PENALTY SDCELL FRACN LATT a b c alpha beta gamma Possible spacegroups
The solution and direct beam position will now be refined; reflections which deviate by more
than the sigma cutoff from their calculated position will be excluded from the refinement.
Refining solution #22 with F23 (number 196) symmetry imposed
Initial cell (before refinement) is 181.2012 181.2012 181.2012 90.000 90.000 90.000
Using 496 indexed reflections (out of 540 spots found, {delta(XY) <= 2.5 sigma}),
final sd in spot positions is 0.05mm and in phi 0.27 degrees
Refined cell parameters 181.12 181.12 181.12 90.00 90.00 90.00
Beam coordinates of 93.63 95.18 have been refined to 93.70 95.10
This is a shift of 0.11mm or 0.086 times the minimum spot separation of ca 1.29mm.
Final cell (after refinement) is 181.1231 181.1231 181.1231 90.000 90.000 90.000
FORMATTED UNKNOWN file opened on unit 12
Logical name: autoindex.mat, Filename: autoindex.mat
Updating the stored central beam position from 9363.000 9518.500 to 9430.712 9509.822
****** 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-ferritin_1.gen Filename: ref-ferritin_1.gen
Title for MTZ and GENERATE Files (TITLE):
.
Crystal identifier (IDENT): ref-ferritin_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= 62
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 204 402 400 370 400 422 383 413 392 401 401 3 8 5 1 3 4 5 4
No gained 9 8
Total intensity 74879 82786 88193 90956 93326 95363 97582 98593 99251 99723 99988 99993 99998 99972 99977 99967 99967 99956 99946
Total intensity 99708 99687
SD of intensity 270 280 285 296 301 311 316 321 332 337 342 342 342 342 342 342 342 342 342
SD of intensity 342 342
The mosaicity has been estimated as ---> 0.57 <--- for this image only;
This value can be used cautiously as an initial estimate.
Storing space group from DPS autoindexing: F23 number 196
Storing space group from DPS autoindexing: F23 number 196
*********** END OF PROCESSING *****************
/n