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== dataset E1 == | == dataset E1 == | ||
Use generate_XDS.INP and run xds once. Based on R-factors and an inspection of BKGPIX.cbf, I modified the resulting XDS.INP to have | |||
INCLUDE_RESOLUTION_RANGE=50 2.1 | |||
VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS=8000. 30000. | |||
and ran xds again. This is the excerpt from CORRECT.LP : | |||
SPACE-GROUP UNIT CELL CONSTANTS UNIQUE Rmeas COMPARED LATTICE- | SPACE-GROUP UNIT CELL CONSTANTS UNIQUE Rmeas COMPARED LATTICE- | ||
NUMBER a b c alpha beta gamma CHARACTER | NUMBER a b c alpha beta gamma CHARACTER | ||
| Line 19: | Line 23: | ||
1 102.9 103.2 131.4 90.0 90.0 90.1 18040 6.9 14871 44 aP | 1 102.9 103.2 131.4 90.0 90.0 90.1 18040 6.9 14871 44 aP | ||
... | |||
REFINED PARAMETERS: DISTANCE BEAM ORIENTATION CELL AXIS | |||
USING 219412 INDEXED SPOTS | |||
STANDARD DEVIATION OF SPOT POSITION (PIXELS) 1.01 | |||
STANDARD DEVIATION OF SPINDLE POSITION (DEGREES) 0.11 | |||
CRYSTAL MOSAICITY (DEGREES) 0.191 | |||
DIRECT BEAM COORDINATES (REC. ANGSTROEM) -0.004789 0.003758 1.021015 | |||
DETECTOR COORDINATES (PIXELS) OF DIRECT BEAM 1027.25 1064.20 | |||
DETECTOR ORIGIN (PIXELS) AT 1036.84 1056.68 | |||
CRYSTAL TO DETECTOR DISTANCE (mm) 209.38 | |||
LAB COORDINATES OF DETECTOR X-AXIS 1.000000 0.000000 0.000000 | |||
LAB COORDINATES OF DETECTOR Y-AXIS 0.000000 1.000000 0.000000 | |||
LAB COORDINATES OF ROTATION AXIS 0.999997 0.000527 0.002187 | |||
COORDINATES OF UNIT CELL A-AXIS 21.922 52.895 85.337 | |||
COORDINATES OF UNIT CELL B-AXIS 3.771 87.158 -54.992 | |||
COORDINATES OF UNIT CELL C-AXIS -128.130 18.914 21.191 | |||
REC. CELL PARAMETERS 0.009731 0.009697 0.007620 90.000 90.000 90.000 | |||
UNIT CELL PARAMETERS 102.766 103.125 131.241 90.000 90.000 90.000 | |||
E.S.D. OF CELL PARAMETERS 1.3E-01 8.6E-02 9.3E-02 0.0E+00 0.0E+00 0.0E+00 | |||
SPACE GROUP NUMBER 16 | |||
So CORRECT chooses an orthorhombic spacegroup. Please note that the "UNIT CELL PARAMETERS" and the "E.S.D. OF CELL PARAMETERS" lines give a difference between the a and the b axis of 0.359 A, whereas the sum of their E.S.D.s is only 0.13+0.086 = 0.22 A. | |||
The file continues: | |||
... | |||
a b ISa | |||
6.058E+00 3.027E-04 23.35 | |||
... | ... | ||
| Line 43: | Line 78: | ||
NUMBER OF SYSTEMATIC ABSENT REFLECTIONS 0 | NUMBER OF SYSTEMATIC ABSENT REFLECTIONS 0 | ||
NUMBER OF ACCEPTED OBSERVATIONS 479004 | NUMBER OF ACCEPTED OBSERVATIONS 479004 | ||
NUMBER OF UNIQUE ACCEPTED REFLECTIONS 157108 | |||
Some comments: | |||
* CORRECT obviously indicates an orthorhombic spacegroup. | |||
* the number of MISFITS is higher than 1%. Running "xdsstat > XDSSTAT.LP" we obtain, among other files, the file "misfits.pck" which can be visualized using VIEW or XDS-Viewer. This clearly shows that many misfits are due to faint high-resolution ice rings - so nothing to worry about. | |||
To my surprise, pointless does not agree with CORRECT's standpoint: | |||
<pre> | |||
Scores for each symmetry element | |||
Nelmt Lklhd Z-cc CC N Rmeas Symmetry & operator (in Lattice Cell) | |||
1 0.959 9.91 0.99 65030 0.034 identity | |||
2 0.959 9.91 0.99 132222 0.035 *** 2-fold l ( 0 0 1) {-h,-k,+l} | |||
3 0.958 9.87 0.99 110073 0.044 *** 2-fold h ( 1 0 0) {+h,-k,-l} | |||
4 0.942 9.55 0.96 132646 0.109 *** 2-fold ( 1 1 0) {+k,+h,-l} | |||
5 0.958 9.87 0.99 111819 0.043 *** 2-fold k ( 0 1 0) {-h,+k,-l} | |||
6 0.941 9.54 0.95 131842 0.109 *** 2-fold ( 1-1 0) {-k,-h,-l} | |||
7 0.937 9.50 0.95 224393 0.107 *** 4-fold l ( 0 0 1) {-k,+h,+l} {+k,-h,+l} | |||
</pre> | |||
and | |||
<pre> | |||
Laue Group Lklhd NetZc Zc+ Zc- CC CC- Rmeas R- Delta ReindexOperator | |||
> 1 P 4/m m m *** 1.000 9.73 9.73 0.00 0.97 0.00 0.07 0.00 0.2 [h,k,l] | |||
- 2 P m m m 0.000 0.35 9.88 9.53 0.99 0.95 0.04 0.11 0.0 [h,k,l] | |||
3 C m m m 0.000 -0.02 9.72 9.74 0.97 0.97 0.07 0.07 0.2 [h+k,-h+k,l] | |||
4 P 4/m 0.000 0.07 9.77 9.70 0.98 0.97 0.06 0.08 0.2 [h,k,l] | |||
5 P 1 2/m 1 0.000 0.25 9.91 9.66 0.99 0.97 0.03 0.08 0.0 [-h,-l,-k] | |||
6 P 1 2/m 1 0.000 0.22 9.89 9.67 0.99 0.97 0.04 0.08 0.0 [h,k,l] | |||
7 P 1 2/m 1 0.000 0.21 9.88 9.67 0.99 0.97 0.04 0.08 0.0 [-k,-h,-l] | |||
8 C 1 2/m 1 0.000 -0.01 9.72 9.73 0.97 0.97 0.07 0.07 0.2 [h-k,h+k,l] | |||
9 C 1 2/m 1 0.000 -0.02 9.71 9.73 0.97 0.97 0.07 0.07 0.2 [h+k,-h+k,l] | |||
10 P -1 0.000 0.21 9.91 9.70 0.99 0.97 0.03 0.08 0.0 [h,k,l] | |||
</pre> | |||
and | |||
Spacegroup TotProb SysAbsProb Reindex Conditions | |||
<P 41 21 2> ( 92) 0.823 0.823 00l: l=4n, h00: h=2n (zones 1,2) | |||
<P 43 21 2> ( 96) 0.823 0.823 00l: l=4n, h00: h=2n (zones 1,2) | |||
.......... | |||
<P 4 21 2> ( 90) 0.095 0.095 h00: h=2n (zone 2) | |||
.......... | |||
<P 42 21 2> ( 94) 0.077 0.077 00l: l=2n, h00: h=2n (zones 1,2) | |||
Thus suggesting #92 or #96 - the latter of which agrees with the PDB deposition. Running CORRECT in #96, we obtain: | |||
REFINED PARAMETERS: DISTANCE BEAM ORIENTATION CELL AXIS | |||
USING 220320 INDEXED SPOTS | |||
STANDARD DEVIATION OF SPOT POSITION (PIXELS) 1.17 | |||
STANDARD DEVIATION OF SPINDLE POSITION (DEGREES) 0.14 | |||
CRYSTAL MOSAICITY (DEGREES) 0.191 | |||
DIRECT BEAM COORDINATES (REC. ANGSTROEM) -0.004790 0.004009 1.021014 | |||
DETECTOR COORDINATES (PIXELS) OF DIRECT BEAM 1027.19 1064.23 | |||
DETECTOR ORIGIN (PIXELS) AT 1036.79 1056.20 | |||
CRYSTAL TO DETECTOR DISTANCE (mm) 209.52 | |||
LAB COORDINATES OF DETECTOR X-AXIS 1.000000 0.000000 0.000000 | |||
LAB COORDINATES OF DETECTOR Y-AXIS 0.000000 1.000000 0.000000 | |||
LAB COORDINATES OF ROTATION AXIS 0.999996 0.000901 0.002534 | |||
COORDINATES OF UNIT CELL A-AXIS 21.926 53.087 85.553 | |||
COORDINATES OF UNIT CELL B-AXIS 3.794 87.060 -54.995 | |||
COORDINATES OF UNIT CELL C-AXIS -128.212 18.926 21.115 | |||
REC. CELL PARAMETERS 0.009704 0.009704 0.007616 90.000 90.000 90.000 | |||
UNIT CELL PARAMETERS 103.045 103.045 131.310 90.000 90.000 90.000 | |||
E.S.D. OF CELL PARAMETERS 2.1E-01 2.1E-01 2.1E-01 0.0E+00 0.0E+00 0.0E+00 | |||
SPACE GROUP NUMBER 96 | |||
... | |||
a b ISa | |||
7.890E+00 8.793E-04 12.01 | |||
... | |||
NOTE: Friedel pairs are treated as different reflections. | |||
SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF RESOLUTION | |||
RESOLUTION NUMBER OF REFLECTIONS COMPLETENESS R-FACTOR R-FACTOR COMPARED I/SIGMA R-meas Rmrgd-F Anomal SigAno Nano | |||
LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected Corr | |||
6.23 16770 2983 3017 98.9% 5.2% 6.1% 16752 26.20 5.7% 2.6% 55% 1.247 1223 | |||
4.43 30598 5392 5393 100.0% 5.8% 6.2% 30596 25.25 6.3% 3.0% 50% 1.072 2420 | |||
3.62 39822 6992 6994 100.0% 6.9% 6.6% 39820 22.27 7.6% 4.0% 32% 0.975 3215 | |||
3.14 49620 8240 8242 100.0% 9.2% 8.7% 49619 17.14 10.1% 6.2% 19% 0.876 3847 | |||
2.81 59388 9379 9379 100.0% 17.7% 18.1% 59387 10.44 19.3% 12.3% 0% 0.736 4410 | |||
2.56 65652 10308 10310 100.0% 34.6% 39.1% 65652 6.08 37.7% 23.6% -1% 0.680 4872 | |||
2.37 71744 11258 11259 100.0% 71.3% 83.8% 71744 3.23 77.6% 52.1% -2% 0.652 5352 | |||
2.22 74888 12065 12082 99.9% 111.0% 116.9% 74888 1.98 121.2% 86.9% 2% 0.718 5753 | |||
2.09 65727 12386 12874 96.2% 151.3% 176.1% 65517 1.12 168.0% 148.4% -3% 0.631 5797 | |||
total 474209 79003 79550 99.3% 10.3% 11.0% 473975 9.44 11.3% 17.2% 13% 0.772 36889 | |||
NUMBER OF REFLECTIONS IN SELECTED SUBSET OF IMAGES 492346 | |||
NUMBER OF REJECTED MISFITS 17898 | |||
NUMBER OF SYSTEMATIC ABSENT REFLECTIONS 141 | |||
NUMBER OF ACCEPTED OBSERVATIONS 474307 | |||
NUMBER OF UNIQUE ACCEPTED REFLECTIONS 79022 | |||