さきほど、d*TREK をビルドしたが、dtprocess と dtdisplay という GUI 部分がうまく動かなかった。そこで、CUI だけから使ってみることになる。
基本的には、xia2 のドキュメント ftp://ftp.ccp4.ac.uk/ccp4/6.3.0/ccp4-6.3.0/share/xia2/xia2/Wrappers/dTREK/Doc/dTREK.pdf に従えばよい。
まず、ヘッダを抽出する。今回は、R-AXIS IV で撮影した Thaumatin のデータセットを用いた。
$ ../dtextractheader test0001.osc start.head dtextractheader: Copyright (c) 2010 Rigaku d*TREK version 9.9.9.10L -- Jul 6 2015 Please see the file ${DTREK_ROOT}/ACKNOWLEDGEMENTS for further acknowledgements, copyrights and license information. Header of file test0001.osc successfully read.
次にスポットを検出する。XDS でいう COLSPOT。
$ ../dtfind start.head dtfind: Copyright (c) 2010 Rigaku d*TREK version 9.9.9.10L -- Jul 6 2015 Please see the file ${DTREK_ROOT}/ACKNOWLEDGEMENTS for further acknowledgements, copyrights and license information. Command line: ../dtfind start.head Header of file start.head successfully read. RX_NONUNF_TYPE: >>None<< Min raw image pixel OK value in mask/nonunf/image file: 1 Resolution limits of an image are 1541.78 to 1.4965 Resolution limits of peak search are 1541.78 to 1.4965 dtfind: 2D method used ...reading image test0001.osc... File test0001.osc successfully opened. Find object listing: Sigma: 5 Resolution: 1541.78 to 1.4965 Minimum: 50 Circle lim: 1500, 1500, 0, 2121 Rect lim: 30, 30, 2970, 2970 Spot wind.: 0, 0 Peak filt.: 6 Back. tile: 187, 187 Seq. num.: 1, 1 Every Nth: 1 Image dim.: 3000, 3000 3D dump: 0 653 preliminary spots found in 2D search with rotation angle 65.25 degs. dtfind: There were 643 spots found. There were 643 preliminary spots of which 0 were marked as saturated, or 0.00% of them. Number of reflections written in 'dtfind.ref': 643 dtfind: Spots written to dtfind.ref
dtfind.ref が SPOTS.XDS に相当する。
次に、指数付けを行う。-prompt をつけたので、対話的に操作する。
$ ../dtindex start.head dtfind.ref -prompt dtindex: Copyright (c) 2010 Rigaku d*TREK version 9.9.9.10L -- Jul 6 2015 Please see the file ${DTREK_ROOT}/ACKNOWLEDGEMENTS for further acknowledgements, copyrights and license information. Command line: ../dtindex start.head dtfind.ref -prompt Header of file start.head successfully read. Reflection list: dtfind.ref Creflnlist::nRead with filename: dtfind.ref INFO in Creflnlist::nRead, EOF after 643 reflections read in (643 total now in list). Command line string: >>-prompt<< INFO: deleted 0 reflns outside of resolution bounds. This leaves 643 reflns for indexing. INFO: 131 reflns deleted out of 643 that might be in ice rings. Max cell length allowed for reciprocal lattice vectors: 272.78 Method: 1D FFT with DPS algorithm Out header: dtindex.head Max cell: 272.78 Num vecs: 1000 Spacegroup: 0 Verbose: 1 Performing 1D FFT indexing (not cell reduction) with the DPS algorithm...see Steller, Bolotovsky, & Rossmann (1997) J. Appl. Cryst. 30, 1036-1040. Max cell is: 272.78 Number of reflections/vectors used: 445 ..................................... ...refining best 30 directions and lengths... .............................. done. Number of vectors used for integer residual calculation: 445 a b c alpha beta gamma Volume Remarks #Indexed %Residual ============================================================================== 57.79 82.42 222.72 42.78 58.14 45.06 509955 Okay 308 0.363 222.72 57.79 82.42 45.06 42.78 58.14 509955 Okay 308 0.363 82.42 222.72 57.79 58.14 45.06 42.78 509955 Okay 308 0.363 222.74 57.79 129.84 26.70 45.49 58.13 509865 Okay 307 0.365 129.84 222.74 57.79 58.13 26.70 45.49 509862 Okay 307 0.365 57.79 129.84 222.74 45.49 58.13 26.70 509865 Okay 307 0.365 82.41 222.74 129.84 45.49 18.37 42.76 509866 Okay 307 0.366 222.72 129.85 82.42 18.37 42.78 45.51 509957 Okay 308 0.362 129.85 82.42 222.72 42.78 45.51 18.37 509957 Okay 308 0.362 222.72 57.79 58.35 89.59 59.07 58.14 509957 Okay 308 0.362 57.79 58.35 222.72 59.07 58.14 89.59 509957 Okay 308 0.362 58.35 222.72 57.79 58.14 89.59 59.07 509957 Okay 308 0.362 222.72 82.42 58.35 44.52 59.07 42.78 509957 Okay 308 0.362 82.42 58.35 222.72 59.07 42.78 44.52 509957 Okay 308 0.362 58.35 222.72 82.42 42.78 44.52 59.07 509956 Okay 308 0.362 Executing beam refinement with beam search radius, acceptable shift radius: 10 9 ... RX_NONUNF_TYPE: >>None<< Min raw image pixel OK value in mask/nonunf/image file: 1 Original (input header) beam center: [1557.1 1496.2] First Pass. Search dim0 in [1547 1567] dim1 in [1486 1506] ............................................. Second Pass. Search dim0 in [1562 1564] dim1 in [1497 1499] Calculated pre-reduced cell solution is in agreement with detector beam center! Original (input header) beam center: [1557.1 1496.2] New (calculated) beam center: [1562.7 1497.8] Header updated to reflect beam center change. WARNING!: Beam position moved more than 5 pixels! ======= INFO: Restart with adjusted beam center. Max cell length allowed for reciprocal lattice vectors: 272.78 Method: 1D FFT with DPS algorithm Out header: dtindex.head Max cell: 272.78 Num vecs: 1000 Spacegroup: 0 Verbose: 1 Performing 1D FFT indexing (not cell reduction) with the DPS algorithm...see Steller, Bolotovsky, & Rossmann (1997) J. Appl. Cryst. 30, 1036-1040. Max cell is: 272.78 Number of reflections/vectors used: 445 ..................................... ...refining best 30 directions and lengths... .............................. done. Number of vectors used for integer residual calculation: 445 a b c alpha beta gamma Volume Remarks #Indexed %Residual ============================================================================== 237.26 58.13 58.29 89.95 42.93 104.16 510869 Okay 300 0.216 58.29 237.26 58.13 104.16 89.95 42.93 510869 Okay 300 0.216 58.13 58.29 237.26 42.93 104.16 89.95 510869 Okay 300 0.216 82.36 58.28 237.27 42.93 69.78 44.90 510842 Okay 298 0.216 58.28 237.27 82.36 69.78 44.90 42.93 510842 Okay 298 0.216 237.27 82.36 58.28 44.90 42.93 69.78 510842 Okay 298 0.216 237.26 58.12 82.36 45.07 69.78 104.15 510984 Okay 301 0.217 58.12 82.36 237.26 69.78 104.15 45.07 510984 Okay 301 0.217 82.36 237.26 58.12 104.15 45.07 69.78 510984 Okay 301 0.217 58.28 237.27 130.31 56.91 26.49 42.93 510775 Okay 298 0.218 130.31 58.28 237.27 42.93 56.91 26.49 510775 Okay 298 0.218 237.27 130.31 58.28 26.49 42.93 56.91 510775 Okay 298 0.218 82.29 58.30 237.22 42.90 133.77 135.07 510447 Okay 299 0.215 58.30 237.22 82.29 133.77 135.07 42.90 510447 Okay 299 0.215 237.22 82.29 58.30 135.07 42.90 133.77 510447 Okay 299 0.215 82.30 58.13 237.22 104.16 133.75 45.11 510836 Okay 300 0.215 237.22 82.30 58.13 45.11 104.16 133.75 510836 Okay 300 0.215 58.13 237.22 82.30 133.75 45.11 104.16 510837 Okay 300 0.215 237.22 130.01 58.11 26.65 104.14 123.15 510699 Okay 302 0.218 58.11 237.22 130.01 123.15 26.65 104.14 510699 Okay 302 0.218 130.01 58.11 237.22 104.14 123.15 26.65 510696 Okay 302 0.218 82.34 130.29 237.26 56.87 69.74 18.41 510582 Okay 302 0.222 130.10 237.26 58.13 104.16 26.62 83.71 510840 Okay 299 0.215 58.13 130.10 237.26 83.71 104.16 26.62 510840 Okay 299 0.215 237.26 58.13 130.10 26.62 83.71 104.16 510840 Okay 299 0.215 130.09 82.36 237.23 69.78 83.71 18.44 510946 Okay 302 0.220 237.24 82.29 130.01 18.47 123.16 133.75 510907 Okay 300 0.216 82.29 130.01 237.24 123.16 133.75 18.47 510907 Okay 300 0.216 Least square fit to lattice characters...see Andrews & Bernstein (1988) Acta Cryst. A44, 1009-1018 and Paciorek & Bonin (1992) J. Appl. Cryst. 25, 632-637. ............................................................ ............................................................ done. Least-squares fit of reduced primitive cell to 44 lattice characters sorted on decreasing (highest to lowest) symmetry. Best possible least-squares residual is 0.000%, worst residual is 100.0%. Only solutions with % residuals <= 3.0% are listed. ======================================================================= Soln LeastSq Spgrp Cent Bravais type a b c num resid(%) num* type Cell volume alpha beta gamma ======================================================================= 7 0.588 75 P tetragonal 58.215 58.215 150.739 510854 90.000 90.000 90.000 9 0.588 21 C orthorhombic 82.295 82.361 150.739 1021708 90.000 90.000 90.000 11 0.585 16 P orthorhombic 58.129 58.301 150.739 510852 90.000 90.000 90.000 12 0.222 5 C monoclinic 82.227 81.891 150.559 1013806 90.000 90.227 90.000 13 0.024 3 P monoclinic 58.301 58.129 150.739 510837 90.000 90.442 90.000 14 0.000 1 P triclinic 58.129 58.301 150.739 510836 89.558 89.984 89.954 ======================================================================= *Suggested spacegroup number until systematic absences are examined. To view least-squares fits to other lattices, enter a new percent residual between 15 and 100% at the following prompt. PLEASE ANSWER THE FOLLOWING PROMPT: Enter solution number (Soln num) of your choice (1-14) from the above table or a new limiting % residual to show more (but worse) solutions (>= 15%) Note: Good solutions usually have 'LeastSq resid(%)' less than 0.5% to 1.0%. or enter L to get a lattice character listing. <Enter> or <cr> or 7 will select the 'P tetragonal' lattice. Select> ...determining orientation angles... . Unit cell parameters and orientation angles ====================================================================== Integer a b c Num residual alpha beta gamma Rot1 Rot2 Rot3 ====================================================================== 1 0.001 58.215 58.215 150.739 17.847 -57.384 -145.253 90.000 90.000 90.000 2 0.001 58.215 58.215 150.739 -17.847 57.384 34.747 90.000 90.000 90.000 3 0.001 58.215 58.215 150.739 -162.153 -57.384 -145.253 90.000 90.000 90.000 4 0.001 58.215 58.215 150.739 162.153 57.384 34.747 90.000 90.000 90.000 5 0.001 58.215 58.215 150.739 -58.654 -9.508 -40.080 90.000 90.000 90.000 6 0.001 58.215 58.215 150.739 58.654 9.508 139.920 90.000 90.000 90.000 7 0.001 58.215 58.215 150.739 121.346 -9.508 -40.080 90.000 90.000 90.000 8 0.001 58.215 58.215 150.739 -121.346 9.508 139.920 90.000 90.000 90.000 ====================================================================== The above table shows symmetry EQUIVALENT crystal orientation angles for the indexing orientation. All the solutions are equivalent for the selected Bravais lattice. The default selection usually has the values closest to crystal orientation found in the input .head file or the one where (|Rot1| + |Rot2| + |Rot3|) is a minimum. PLEASE ANSWER THE FOLLOWING PROMPT: Enter your choice 0=Abort [5]: Orientation angles choice 5 selected. Crystal listing: Unit cell lengths: 58.2150 58.2150 150.7394 Unit cell angles: 90.0000 90.0000 90.0000 Unit cell volume: 510854.035 Orientation angles: -58.6536 -9.5083 -40.0800 Mosaicity: 0.300 Description: unknown Spacegroup number: 75 name: P4 Num. equiv. posns: 4 dtindex - Wrote header file dtindex.head INFO - The above indexing solution is ONLY a hypothesis. One must confirm the hypothesis by examining symmetry of observed intensities as well as possible systematic absences. One does this by collecting data, processing the data and using dtcell and dtscaleaverage. INFO - The suggested next step is to run dtrefine with dtindex.head as the input .head file: dtrefine dtindex.head dtfind.ref ...
ここで、方位行列などが書き加えられた dtindex.head ができる。これを dtrefine に与えて、精密化を行う。精密化ストラテジにもいろいろあるようだが、xia2 ドキュメントを参考にやってみる。-seq で画像範囲を指定すると、そこでスポットを探しながら精密化してくれるようだ。
$ ../dtrefine dtindex.head -seq 1 5 -seq 180 185 +CrysAll +DetAll -go dtrefine: Copyright (c) 2010 Rigaku d*TREK version 9.9.9.10L -- Jul 6 2015 Please see the file ${DTREK_ROOT}/ACKNOWLEDGEMENTS for further acknowledgements, copyrights and license information. Command line: ../dtrefine dtindex.head -seq 1 5 -seq 180 185 +CrysAll +DetAll -go Header of file dtindex.head successfully read. Reflection centroids will come from a search of image(s), and not from a reflnlist file. RX_NONUNF_TYPE: >>None<< Min raw image pixel OK value in mask/nonunf/image file: 1 File test0001.osc successfully opened. ... predicting reflections and getting centroids for image 1 ... File test0002.osc successfully opened. ... predicting reflections and getting centroids for image 2 ... File test0003.osc successfully opened. ... predicting reflections and getting centroids for image 3 ... File test0004.osc successfully opened. ... predicting reflections and getting centroids for image 4 ... File test0005.osc successfully opened. ... predicting reflections and getting centroids for image 5 ... File test0180.osc successfully opened. ... predicting reflections and getting centroids for image 180 ... File test0181.osc successfully opened. ... predicting reflections and getting centroids for image 181 ... File test0182.osc successfully opened. ... predicting reflections and getting centroids for image 182 ... File test0183.osc successfully opened. ... predicting reflections and getting centroids for image 183 ... File test0184.osc successfully opened. ... predicting reflections and getting centroids for image 184 ... File test0185.osc successfully opened. ... predicting reflections and getting centroids for image 185 ... Total number of reflns in m_poReflnlist: 80545 Reflection status after merging ------------------------------- Raw 2D centroids 8976 Merged 4773 Reflns. on 1 consecutive image(s) 3710 Reflns. on 2 consecutive image(s) 780 Reflns. on 3 consecutive image(s) 204 Reflns. on 4 consecutive image(s) 61 Reflns. on 5 consecutive image(s) 18 Total number of predicted merged reflections: 4773 Refine listing: Crystal listing: Unit cell lengths: 58.2150 58.2150 150.7394 Unit cell angles: 90.0000 90.0000 90.0000 Unit cell volume: 510853.750 Orientation angles: -58.6536 -9.5083 -40.0800 Mosaicity: 0.300 Description: unknown Spacegroup number: 75 name: P4 Num. equiv. posns: 4 CRYSTAL_ Goniometer listing: Description: Crystal Goniometer Number of values: 3 Name Datum Current Units Vector ===================================================================== Omega 0.000 Unknown deg ( 1.000, 0.000, 0.000) Chi 0.000 Unknown deg ( 0.000, 0.000, 1.000) Phi 0.000 Unknown deg ( 1.000, 0.000, 0.000) ===================================================================== Source listing: Single wavelength: 1.5418 Polarization: 0.5, 1, 0, 0 Intensity: 0 RX_Detector listing: Pixel dimensions: 3000, 3000 Nominal size in mm: 300, 300 Description: RAXIS conversion Spatial distortion descriptive text: Simple pixel scaling spatial distortion Simple spatial distortion: Center of primary beam: 1562.7, 1497.8 Pixel size (mm): 0.1, 0.1 Direction vectors: 0, 1, -1, 0 RX_ Goniometer listing: Description: UNKNOWN Number of values: 6 Name Datum Current Units Vector ===================================================================== RotZ 0.000 Unknown deg ( 0.000, 0.000, 1.000) RotX/Swing 0.000 Unknown deg ( -1.000, 0.000, 0.000) RotY 0.000 Unknown deg ( 0.000, 1.000, 0.000) TransX 0.000 Unknown mm ( 1.000, 0.000, 0.000) TransY 0.000 Unknown mm ( 0.000, 1.000, 0.000) TransZ/Dist 115.000 Unknown mm ( 0.000, 0.000, -1.000) ===================================================================== DetResolution min: 1541.78 DetResolution max: 1.4958 DetResolution edge: 1.70829 Refine resol min: 99999 Refine resol max: 1e-05 I/sigma cutoff: 5 Sharpness cutoff: 0.2 Rejection limits: 2.5, 2.5, 2 Weighting scheme: Unit weights ....*........................ INFO: no convergence after 30 cycles. Number of found reflections and best mosaicity vs Trial rotation offset ------------------------------------------------------------------------------ % of Max number of observed reflections* Offset Mosaicity^ reflns 0...10...20...30...40...50...60...70...80...90...100 ------------------------------------------------------------------------------ -0.40 1.69 5281 *********** -0.35 1.60 5412 ******************** -0.30 1.53 5503 ************************** -0.25 1.43 5581 ******************************* -0.20 1.34 5630 *********************************** -0.15 1.25 5682 ************************************** -0.10 1.18 5735 ****************************************** -0.05 1.08 5782 ********************************************* -0.00 0.99 5818 *********************************************** 0.05 0.90 5862 ************************************************** 0.10 0.85 5882 **************************************************** 0.15 0.81 5895 **************************************************** 0.20 0.85 5896 **************************************************** 0.25 0.90 5882 **************************************************** 0.30 0.99 5855 ************************************************** 0.35 1.08 5789 ********************************************* 0.40 1.15 5685 ************************************** ------------------------------------------------------------------------------ ^Mosaicity value needed to get maximum number of reflns with this offset. *When mosaicity is set to 0.81 degrees. INFO: Mosaicity set to 0.81 degrees. INFO: Rotation Offset of 0.15 degrees applied to obtain lowest mosaicity. Refinement results ================================================================== Crystal a, b, c: 58.1596 58.1596 150.6231 Sigmas: 0.0169 0.0169 0.0470 Shifts: -0.0554 -0.0554 -0.1163 alpha, beta, gamma: 90.0000 90.0000 90.0000 Sigmas: 0.0000 0.0000 0.0000 Shifts: 0.0000 0.0000 0.0000 Crys Rot1, Rot2, Rot3: -58.862 -9.454 -40.141 Sigmas: 0.0107 0.0109 0.0078 Shifts: -0.2085 0.0544 -0.0612 Mosaicity: 0.8054 Sigma: 0.1000 Shift: 0.5054 ================================================================== Detector: 0 DetTrans: TransX, TransY, TransZ: 0.155 0.420 114.813 Sigmas: 0.0098 0.0105 0.0497 Shifts: 0.1554 0.4196 -0.1869 DetRots: RotZ, RotX/Swing, RotY: -0.002 0.196 0.102 Sigmas: 0.0121 0.0196 0.0209 Shifts: -0.0019 0.1955 0.1023 ================================================================== Source Wavelength, Rot1, Rot2: 1.541800 0.000 0.000 Sigmas: fixed fixed fixed Shifts: fixed fixed fixed ================================================================== Refinement residuals rmsResid (A-1) = 0.00206 rmsResid (mm) = 0.2881 FAIR, less than or equal to 3 pixels (0.300 mm). rmsResid (Deg) = 0.2586 GOOD, less than 1/2 the mosaicity. ================================================================== Reflections in list: 4773 Reflections accepted [blue]: 4214 (Resolution limits of these: 15.6974 to 1.61412 A) Reflections rejected [ red]: 214 (|Xobs-Xcalc| >= 2.5 mm), or (|Yobs-Ycalc| >= 2.5 mm) Reflections rejected [ red]: 316 (|Rotobs-Rotcalc| >= 2 deg) Reflections ignored [green]: 29 (I/sigI < 5 or outside resolution of 99999 to 1e-05, or Lorentz factor too large, or sharpness > 0.2, etc) Listing for all refinement iterations ----------------------------------------------------------------- Iter Twin Volume Rms Rms Total Ignored Rejects Rejects (MM) (DEG) refln refln (MM) (DEG) ----------------------------------------------------------------- 31 01/01 509489 0.2881 0.2586 4214 29 213 316 ----------------------------------------------------------------- dtrefine - INFO wrote header file: dtrefine.head INFO - The suggested next step is to run dtrefine again: dtrefine dtrefine.head -seq ... -or- Run dtpredict to check that the results predict the first few images in each scan correctly: dtpredict dtrefine.head -seq ... -or- Run dtmultistrategy or dtintegrate with dtrefine.head as the input .head file: dtmultistrategy dtrefine.head ... dtintegrate dtrefine.head ...
これで準備が終わった。積分を行う。
$ ../dtintegrate dtrefine.head -seq 1 230 dtintegrate: Copyright (c) 2010 Rigaku d*TREK version 9.9.9.10L -- Jul 6 2015 Please see the file ${DTREK_ROOT}/ACKNOWLEDGEMENTS for further acknowledgements, copyrights and license information. Command line: ../dtintegrate dtrefine.head -seq 1 230 Header of file dtrefine.head successfully read. Command line string: >>-seq<< =============================================== Integrate object listing: =============================================== Verbose level: 1 Scan sequence range: 1, 230 Resolution range: 0, 100000 Images/ Scale batch: 1 Images/ Refine batch: 4 Batch prefix: Image padding: 0 Image padding multiplier: 1 Minimum peak radius in pixels: 2 Spot size multiplier: 2.8 Input max window size: 0, 0 Input min window size: 0, 0 Maximum refln overlap fraction: 0.03 Alpha1 / Alpha2 splitting option: Off Mosaicity model: 1, 0 mosaicity used = (Refined_mosaicity * 1) + 0 Num oblique incidence factors: 0 Num excluded resolution rings: 0 =============================================== dtintegrate: 3D method used RX_NONUNF_TYPE: >>None<< Min raw image pixel OK value in mask/nonunf/image file: 1 ... reflnlist dtintegrate.ref prepared for writing. ... reflnlist dtintrejects.ref prepared for writing. ... reflnlist dtintpartials.ref prepared for writing. File test0001.osc successfully opened. ================================================================== PRE-REFINE IMAGE #: 1 (restart expected after image 8 of 230) Name: test0001.osc Date: 6-Jul-2015 Time: 16:25:56 Elapsed: 1 ================================================================== Rotation list: Start: 65.000 End: 65.500 Increment: 0.500 Time: 60.000 INFO: eImage_data_type is unsigned short int Reflection dispositions ================================================= Status: New Active Full DNormal Dspecial Number: 1274 1274 0 0 0 ================================================= File test0002.osc successfully opened. ================================================================== PRE-REFINE IMAGE #: 2 (restart expected after image 8 of 230) Name: test0002.osc Date: 6-Jul-2015 Time: 16:25:56 Elapsed: 1 ================================================================== Rotation list: Start: 65.500 End: 66.000 Increment: 0.500 Time: 60.000 Reflection dispositions ================================================= Status: New Active Full DNormal Dspecial Number: 1254 2528 180 82 98 ================================================= File test0003.osc successfully opened. ================================================================== PRE-REFINE IMAGE #: 3 (restart expected after image 8 of 230) Name: test0003.osc Date: 6-Jul-2015 Time: 16:25:57 Elapsed: 2 ================================================================== Rotation list: Start: 66.000 End: 66.500 Increment: 0.500 Time: 60.000 Reflection dispositions ================================================= Status: New Active Full DNormal Dspecial Number: 1223 3571 939 391 548 ================================================= Strong peak info listing =============================================================================== Pix Pix Num Counts Sigma Back Back Box Box Major Minor Rot. Shift Shift [0] [1] Avg Sig [0] [1] Axis Axis Axis [0] [1] =============================================================================== 300 300 32 15006 317 239 22 33 33 14.0 10.4 1.4 0.8 0.7 300 900 23 7637 266 187 20 33 33 15.3 9.4 1.3 0.9 0.6 300 1500 19 20329 458 317 35 33 33 14.8 10.4 1.4 1.0 0.7 300 2100 27 30162 562 356 38 33 33 14.4 10.5 1.3 0.9 0.7 300 2700 11 15764 410 292 28 33 33 13.4 10.8 1.5 0.7 0.7 900 300 32 15006 317 239 22 33 33 14.0 10.4 1.4 0.8 0.7 900 900 36 59506 653 510 44 33 33 12.6 10.5 1.5 0.7 0.6 900 1500 93 144136 1327 803 83 33 33 12.5 10.5 1.3 0.7 0.7 900 2100 27 49868 706 487 42 33 33 12.7 10.6 1.5 0.7 0.6 900 2700 11 15764 410 292 28 33 33 13.4 10.8 1.5 0.7 0.7 1500 300 122 112172 975 538 56 33 33 12.3 10.8 1.3 0.7 0.8 1500 900 122 112172 975 538 56 33 33 12.3 10.8 1.3 0.7 0.8 1500 1500 37 307663 1783 509 94 33 33 13.6 10.9 1.4 0.7 0.9 1500 2100 106 120329 1023 509 62 33 33 12.7 11.1 1.3 0.7 0.7 1500 2700 106 120329 1023 509 62 33 33 12.7 11.1 1.3 0.7 0.7 2100 300 16 42017 587 298 36 33 33 12.2 10.8 1.5 0.6 0.6 2100 900 35 118413 1054 596 58 33 33 13.4 11.0 1.5 0.7 0.8 2100 1500 94 190291 1414 691 81 33 33 12.7 11.2 1.3 0.7 0.8 2100 2100 29 59880 730 474 45 33 33 12.8 11.1 1.4 0.8 0.8 2100 2700 21 25663 459 299 30 33 33 13.6 11.3 1.5 0.7 0.9 2700 300 16 42017 587 298 36 33 33 12.2 10.8 1.5 0.6 0.6 2700 900 10 12497 351 239 28 33 33 12.7 9.6 1.4 0.7 0.7 2700 1500 40 19112 440 291 32 33 33 12.5 9.7 1.1 0.8 0.8 2700 2100 46 26227 511 325 34 33 33 13.0 10.6 1.2 0.7 0.6 2700 2700 21 25663 459 299 30 33 33 13.6 11.3 1.5 0.7 0.9 =============================================================================== All area avg: 68305 712 405 44 33 33 12.7 10.8 1.4 0.7 0.7 =============================================================================== File test0004.osc successfully opened. ================================================================== PRE-REFINE IMAGE #: 4 (restart expected after image 8 of 230) Name: test0004.osc Date: 6-Jul-2015 Time: 16:25:58 Elapsed: 3 ================================================================== Rotation list: Start: 66.500 End: 67.000 Increment: 0.500 Time: 60.000 Reflection dispositions ================================================= Status: New Active Full DNormal Dspecial Number: 1200 3832 1090 358 732 ================================================= Refinement options found: +CrysAll +DetAll -go Refine listing: Crystal listing: Unit cell lengths: 58.1596 58.1596 150.6231 Unit cell angles: 90.0000 90.0000 90.0000 Unit cell volume: 509488.521 Orientation angles: -58.8622 -9.4539 -40.1412 Mosaicity: 0.805 Description: unknown Spacegroup number: 75 name: P4 Num. equiv. posns: 4 CRYSTAL_ Goniometer listing: Description: Crystal Goniometer Number of values: 3 Name Datum Current Units Vector ===================================================================== Omega 0.000 Unknown deg ( 1.000, 0.000, 0.000) Chi 0.000 Unknown deg ( 0.000, 0.000, 1.000) Phi 0.000 Unknown deg ( 1.000, 0.000, 0.000) ===================================================================== Source listing: Multiple wavelengths: Polarization: 0.5, 1, 0, 0 Intensity: 0 RX_Detector listing: Pixel dimensions: 3000, 3000 Nominal size in mm: 300, 300 Description: RAXIS conversion Spatial distortion descriptive text: Simple pixel scaling spatial distortion Simple spatial distortion: Center of primary beam: 1562.7, 1497.8 Pixel size (mm): 0.1, 0.1 Direction vectors: 0, 1, -1, 0 RX_ Goniometer listing: Description: UNKNOWN Number of values: 6 Name Datum Current Units Vector ===================================================================== RotZ -0.002 Unknown deg ( 0.000, 0.000, 1.000) RotX/Swing 0.196 Unknown deg ( -1.000, 0.000, 0.000) RotY 0.102 Unknown deg ( 0.000, 1.000, 0.000) TransX 0.155 Unknown mm ( 1.000, 0.000, 0.000) TransY 0.420 Unknown mm ( 0.000, 1.000, 0.000) TransZ/Dist 114.813 Unknown mm ( 0.000, 0.000, -1.000) ===================================================================== DetResolution min: 1541.78 DetResolution max: 1.49136 DetResolution edge: 1.7034 Refine resol min: 99999 Refine resol max: 1e-05 I/sigma cutoff: 0 Sharpness cutoff: 0.2 Rejection limits: 2.5, 2.5, 2 Weighting scheme: Unit weights ............................. INFO: no convergence after 30 cycles. Number of found reflections and best mosaicity vs Trial rotation offset ------------------------------------------------------------------------------ % of Max number of observed reflections* Offset Mosaicity^ reflns 0...10...20...30...40...50...60...70...80...90...100 ------------------------------------------------------------------------------ -0.40 1.32 841 *********** -0.35 1.22 911 ********************* -0.30 1.13 974 ****************************** -0.25 1.06 1045 **************************************** -0.20 0.97 1072 ******************************************** -0.15 0.88 1097 *********************************************** -0.10 0.78 1114 ************************************************** -0.05 0.71 1126 **************************************************** -0.00 0.64 1133 **************************************************** 0.05 0.67 1127 **************************************************** 0.10 0.76 1124 *************************************************** 0.15 0.85 1117 ************************************************** 0.20 0.97 1112 ************************************************** 0.25 1.04 1097 *********************************************** 0.30 1.15 1084 ********************************************** 0.35 1.25 1037 *************************************** 0.40 1.34 986 ******************************** ------------------------------------------------------------------------------ ^Mosaicity value needed to get maximum number of reflns with this offset. *When mosaicity is set to 0.64 degrees. INFO: Mosaicity set to 0.64 degrees. INFO: Rotation Offset of 0.00 degrees applied to obtain lowest mosaicity. Refinement results ================================================================== Crystal a, b, c: 58.0217 58.0217 150.0661 Sigmas: 0.0211 0.0211 0.1192 Shifts: -0.1379 -0.1379 -0.5570 alpha, beta, gamma: 90.0000 90.0000 90.0000 Sigmas: 0.0000 0.0000 0.0000 Shifts: 0.0000 0.0000 0.0000 Crys Rot1, Rot2, Rot3: -58.819 -9.446 -40.123 Sigmas: 0.0078 0.0070 0.0136 Shifts: 0.0428 0.0083 0.0185 Mosaicity: 0.6427 Sigma: 0.1000 Shift: -0.1627 ================================================================== Detector: 0 DetTrans: TransX, TransY, TransZ: -0.066 0.708 114.340 Sigmas: 0.0106 0.0123 0.0667 Shifts: -0.2218 0.2889 -0.4732 DetRots: RotZ, RotX/Swing, RotY: 0.011 0.341 -0.002 Sigmas: 0.0052 0.0191 0.0373 Shifts: 0.0130 0.1454 -0.1041 ================================================================== Source Wavelength, Rot1, Rot2: 1.541800 0.000 0.000 Sigmas: fixed fixed fixed Shifts: fixed fixed fixed ================================================================== Refinement residuals rmsResid (A-1) = 0.00098 rmsResid (mm) = 0.1376 GOOD, less than or equal to 2 pixels (0.200 mm). rmsResid (Deg) = 0.0583 EXCELLENT, less than 1/4 the mosaicity. ================================================================== Reflections in list: 831 Reflections accepted [blue]: 794 (Resolution limits of these: 15.6545 to 1.65463 A) Reflections rejected [ red]: 36 (|Xobs-Xcalc| >= 2.5 mm), or (|Yobs-Ycalc| >= 2.5 mm) Reflections rejected [ red]: 1 (|Rotobs-Rotcalc| >= 2 deg) Reflections ignored [green]: 0 (I/sigI < 0 or outside resolution of 99999 to 1e-05, or Lorentz factor too large, or sharpness > 0.2, etc) PLOTCRYS: Seq a b c alp bet gam Rot1 Rot2 Rot3 Mos 4 58.02 58.02 150.07 90.00 90.00 90.00 -58.82 -9.45 -40.12 0.643 PLOTDET: Seq TransX TransY Dist RotZ RotX RotY SrcRot1 SrcRot2 rmsMM rmsDeg 4 -0.07 0.71 114.34 0.01 0.34 -0.00 0.00 0.00 0.138 0.058 INFO: Integrate Mosaicity accepts the 0.642676 deg value from refinement. Number of reflections written in 'dtintrefine.ref': 831 ...(中略)... Working ... Almost done. Rocking curve width analysis (for reflections 0 through 89999 only) ------------------------------------ Full-width (Degrees) at % of Total_area Max_height ------------------------------------ 70% 0.154 0.653 50% 0.267 0.810 30% 0.410 0.962 10% 0.627 1.167 5% 0.729 1.253 1% 0.913 1.399 ------------------------------------ Total spatial overlaps (intersections): 247 -------------------------------------------------------------------- <=0.001 0.002 0.004 0.008 0.016 0.032 0.064 0.128 0.256 0.512 >=1.0 0 0 0 1 3 14 25 48 67 78 15 -------------------------------------------------------------------- Number of reflections written in 'Part0_dtprofit.ref': 90000 Creflnlist::nRead with filename: dtintegrate.ref Creflnlist::nRead with filename: dtintpartials.ref Working ... Almost done. Rocking curve width analysis (for reflections 90000 through 179999 only) ------------------------------------ Full-width (Degrees) at % of Total_area Max_height ------------------------------------ 70% 0.177 0.291 50% 0.318 0.537 30% 0.484 0.737 10% 0.703 0.901 5% 0.787 0.963 1% 0.921 1.054 ------------------------------------ Total spatial overlaps (intersections): 259 -------------------------------------------------------------------- <=0.001 0.002 0.004 0.008 0.016 0.032 0.064 0.128 0.256 0.512 >=1.0 0 0 0 0 0 0 0 21 54 170 14 -------------------------------------------------------------------- Number of reflections written in 'Part1_dtprofit.ref': 90000 Creflnlist::nRead with filename: dtintegrate.ref INFO in Creflnlist::nRead, EOF after 90451 reflections read in (90451 total now in list). Creflnlist::nRead with filename: dtintpartials.ref INFO in Creflnlist::nRead, EOF after 122082 reflections read in (122082 total now in list). h00, 0k0, 00l (axial) reflections. Examine them for systematic absences. -------------------------------------------------------------- h k l Intensity SigmaInt I/sigI Pix0 Pix1 Angle -------------------------------------------------------------- -35 0 0 0 0 0.0 684 2913 149.14 -34 0 0 0 0 0.0 722 2815 150.76 -33 0 0 0 0 0.0 759 2726 152.32 -32 0 0 33434 605 55.3 799 2648 153.79 -31 0 0 0 0 0.0 829 2571 155.29 -30 0 0 99873 973 102.7 863 2506 156.77 ...(中略)... 0 0 -89 0 0 0.0 2901 2377 175.63 0 0 -91 0 0 0.0 2966 2427 176.34 0 0 -90 0 0 0.0 2933 2401 176.00 -------------------------------------------------------------- Number of reflections written in 'axial.ref': 237 INFO: Use dtdisplay and File>Read refln list ... to view these axial reflns. Working ... Almost done. Rocking curve width analysis (for reflections 180000 through 279999 only) ------------------------------------ Full-width (Degrees) at % of Total_area Max_height ------------------------------------ 70% 0.173 0.317 50% 0.313 0.511 30% 0.477 0.701 10% 0.697 0.890 5% 0.784 0.951 1% 0.928 1.033 ------------------------------------ Total spatial overlaps (intersections): 159 -------------------------------------------------------------------- <=0.001 0.002 0.004 0.008 0.016 0.032 0.064 0.128 0.256 0.512 >=1.0 0 0 0 0 0 0 5 7 35 108 4 -------------------------------------------------------------------- Analysis of partials contributing to integrated data ----------------------------------------------------------------------------- Reflections removed with highly deviant pixel positions: 765 Reflections removed due to highly deviant profile fit: 0 Reflections removed due to overlaps: 665 Maximum deviation allowed between calculated and observed positions: 9.0 Reflections with noisy tails removed: 23571 Reflections containing both profiled and non-profiled data: 0 Reflections containing only profiled data: 0 Reflections containing only non-profiled data: 269021 Reflections which lacked adequate profile information: 0 Reflections containing intensity beyond predicted mosaicity bounds: 1189 Reflections containing intensity only in the centroid slice: 156435 ----------------------------------------------------------------------------- Total profiles examined: 0 Total profiles used: 0 Total reflections to be output: 269021 ----------------------------------------------------------------------------- Number of reflections written in 'Part2_dtprofit.ref': 90451 Creflnlist::nRead with filename: Part0_dtprofit.ref INFO in Creflnlist::nRead, EOF after 89618 reflections read in (89618 total now in list). Creflnlist::nRead with filename: Part1_dtprofit.ref INFO in Creflnlist::nRead, EOF after 89453 reflections read in (89453 total now in list). Creflnlist::nRead with filename: Part2_dtprofit.ref INFO in Creflnlist::nRead, EOF after 89950 reflections read in (89950 total now in list). Number of reflections written in 'dtprofit.ref': 269021 Average rocking curve for strong reflns on 2 images (67414 contributors). ========================================================================== Image 0 50.7% ****************************** Image 1 49.3% ***************************** ========================================================================== Average rocking curve for strong reflns on 3 images (12708 contributors). ========================================================================== Image 0 19.1% *********** Image 1 64.1% ************************************** Image 2 16.8% ********** ========================================================================== Average rocking curve for strong reflns on 4 images (2433 contributors). ========================================================================== Image 0 16.0% ********* Image 1 37.8% ********************** Image 2 32.6% ******************* Image 3 13.6% ******** ========================================================================== Average rocking curve for strong reflns on 5 images (824 contributors). ========================================================================== Image 0 13.5% ******** Image 1 25.4% *************** Image 2 29.7% ***************** Image 3 20.5% ************ Image 4 10.9% ****** ========================================================================== Average rocking curve for strong reflns on 6 images (360 contributors). ========================================================================== Image 0 11.0% ****** Image 1 18.7% *********** Image 2 23.3% ************* Image 3 22.0% ************* Image 4 15.4% ********* Image 5 9.7% ***** ========================================================================== Average rocking curve for strong reflns on 7 images (211 contributors). ========================================================================== Image 0 10.0% ****** Image 1 15.1% ********* Image 2 18.7% *********** Image 3 19.5% *********** Image 4 16.4% ********* Image 5 11.7% ******* Image 6 8.4% ***** ========================================================================== Average rocking curve for strong reflns on 8 images (106 contributors). ========================================================================== Image 0 8.2% **** Image 1 12.0% ******* Image 2 15.6% ********* Image 3 17.2% ********** Image 4 16.1% ********* Image 5 13.2% ******* Image 6 10.3% ****** Image 7 7.5% **** ========================================================================== Average rocking curve for strong reflns on 9 images (47 contributors). ========================================================================== Image 0 7.8% **** Image 1 10.7% ****** Image 2 13.1% ******* Image 3 14.6% ******** Image 4 14.6% ******** Image 5 13.4% ******** Image 6 11.0% ****** Image 7 8.5% ***** Image 8 6.4% *** ========================================================================== Average rocking curve for strong reflns on 10 images (33 contributors). ========================================================================== Image 0 6.9% **** Image 1 8.6% ***** Image 2 10.5% ****** Image 3 11.9% ******* Image 4 13.2% ******* Image 5 13.0% ******* Image 6 11.8% ******* Image 7 9.7% ***** Image 8 8.0% **** Image 9 6.4% *** ========================================================================== Average rocking curve for strong reflns on 12 images (21 contributors). ========================================================================== Image 0 4.9% ** Image 1 6.3% *** Image 2 7.7% **** Image 3 9.2% ***** Image 4 10.4% ****** Image 5 11.1% ****** Image 6 11.0% ****** Image 7 10.4% ****** Image 8 9.5% ***** Image 9 8.0% **** Image 10 6.3% *** Image 11 5.1% *** ========================================================================== *** dtintegrate *** Summary of crystal refinement results during integration ------------------------------------------------------------------------------------ Seq a b c alp bet gam Rot1 Rot2 Rot3 Mos MosMod ------------------------------------------------------------------------------------ 4 57.98 57.98 149.85 90.00 90.00 90.00 -58.81 -9.45 -40.11 0.57 0.57 8 57.97 57.97 149.84 90.00 90.00 90.00 -58.81 -9.45 -40.11 0.60 0.60 12 57.97 57.97 149.84 90.00 90.00 90.00 -58.81 -9.44 -40.11 0.57 0.57 ...(中略)... 224 58.02 58.02 150.36 90.00 90.00 90.00 -58.71 -9.24 -40.14 0.20 0.20 228 58.02 58.02 150.36 90.00 90.00 90.00 -58.71 -9.24 -40.13 0.20 0.20 230 58.02 58.02 150.36 90.00 90.00 90.00 -58.71 -9.24 -40.13 0.18 0.18 ------------------------------------------------------------------------------------ Avg: 57.99 57.99 150.34 90.00 90.00 90.00 -58.82 -9.34 -40.20 0.26 0.26 Updating header with average crystal results... Summary of detector and source refinement results during integration ------------------------------------------------------------------------------ Seq TransX TransY Dist RotZ RotX RotY SrcRot1 SrcRot2 rmsMM rmsDeg ------------------------------------------------------------------------------ 4 -0.11 0.80 114.21 0.01 0.38 -0.02 0.00 0.00 0.135 0.051 8 -0.12 0.81 114.22 0.01 0.39 -0.03 0.00 0.00 0.148 0.056 12 -0.13 0.81 114.23 0.01 0.39 -0.04 0.00 0.00 0.146 0.060 ...(中略)... 224 0.08 0.89 114.63 -0.06 0.31 0.08 0.00 0.00 0.182 0.057 228 0.08 0.90 114.63 -0.06 0.32 0.09 0.00 0.00 0.179 0.053 230 0.11 0.89 114.62 -0.06 0.31 0.09 0.00 0.00 0.176 0.053 ------------------------------------------------------------------------------ INFO: There is a correlation of 1.000 between variables a and b INFO: There is a correlation of 0.965 between variables TransX and RotY INFO: There is a correlation of 0.966 between variables Mos and RotZ INFO: There is a correlation of 0.940 between variables c and Dist INFO: There is a correlation of 0.941 between variables Rot1 and TransX ================================================================ Summary of results for scan rotation from 65.000 to 180.000 with image sequence numbers from 1 to 230 ---------------------------------------------------------------- Total reflections predicted: 283581 Total reflections with no errors: 123874 Total reflections processed weak: 144704 Total reflections with bad errors*: 9577 Total reflections partial in scan*: 3148 Reflection integration status codes ==================================== Status Num reflns ------------------------------------ No errors, no warnings: 123874 ------------------------------------ On edge 0: 237 *Some peak on box edge in 1st dim Off edge 0: 438 *Some peak outside box edge in 1st dim On edge 1: 355 *Some peak on box edge in 2nd dim Off edge 1: 155 *Some peak outside box edge in 2nd dim Off edge 2: 846 *Some peak outside box edge in 3rd dim Outside HKL bounds: 0 *Mask lies outside HKL bounds Ring: 0 *Intersection with excluded resolution ring Too dark: 0 *Some peak pixels saturated Bad background: 0 *Error in background determination Bad non-uniformity A: 0 Any shoebox pixels flagged as bad Bad non-uniformity B: 676 *Peak pixels flagged as bad or in shadow Partial at scan start: 5424 *Reflns incomplete at start of the rotation Partial at scan end: 757 *Reflns incomplete at end of the rotation Rotation too wide: 0 *Reflns predicted to be on too many images Integration problem: 7575 *Bad mask computation Fuzzy spot shape: 2579 Fuzzy spot profile Overlap: 159 *Spatial overlaps (dtprofit) ==================================== *Rejected from output. dtintegrate: All done. INFO - If dtintegrate was successful, the suggested next step is to run dtcell to check your spacegroup hypothesis (also be sure look at the axial reflections listed above): dtcell dtintegrate.head dtprofit.ref -or- run dtscaleaverage with dtintegrate.head as the input .head file: dtscaleaverage dtintegrate.head ...
dtcell というのは、空間群を確定するステップのようだ。
$ ../dtcell dtintegrate.head dtprofit.ref dtcell: Copyright (c) 2010 Rigaku d*TREK version 9.9.9.10L -- Jul 6 2015 Please see the file ${DTREK_ROOT}/ACKNOWLEDGEMENTS for further acknowledgements, copyrights and license information. Command line: ../dtcell dtintegrate.head dtprofit.ref Header "dtintegrate.head" opened. Header of file dtintegrate.head successfully read. Lattice tP assumed for space group 75. Assuming chiral cell since cell volume is greater than 25000.0 cubic angstroms. Please use -chiral or -chiralunknown to override this default. Reading Reflection file dtprofit.ref ... Creflnlist::nRead with filename: dtprofit.ref INFO in Creflnlist::nRead, EOF after 269021 reflections read in (269021 total now in list). ////////////////////////////// Finished reading command line. Input Cell: [ 57.99 57.99 150.34 90.00 90.00 90.00 ] Input Sigmas: [ 0.0308 0.0308 0.0780 0.0000 0.0000 0.0000 ] Input Orientation: [ -58.82 -9.34 -40.20 ] Least square fit to lattice characters...see Andrews & Bernstein (1988) Acta Cryst. A44, 1009-1018 and Paciorek & Bonin (1992) J. Appl. Cryst. 25, 632-637. ............................................................ ............................................................ done. Least-squares fit of reduced primitive cell to 44 lattice characters sorted on decreasing (highest to lowest) symmetry. Best possible least-squares residual is 0.000%, worst residual is 100.0%. Only solutions with % residuals <= 5.0% are listed. ======================================================================= Soln LeastSq Spgrp Cent Bravais type a b c num resid(%) num* type Cell volume alpha beta gamma ======================================================================= 7 0.000 75 P tetragonal 57.989 57.989 150.343 505564 90.000 90.000 90.000 9 0.000 21 C orthorhombic 82.009 82.009 150.343 1011129 90.000 90.000 90.000 11 0.000 16 P orthorhombic 57.989 57.989 150.343 505564 90.000 90.000 90.000 12 0.000 5 C monoclinic 82.009 82.009 150.343 1011129 90.000 90.000 90.000 13 0.000 3 P monoclinic 57.989 57.989 150.343 505564 90.000 90.000 90.000 14 0.000 1 P triclinic 57.989 57.989 150.343 505564 90.000 90.000 90.000 ======================================================================= *Suggested spacegroup number until systematic absences are examined. Laue Check ------------------------------------------------------------------------------ Laue Unique Latt Refln Non Calc Obs *Rmerge **Rmerge Incres Pass? class axis used groups index mult mult raw scaled frac ------------------------------------------------------------------------------ -1 - aP 58508 0 2 2.00 0.25 0.25 N/A N/A 2/m a mP 73644 0 4 2.69 0.26 0.26 1.08 [POOR] 2/m b mP 77567 0 4 2.52 0.24 0.24 0.97 [POOR] 2/m c mP 78946 0 4 2.54 0.26 0.26 1.04 [POOR] 2/m b mC 71748 0 4 2.71 0.26 0.26 1.07 [POOR] mmm - oP 56693 0 8 3.98 0.28 0.28 1.05 [POOR] mmm - oC 55174 0 8 4.09 0.28 0.28 1.04 [POOR] 4/m c tP 54739 0 8 4.13 0.29 0.29 1.04 [POOR] 4/mmm c tP 32759 0 16 7.07 0.30 0.30 1.04 [POOR] ------------------------------------------------------------------------------ 4/mmm selected with Rmerge of .......................... 0.30 * Rmerge is from reflections with I/sig >= 3.00. 1.00 percent of data rejected. ** Rmerge-scaled value will equal Rmerge-raw value because batch scaling has been disabled. Enter your choice [4/mmm]: New Crystal Parameters: [57.99 57.99 150.34 90.00 90.00 90.00] New Cell Sigmas: [0.0308 0.0308 0.0780 0.0000 0.0000 0.0000 ] New Crystal Orientation: [-58.82 -9.34 -40.20] N(Z) test: fraction of intensities less than Z x <I> ------------------------------------------------------------------------------- Z= 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 centric .248 .345 .419 .479 .520 .561 .597 .629 .657 .683 acentric .095 .181 .259 .330 .394 .451 .503 .551 .593 .632 deviation -.153 -.164 -.160 -.149 -.126 -.110 -.094 -.078 -.064 -.051 theoretical average deviation ==> -.115 measured 0.413 0.534 0.602 0.647 0.681 0.708 0.731 0.751 0.768 0.783 deviation -0.165 -0.189 -0.183 -0.168 -0.161 -0.147 -0.134 -0.122 -0.111 -0.100 measured average deviation ==> -0.148 ------------------------------------------------------------------------------- Although statistics might suggest a centric distribution, Acentric Distribution Selected because CHIRAL has precedence. Checking systematic absences... Systematic absences for spacegroup #90 P4212 (<I/sig(I)> <= 4.00) --------------------------------------------------------------------------- Conditions hkl hk0 0kl hhl 00l 0k0 hh0 --------------------------------------------------------------------------- Total Reflns 269021 1785 13767 5042 177 59 44 Restrictions ---- ---- ---- ---- ---- k!=2n ---- Num Reflns ---- ---- ---- ---- ---- 31 ---- Num Observed ---- ---- ---- ---- ---- 3 ---- <I/sig(I)> ---- ---- ---- ---- ---- -0.27 ---- --------------------------------------------------------------------------- Spacegroups found (Laue class: 4/mmm, Chirality: chiral) ------------------------------------------------------------- Number Name Presentation Centricity Probability Absences ------------------------------------------------------------- 90 P4212 P4212 Acentric 100.0 -----A- ------------------------------------------------------------- Probability column shows the relative probability (in percent) for each of the found spacegroups based on the frequencies of just these spacegroups in the small molecule Cambridge Structural Database. Absences column summarizes systematic absences for reflection conditions shown in the "Systematic Absences" table. 'A' stands for a conclusive systematic absence of non-restricted reflections in a condition. '?' means inconclusiveness because of too few reflections in the file in a condition. '-' means a condition is not restricted by the spacegroup. Options: T) Print reflection parities (Texsan output) S) Print found spacegroups A) Print Table of absences applicable to found spacegroups B) Print Table of all absences applicable to Laue class Q) Quit #) Type spacegroup number Enter) Select spacegroup 90 Choice: 92 # ←指定 Spacegroup #92 not found in list of candidates... no reindexing information available. No reindexing done. Reflection file not updated. Header "dtcell.head" written. dtcell: Done.
ここで、消滅則から P4212 を選択したようだが、正しくは P41212 (92) だから指定した。
最後にスケールとマージを行う。
$ ../dtscaleaverage dtcell.head dtprofit.ref dtscaleaverage: Copyright (c) 2010 Rigaku d*TREK version 9.9.9.10L -- Jul 6 2015 Please see the file ${DTREK_ROOT}/ACKNOWLEDGEMENTS for further acknowledgements, copyrights and license information. Command line: ../dtscaleaverage dtcell.head dtprofit.ref --------- Command line option parsing -------- Header of file dtcell.head successfully read. Reading reflection list dtprofit.ref ... Creflnlist::nRead with filename: dtprofit.ref INFO in Creflnlist::nRead, EOF after 269021 reflections read in (269021 total now in list). ----- End of command line options ----- Crystal listing: Unit cell lengths: 57.9892 57.9892 150.3426 Unit cell angles: 90.0000 90.0000 90.0000 Unit cell volume: 505564.175 Orientation angles: -58.8225 -9.3389 -40.1962 Mosaicity: 0.262 Description: unknown Spacegroup number: 92 name: P41212 Num. equiv. posns: 8 Rejection sigma set to 50.00 Reflections excluded from scale factor calculation (NOT results and statistics) with I/SigmaI less than 3.00 Using Auto Emul Auto Eadd. Sorting on batch ID ... ...done. Examining batch IDs and reflection resolution limits... 230 batch IDs were found in the input reflnlist. ...done. Reflections exceeding resolution limits: 0 Kept: 269021 for scaling. Sorting on intensity ... ...done. Sorting and reducing reflnlist to asymmetric unit ... ...done. INFO <Intensity> = 24482.0 <SigmaInt> = 175.4, so <Intensity>/<SigmaInt> = 139.58 for 36015 reflns ChiSq fitting parameters vs Resolution ----------------------------------------------------------- Resolution Range Contrib |ChiSq| Emul Eadd Eadd/Emul ----------------------------------------------------------- 57.99 - 3.22 20380 3.72 12.90 0.189 0.015 3.22 - 2.55 19866 2.11 12.90 0.212 0.016 2.55 - 2.23 19613 1.63 12.90 0.200 0.015 2.23 - 2.03 19878 0.96 12.90 0.199 0.015 2.03 - 1.88 19595 0.60 12.90 0.157 0.012 1.88 - 1.77 19658 0.36 12.90 0.120 0.009 1.77 - 1.68 15059 0.26 12.90 0.080 0.006 1.68 - 1.61 7673 0.13 12.90 0.060 0.005 1.61 - 1.55 2937 0.07 12.90 0.060 0.005 1.55 - 1.49 302 0.05 12.90 0.023 0.002 ----------------------------------------------------------- ChiSq fitting parameters vs I/sigI ------------------------------------------------------------------ Int/sigmaI Range Counts Contrib |ChiSq| Emul Eadd Eadd/Emul ------------------------------------------------------------------ > 20 - 18 533334 89 10.83 12.90 0.000 0.000 18 - 16 273555 45 8.07 12.90 0.000 0.000 16 - 14 278468 74 12.64 12.90 0.000 0.000 14 - 12 245346 111 8.82 12.90 0.000 0.000 12 - 10 168535 153 9.65 12.90 0.000 0.000 10 - 8 115969 276 8.53 12.90 0.000 0.000 8 - 6 258743 600 7.22 12.90 0.033 0.003 6 - 4 143905 1215 8.79 12.90 0.050 0.004 4 - 2 179446 12874 4.45 12.90 0.179 0.014 2 - < 0 21009 129524 0.88 12.90 0.161 0.012 ------------------------------------------------------------------ Number of reflections written in 'dtscaleaverage_rejects.ref': 0 Multiplicity of observed reflections -------------------------------------------------------------------------------- Mult | 1* 2 3 4 5 6 7 8 >8 -------------------------------------------------------------------------------- Refs | 0 2071 2146 2863 2687 3830 5462 5291 11665 |ChiSq| | ---- 127.66 128.42 130.18 132.67 135.07 136.14 138.20 138.44 -------------------------------------------------------------------------------- *Reflections with a multiplicity of 1 are not used in scale factor refinement nor in Rmerge calculations. Iout = Iin*Scale_factor*exp(2B_factor*sin^2(Theta)/lambda^2) Reflections in input file -------------------------------------------------------------------------------- Batch Scale B Num Num Num Num Num name factor factor refs excluded rejs ovlps singles -------------------------------------------------------------------------------- 0001 1.000 0.000 241 31 0 238 3 0002 1.000 0.000 1095 181 0 1091 4 0003 1.000 0.000 1153 182 0 1145 8 ...(中略)... 0228 1.000 0.000 1170 147 0 1165 5 0229 1.000 0.000 1185 160 0 1178 7 0230 1.000 0.000 851 108 0 845 6 -------------------------------------------------------------------------------- All batches --- --- 269021 36647 0 266249 2772 Distribution of reduced ChiSquared (|ChiSq|) ----------------------------------------------------------------------------- |ChiSq| <1.30 1.60 2.00 3.00 4.00 5.00 6.50 8.00 >10.00 ----------------------------------------------------------------------------- Num unique ref 6428 1066 1195 2152 1559 1254 1370 1089 19902 Num reflns 33708 6886 7807 14341 10934 8976 10023 8113 165461
