The following is a (nearly) verbatim session with Elves that was used to solve a selenomethionine derivative of dnaG:
Keck JL, Roche DD, Lynch AS, Berger JM. "Structure of the RNA polymerase domain of E. coli primase". Science. 2000 Mar 31;287(5462):2482-6.It is repoduced here with the kind permission of Jim Keck and James Berger.
Text produced by Elves is in white, and text typed in by the user is indicated in green. Interspersed commentary from me (not part of the actual session), are in blue. Text in <braces> is something the user typed that doesn't get displayed (like the Enter key).
Last login: Tue Aug 31 10:29:14 1999 from machine.berkeley.edu You have mail. unix 1% cd /laue/jamesh/showoff/Elves/ unix 2% mail Mail version SGI.950426. Type ? for help. "/var/mail/jamesh": 1 message 1 new >N 1 jamesh@ucxray.berkeley.edu Tue Aug 31 12:09 & s Elves "Elves" [New file] 44328/1358509 & d & q
unix 3% awk '/#! /,""' Elves >! elves unix 4% mv elves Elves unix 5% chmod a+x Elves
unix 6% ./Elves data in /data/semet/ is from the protein in ~/orf.seq Elves v 0.9 Because you have better things to do.(TM) James Holton 8-31-99 Cataloging frames in /data/semet/ ....... Getting protein sequence from /usr/users/alber/jamesh/orf.seq Hang on ... ready to set up processing directories for: single crystal of: 36482.5 D chain: YMRDGAGNLPQSFARYEKQGGRSWIYHQQNLLVAQNNQLFMGTGSFLVRSIRRQLTGTAVFDIKPLTPHPAAVDLEQEQL EQGDDEPMRRVESDLRSLIKLIGNYYLDRRYPDRKYFFTGLKNNGQYRLVRVEGDRVQDVEFPMPHAQGNGIGATNVFRG ATNPIACVDYSRDVHFAQFYADQRALEIRTYTLRADTPILDNLGPGYSTRWGLLCDMFAEDTAQDLGRMTVAAALLVNGG LELTGLLEVFLTQGMALYDRSDSAQSSARMQFAMGLEPEELVLNKARKPPFQPRDISQRDLRLGEGLKETSIILARNLPL KPM Total: 36482.5 D directory Energy First_Frame total phi0 osc distance x_beam y_beam 2theta wave1 13000.0 /data/semet/hr_1_001.img 180 180.0 1.0 240.00 93.14 94.20 0.0 wave2 12658.0 /data/semet/pk1_1_001.img 180 180.0 1.0 240.00 93.14 94.20 0.0 wave3 12663.0 /data/semet/in1_1_001.img 180 180.0 1.0 240.00 93.14 94.20 0.0 in unknown space group. with 10 Selenium sites / 36.5 kD Expect: Riso= 5.2% Rano= 0.1% Rdisp= 0.5% at 12660.0 eV Everything look okay? [Yes] -> no What's wrong? [nothing]? -> the beam center is really 93.1 95.0 and there are only 8 sites Hang on ... Is this beam center from Mosflm, adxv, R-axis(horiz, vert), or denzo? [mosflm] -> <Enter> ready to set up processing directories for: single crystal of: 36482.5 D chain: YMRDGAGNLPQSFARYEKQGGRSWIYHQQNLLVAQNNQLFMGTGSFLVRSIRRQLTGTAVFDIKPLTPHPAAVDLEQEQL EQGDDEPMRRVESDLRSLIKLIGNYYLDRRYPDRKYFFTGLKNNGQYRLVRVEGDRVQDVEFPMPHAQGNGIGATNVFRG ATNPIACVDYSRDVHFAQFYADQRALEIRTYTLRADTPILDNLGPGYSTRWGLLCDMFAEDTAQDLGRMTVAAALLVNGG LELTGLLEVFLTQGMALYDRSDSAQSSARMQFAMGLEPEELVLNKARKPPFQPRDISQRDLRLGEGLKETSIILARNLPL KPM Total: 36482.5 D directory Energy First_Frame total phi0 osc distance x_beam y_beam 2theta wave1 13000.0 /data/semet/hr_1_001.img 180 180.0 1.0 240.00 93.10 95.00 0.0 wave2 12658.0 /data/semet/pk1_1_001.img 180 180.0 1.0 240.00 93.10 95.00 0.0 wave3 12663.0 /data/semet/in1_1_001.img 180 180.0 1.0 240.00 93.10 95.00 0.0 in unknown space group. with 8 Selenium sites / 36.5 kD Expect: Riso= 4.1% Rano= 0.1% Rdisp= 0.4% at 12660.0 eV Everything look okay? [Yes] -> I want to edit this table Do you want to exit and edit wedges.txt [Yes] -> yup Please edit wedges.txt with your favorite text editor. (Remember to keep the wedge table nice and vertical) When you are done, type: ./Elves wedges.txt unix 15% vi wedges.txt
unix 19% ./Elves wedges.txt Elves v 0.9 Because you have better things to do.(TM) James Holton 8-27-99 Getting image file layout from wedges.txt Getting protein sequence from wedges.txt Hang on ... ready to set up processing directories for: single crystal of: 36482.5 D chain: YMRDGAGNLPQSFARYEKQGGRSWIYHQQNLLVAQNNQLFMGTGSFLVRSIRRQLTGTAVFDIKPLTPHPAAVDLEQEQL EQGDDEPMRRVESDLRSLIKLIGNYYLDRRYPDRKYFFTGLKNNGQYRLVRVEGDRVQDVEFPMPHAQGNGIGATNVFRG ATNPIACVDYSRDVHFAQFYADQRALEIRTYTLRADTPILDNLGPGYSTRWGLLCDMFAEDTAQDLGRMTVAAALLVNGG LELTGLLEVFLTQGMALYDRSDSAQSSARMQFAMGLEPEELVLNKARKPPFQPRDISQRDLRLGEGLKETSIILARNLPL KPM Total: 36482.5 D directory Energy First_Frame total phi0 osc distance x_beam y_beam 2theta hr 13000.0 /data/semet/hr_1_001.img 180 180.0 1.0 240.00 93.10 95.00 0.0 inf 12658.0 /data/semet/in1_1_001.img 180 180.0 1.0 240.00 93.10 95.00 0.0 peak 12663.0 /data/semet/pk1_1_001.img 180 180.0 1.0 240.00 93.10 95.00 0.0 in unknown space group. with 8 Selenium sites / 36.5 kD Expect: Riso= 4.1% Rano= 0.1% Rdisp= 0.4% at 12660.0 eV Everything look okay? [Yes] -> <Enter> Good.
Don't go away ... /laue/jamesh/showoff/Elves/hr/wedge1 is for /data/semet/hr_1_001.img /laue/jamesh/showoff/Elves/inf/wedge1 is for /data/semet/in1_1_001.img /laue/jamesh/showoff/Elves/peak/wedge1 is for /data/semet/pk1_1_001.img deploying elves into /laue/jamesh/showoff/Elves/Elfsheim ...... ./Elfsheim/Wedger will index and process one wedge of data. ./Elfsheim/Scaler will localscale and merge multiwedge data. ./Elfsheim/Phaser will refine sites and calculate phases. ./Elfsheim/Processer will process all your data. Shall we index your first wedge? [Yes] -> y moving us into indexing directory... cd ./index
Wedger: v1.0b Because you have better things to do.(TM) James Holton 8-30-99 found: ./start Scanning /data/semet/hr_1_001.img ... 0.95372 Å 1-180 Scanning ./start ..... Looking for ipmosflm ... found /programs/mosflm/ipmosflm Checking frames (Ctrl-C to skip) .................................................................................................................................. About to autoindex: /data/semet/hr_1_???.img using: /programs/mosflm/ipmosflm v 6.01 beam center: 93.10 95.00 distance: 240.00 mm wavelength: 0.953725 Å cell: unknown space group: unknown Is this correct? [Yes] creating autoindex.inp... WARNING: non-interactive indexing cannot determine your space group exactly. (but, the elves can pick a close one, and reindex later.) DPS indexing in MOSFLM Version 6.x is very cool, but can only be done in the graphics window! Do you want to autoindex INTERactively (with graphics)? [Yes] -> y #################################################################################### WHAT TO DO NEXT: 1) Say "Yes" to the question below. 2) the big Mosflm graphics window should come up. (if not, read the errors and make sure CCP4 is set up) 3) Click on "Autoindex" follow the directions you see. 4) If nothing too scary happens Click on "Predict" 5) If you see little boxes around your spots, You WIN! (auto.mat is your new matrix) 6) Exit Mosflm, and come back here. P.S. You might also want to take this opportunity to define your backstop shadow using the "KEYWORDED INPUT" button and typing something like: "BACKSTOP CENTER 93.10 95.00 RADIUS 5" #################################################################################### launch mosflm and do some autoindexing now? [Yes] -> <Enter> ************ Version 6.01 for Image plate data 06/07/99 *********** 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. ......
*********** END OF PROCESSING ***************** There, now wasn't that fun? :) What space group did you pick? [P212121] -> <Enter> Scanning auto.mat ... 38.1886 57.6016 147.314 90 90 90 Scanning hr_1_001.sav ..... Scanning logs/autoindex.log .... Hang on ... Wedger elves will create a script called mosflm.com that will run /programs/mosflm/ipmosflm and process from /data/semet/hr_1_001.img to /data/semet/hr_1_180.img using the orientation in auto.mat The Mosflm interactive graphics window will be launched. Data were collected from 180° to 360°, in 1° steps with the ALS ADSC detector (gain = 0.3) at 240.000 mm from the crystal and with the direct beam hitting the detector at: 93.22 95.21 X-rays were 0.95373 Å, with a spectral bandwidth of 1:10000, and the beam was diverging by 0.100 x 0.020° with polarization 0.9 Unit Cell is 38.1886 57.6016 147.314 90 90 90 Spots will be measured out to 2.0 Å with space group P212121 and a mosaic spread of 1.00° Refinement will be in 7 blocks of 4 frames. No integration. additional keywords: BACKSTOP CENTRE 94.00 88.00 RADIUS 10.00 ^ ### #### # ### ##### # # # ### ^ /|\ # # # # # # # # # # # # /|\ | ### ### ##### # # # #### # ### | | # # # # # # # # # # # # | | # # #### # # ### # # # # #### | Make sure all the above numbers are correct. (Especially the beam center)
Do you want our opinion on your collection strategy? [Yes] -> <Enter> This wedge will be 100.0% complete to 2.0 A and contain 99.3% of anomalous data. A wedge from 323.0 to 413.0 degrees would be 97.6% complete. A wedge from 298.0 to 388.0 degrees would contain 63.4% of anomalous pairs.
Do you want to monitor this run in the graphics window? [No] -> n
Shall we run mosflm.com now? [Yes]? -> <Enter> Refining... You can watch the full output in /laue/jamesh/showoff/Elves/hr/wedge1/logs/mosflm.log rmsd |xtal slip around| frame preds mosaic dist beam "Y" phi unit cell 1 0.17 n/d 240.1 0.00 0.07 -0.03 38.189 57.602 147.314 90 90 90 2 0.15 n/d 240.1 0.00 0.07 -0.04 38.189 57.602 147.314 90 90 90 3 0.18 n/d 240.1 0.00 0.05 -0.04 38.189 57.602 147.314 90 90 90 30 0.16 n/d 240.2 0.00 0.05 -0.02 38.189 57.602 147.314 90 90 90 31 0.14 n/d 240.2 0.00 0.06 0.03 38.189 57.602 147.314 90 90 90 32 0.15 n/d 240.1 -0.01 0.03 0.04 38.189 57.602 147.314 90 90 90 59 0.14 n/d 240.2 -0.03 0.02 0.03 38.189 57.602 147.314 90 90 90 60 0.12 n/d 240.1 0.00 0.04 0.04 38.189 57.602 147.314 90 90 90 88 0.12 n/d 240.1 -0.04 0.03 0.06 38.189 57.602 147.314 90 90 90 89 0.13 n/d 240.1 -0.05 0.03 0.05 38.189 57.602 147.314 90 90 90 90 0.13 n/d 240.1 -0.02 0.03 0.03 38.189 57.602 147.314 90 90 90 117 0.14 n/d 240.1 -0.01 0.02 0.04 38.189 57.602 147.314 90 90 90 118 0.13 n/d 240.1 0.02 0.01 0.04 38.189 57.602 147.314 90 90 90 119 0.14 n/d 240.1 0.01 0.01 0.07 38.189 57.602 147.314 90 90 90 146 0.15 n/d 240.2 0.06 -0.06 0.01 38.189 57.602 147.314 90 90 90 147 0.14 n/d 240.1 0.06 -0.06 0.01 38.189 57.602 147.314 90 90 90 148 0.15 n/d 240.2 0.04 -0.03 0.00 38.189 57.602 147.314 90 90 90 177 0.15 n/d 240.1 0.05 -0.17 -0.01 38.189 57.602 147.314 90 90 90 178 0.16 n/d 240.1 0.05 -0.13 0.00 38.189 57.602 147.314 90 90 90 179 0.04 0.33 240.2 0.05 -0.17 0.02 38.263 57.717 147.692 90 90 90 1 0.16 n/d 240.6 0.00 0.09 -0.02 38.263 57.717 147.692 90 90 90 2 0.15 n/d 240.6 0.00 0.07 -0.01 38.263 57.717 147.692 90 90 90 3 0.17 n/d 240.6 0.00 0.07 -0.03 38.263 57.717 147.692 90 90 90 30 0.16 n/d 240.7 0.01 0.06 0.00 38.263 57.717 147.692 90 90 90 31 0.15 n/d 240.7 0.01 0.08 0.03 38.263 57.717 147.692 90 90 90 32 0.14 n/d 240.6 0.00 0.06 0.03 38.263 57.717 147.692 90 90 90 59 0.14 n/d 240.6 -0.02 0.03 0.04 38.263 57.717 147.692 90 90 90 60 0.12 n/d 240.6 0.01 0.04 0.04 38.263 57.717 147.692 90 90 90 61 0.14 n/d 240.6 0.01 0.04 0.04 38.263 57.717 147.692 90 90 90 88 0.12 n/d 240.6 -0.02 0.03 0.04 38.263 57.717 147.692 90 90 90 89 0.12 n/d 240.7 -0.04 0.03 0.04 38.263 57.717 147.692 90 90 90 90 0.12 n/d 240.5 0.01 0.03 0.02 38.263 57.717 147.692 90 90 90 117 0.14 n/d 240.7 0.02 0.01 0.02 38.263 57.717 147.692 90 90 90 118 0.13 n/d 240.6 0.01 0.01 0.03 38.263 57.717 147.692 90 90 90 119 0.14 n/d 240.6 0.02 0.01 0.06 38.263 57.717 147.692 90 90 90 146 0.14 n/d 240.7 0.06 -0.06 0.01 38.263 57.717 147.692 90 90 90 147 0.14 n/d 240.6 0.06 -0.06 0.02 38.263 57.717 147.692 90 90 90 148 0.13 n/d 240.7 0.04 -0.03 0.01 38.263 57.717 147.692 90 90 90 177 0.15 n/d 240.6 0.05 -0.17 0.01 38.263 57.717 147.692 90 90 90 178 0.15 n/d 240.7 0.04 -0.10 0.01 38.263 57.717 147.692 90 90 90 179 0.05 0.37 240.7 0.05 -0.17 0.02 38.265 57.731 147.688 90 90 90 Spots are 0.03 mm (rms) from their predictions. (pixel is 0.0816 mm) orientation changed 0.014° mosaicity changed 0.637° unit cell unchanged. distance changed 0.19% Ding! Refinement was successful! Parameters are still drifting. Refine again. On the CCD, you should probably fix the X-Y scale. Recommend: mv postref.mat best.mat /laue/jamesh/showoff/Elves/Elfsheim/Wedger refine nointeg fixyscale
Do this now? [Yes/go auto]? -> no What's wrong? [nothing]? -> <Enter> Shall we update mosflm.com? [Y]? -> <Enter> mosflm.com is ready... Cleaning up... moving back to root directory... cd .. Shall we process the rest of your data? [Yes] -> <Enter>
Processer running as pid=19898 on machine using "nice" cpu priority ready to process: hr/wedge1 peak/wedge1 inf/wedge1
setting up ./hr/wedge1 with ./hr/wedge1/start ./index/mosflm.com and /data/semet/hr_1_001.img setting up ./peak/wedge1 with ./peak/wedge1/start ./index/mosflm.com and /data/semet/peak_1_001.img setting up ./inf/wedge1 with ./inf/wedge1/start ./index/mosflm.com and /data/semet/inf_1_001.img finished
testing ./hr/wedge1 (/data/semet/hr_1_001.img) testing ./peak/wedge1 (/data/semet/peak_1_001.img) testing ./inf/wedge1 (/data/semet/inf_1_001.img) finished
processing ./hr/wedge1 (/data/semet/hr_1_001.img) processing ./peak/wedge1 (/data/semet/peak_1_001.img) processing ./inf/wedge1 (/data/semet/inf_1_001.img) finished
repeating refinement with average cell: 38.3383 57.8834 148.091 90 90 90 processing ./hr/wedge1 (/data/semet/hr_1_001.img) processing ./peak/wedge1 (/data/semet/peak_1_001.img) processing ./inf/wedge1 (/data/semet/inf_1_001.img) finished
Scaler Elves v 0.9 Because you have better things to do.(TM) James Holton 8-30-99 Reading parameters in wedges.txt Getting protein sequence from wedges.txt Organizing mtz data ... (Cntrl-C to end) hr/wedge1/raw.mtz (180 frames) inf/wedge1/raw.mtz (180 frames) peak/wedge1/raw.mtz (180 frames) Hang on... Scaler elves will localscale and merge your data with 3 wavelengths: 0.97949 Å "Finf" <- reference 0.97911 Å "Fpeak" 0.95373 Å "Fhr" frames from file as wavelength 1 to 180 inf/wedge1/raw.mtz Finf 1 to 180 peak/wedge1/raw.mtz Fpeak 1 to 180 hr/wedge1/raw.mtz Fhr The following SCALA cards will be used: SDCORR 1.3 0 0.03 INTENSITIES SCALE_PARTIALS 0.85 Resolution : 2 Å - 54.233 Å Space group: P212121 Unit Cell : 38.34 57.88 148.09 90 90 90 Vm : 2.25 (44% solvent) Asymmetric unit contains: 1/4 of unit cell, 36500 Da of protein, 8 Selenium sites. (expected) Everything look okay? [Yes] -> Good. Don't go away. setting up scripts in ./scripts/... setting up solve in ./SOLVE setting up shelx in ./SHELX setting up X-PLOR in ./XPLOR Scaler Elves are now ready to start scaling your data. Scripts to run "solve" and "shelx" have been set up, but have no data files yet. Your raw data must be scaled and merged first. However, since scaling can take longer that you will probably want to hang around, there are a few questions we would like you to answer now: Would you like to: 1) Have the Elves give you some merged data to look at ASAP. 2) Use these scripts to process your data yourself, thankyouverymuch. 3) Let the Elves edit the scripts, and improve parameters automatically. Choose a strategy [3] -> 3 Okay, you can go away now. sorting raw data ... prescaling reference set (Finf) ... (see ./logs/sorting.log) roughly scaling everything to Finf. (see ./logs/rough_scale.log) Found 10 contiguous groups of scales. updating run definitions to: frames from file as wavelength 1 to 75 inf/wedge1/raw.mtz Finf 76 to 76 inf/wedge1/raw.mtz Finf 77 to 86 inf/wedge1/raw.mtz Finf 87 to 89 inf/wedge1/raw.mtz Finf 90 to 144 inf/wedge1/raw.mtz Finf 145 to 180 inf/wedge1/raw.mtz Finf 1 to 99 peak/wedge1/raw.mtz Fpeak 100 to 162 peak/wedge1/raw.mtz Fpeak 163 to 180 peak/wedge1/raw.mtz Fpeak 1 to 180 hr/wedge1/raw.mtz Fhr roughly scaling everything to Finf. (see ./logs/rough_scale.log) switching to smooth scales. smooth scaling everything to Finf. (see ./logs/rough_scale.log) localscaling: this can take a long time. (see ./logs/localscale.log) mergeing Fhr as ./mtz/Fhr.mtz ... (see ./logs/merge_Fhr.log) mergeing Fpeak as ./mtz/Fpeak.mtz ... (see ./logs/merge_Fpeak.log) mergeing Finf as ./mtz/Finf.mtz ... (see ./logs/merge_Finf.log) combining Fhr Fpeak Finf into ./mtz/all.mtz ... (see ./logs/scaleit.log) wavelength Rmerge Ranom I/sigma Complete Mult Wilson B Fhr 0.046 0.045 17.400 89.5% 5.5 49.377 Finf 0.103 0.078 6.900 85.6% 4.8 48.024 Fpeak 0.044 0.059 17.500 85.9% 5.4 50.132 adding Free-R flags ... True completeness to 2.10 A: Fhr: 88.80% complete, <F>/<sig> = 35.59 Fpeak: 85.15% complete, <F>/<sig> = 35.28 Finf: 81.03% complete, <F>/<sig> = 12.52 look at end of ./logs/scaleit.log for Dano and Diso vs Finf ./mtz/all.mtz is ready for input into SHARP or mlphare. ./SOLVE/*.fmt are ready for input into SOLVE ./SHELX/*.hkl are ready for input into SHELX ./XPLOR/*.fobs are ready for input into XPLOR's mad_merge.inp Thank you, drive through!
unix% ./Elfsheim/Scaler
hr/*/raw.mtz peak/*/raw.mtz wedges.txt >&! Scaler.log &
unix% tail
-f Scaler.log
unix% ./Elfsheim/Processer
solve >&! process2.log &
unix% tail
-f process2.log
shelx will be run in each space group running shelx in P21212 at SHELX/P21212 CFOM = 0.1281 running shelx in P212121 at SHELX/P212121 CFOM = 0.1554 running shelx in P2122 at SHELX/P2122 CFOM = 0.1335 running shelx in P21221 at SHELX/P21221 CFOM = 0.1386 running shelx in P2212 at SHELX/P2212 CFOM = 0.1515 running shelx in P22121 at SHELX/P22121 CFOM = 0.1491 running shelx in P222 at SHELX/P222 CFOM = 0.1138 running shelx in P2221 at SHELX/P2221 CFOM = 0.1286
running SOLVE in P222 at /laue/jamesh/keck/SOLVE/P222 P222 7 sites, fom = 0.45, Z-score = 10.63 running SOLVE in P2221 at /laue/jamesh/keck/SOLVE/P2221 P2221 8 sites, fom = 0.46, Z-score = 14.55 running SOLVE in P22121 at /laue/jamesh/keck/SOLVE/P22121 P22121 8 sites, fom = 0.47, Z-score = 22.23 running SOLVE in P21212 at /laue/jamesh/keck/SOLVE/P21212 P21212 8 sites, fom = 0.47, Z-score = 21.17 running SOLVE in P2122 at /laue/jamesh/keck/SOLVE/P2122 P2122 8 sites, fom = 0.45, Z-score = 16.01 running SOLVE in P21221 at /laue/jamesh/keck/SOLVE/P21221 P21221 8 sites, fom = 0.44, Z-score = 10.93 running SOLVE in P2212 at /laue/jamesh/keck/SOLVE/P2212 P2212 4 sites, fom = 0.43, Z-score = 12.15 running SOLVE in P212121 at /laue/jamesh/keck/SOLVE/P212121 P212121 8 sites, fom = 0.48, Z-score = 21.52 waiting for other instances to synch up... SOLVE summary: P212121 8 sites, fom = 0.48, Z-score = 21.52 P22121 8 sites, fom = 0.47, Z-score = 22.23 P21212 8 sites, fom = 0.47, Z-score = 21.17 P2221 8 sites, fom = 0.46, Z-score = 14.55 P222 7 sites, fom = 0.45, Z-score = 10.63 P2122 8 sites, fom = 0.45, Z-score = 16.01 P21221 8 sites, fom = 0.44, Z-score = 10.93 P2212 4 sites, fom = 0.43, Z-score = 12.15
Phaser Elves v 0.9 Because trying everything isn't so hard.(TM) James Holton 3-22-00 Evaluating Fs in mtz/all.mtz ..picked Fpeak as the best reference. checking mtz/all.mtz writing scripts/reindex.com writing scripts/rrsps.com writing scripts/more_atoms.com writing scripts/dm.com getting atom coordinates from SOLVE/P212121/solve.status refining occupancies only running scripts/mlphare.com into logs/mlphare.log .......... FOM = 0.4891 (0.1769 - 0.7507) best Phasing Power = 2.29 (a), 1.89 (c) eliminated 1 bad atoms from scripts/mlphare.com switching to XYZ refinement running scripts/mlphare.com into logs/mlphare.log .......... FOM = 0.4909 (0.1775 - 0.7528) best Phasing Power = 2.31 (a), 1.91 (c) running scripts/mlphare.com into logs/mlphare.log .......... FOM = 0.4909 (0.1775 - 0.7526) best Phasing Power = 2.31 (a), 1.92 (c) enabling occupancy refinement running scripts/mlphare.com into logs/mlphare.log .......... FOM = 0.4925 (0.1783 - 0.7543) best Phasing Power = 2.34 (a), 1.95 (c) running scripts/mlphare.com into logs/mlphare.log .......... FOM = 0.4925 (0.1783 - 0.7543) best Phasing Power = 2.34 (a), 1.95 (c) enabling B factor refinement running scripts/mlphare.com into logs/mlphare.log .......... FOM = 0.4958 (0.1765 - 0.7490) best Phasing Power = 2.31 (a), 1.91 (c) running scripts/mlphare.com into logs/mlphare.log .......... FOM = 0.4958 (0.1765 - 0.7490) best Phasing Power = 2.31 (a), 1.91 (c) refinement has converged! running scripts/dm.com with 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, and 70% solvent for auto cycles each 25% : R_dm = 0.210 ( 4/4 ) 30% : R_dm = 0.146 ( 4/4 ) 35% : R_dm = 0.176 ( 4/4 ) 40% : R_dm = 0.164 ( 4/4 ) 45% : R_dm = 0.170 ( 6/6 ) 50% : R_dm = 0.170 ( 7/7 ) 55% : R_dm = 0.131 ( 3/3 ) 60% : R_dm = 0.131 ( 4/4 ) 65% : R_dm = 0.132 ( 6/6 ) 70% : R_dm = 0.130 ( 10/10 ) copying scripts/mlphare.com to scripts/mlphare.com.best copying mtz/dm70.mtz to mtz/dm_best.mtz maps/best.map is a normalized ccp4 map from mtz/dm_best.mtz maps/best.omap is an o version (dsn6) of maps/best.map copying scripts/mlphare.com.best to scripts/mlphare.com.unflipped
inverting real occupancies running scripts/mlphare.com into logs/mlphare.log .......... FOM = 0.4929 (0.1751 - 0.7479) best Phasing Power = 2.35 (a), 1.89 (c) running scripts/mlphare.com into logs/mlphare.log .......... FOM = 0.4929 (0.1751 - 0.7479) best Phasing Power = 2.35 (a), 1.89 (c) refinement has converged! running scripts/dm.com with 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, and 70% solvent for auto cycles each 25% : R_dm = 0.168 ( 13/13 ) 30% : R_dm = 0.170 ( 10/10 ) 35% : R_dm = 0.141 ( 18/18 ) 40% : R_dm = 0.211 ( 12/12 ) 45% : R_dm = 0.219 ( 11/11 ) 50% : R_dm = 0.270 ( 6/6 ) 55% : R_dm = 0.217 ( 17/17 ) 60% : R_dm = 0.222 ( 10/10 ) 65% : R_dm = 0.230 ( 8/8 ) 70% : R_dm = 0.218 ( 9/9 ) none of these were better than mtz/dm_best.mtz scripts/mlphare.com.best is still the best mlphare script. flipping all atoms through the origin running scripts/mlphare.com into logs/mlphare.log .......... FOM = 0.4929 (0.1751 - 0.7479) best Phasing Power = 2.35 (a), 1.89 (c) running scripts/mlphare.com into logs/mlphare.log .......... FOM = 0.4929 (0.1751 - 0.7479) best Phasing Power = 2.35 (a), 1.89 (c) refinement has converged! running scripts/dm.com with 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, and 70% solvent for auto cycles each 25% : R_dm = 0.149 ( 10/10 ) 30% : R_dm = 0.123 ( 11/11 ) 35% : R_dm = 0.169 ( 13/13 ) 40% : R_dm = 0.149 ( 18/18 ) 45% : R_dm = 0.160 ( 16/16 ) 50% : R_dm = 0.182 ( 16/16 ) 55% : R_dm = 0.176 ( 18/19 ) 60% : R_dm = 0.207 ( 8/8 ) 65% : R_dm = 0.174 ( 15/15 ) 70% : R_dm = 0.202 ( 6/6 ) copying scripts/mlphare.com to scripts/mlphare.com.best copying mtz/dm30.mtz to mtz/dm_best.mtz maps/best.map is a normalized ccp4 map from mtz/dm_best.mtz maps/best.omap is an o version (dsn6) of maps/best.map inverting real occupancies and flipping all atoms through the origin running scripts/mlphare.com into logs/mlphare.log .......... FOM = 0.4958 (0.1765 - 0.7490) best Phasing Power = 2.31 (a), 1.91 (c) running scripts/mlphare.com into logs/mlphare.log .......... FOM = 0.4958 (0.1765 - 0.7490) best Phasing Power = 2.31 (a), 1.91 (c) refinement has converged! running scripts/dm.com with 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, and 70% solvent for auto cycles each 25% : R_dm = 0.185 ( 7/7 ) 30% : R_dm = 0.193 ( 6/6 ) 35% : R_dm = 0.191 ( 8/8 ) 40% : R_dm = 0.214 ( 6/6 ) 45% : R_dm = 0.212 ( 5/5 ) 50% : R_dm = 0.187 ( 10/10 ) 55% : R_dm = 0.186 ( 8/8 ) 60% : R_dm = 0.206 ( 5/5 ) 65% : R_dm = 0.175 ( 10/10 ) 70% : R_dm = 0.165 ( 11/11 ) none of these were better than mtz/dm_best.mtz scripts/mlphare.com.best is still the best mlphare script. copying scripts/mlphare.com.best back to scripts/mlphare.com
Looking for more atoms in mtz/dm_best.mtz that are not already within 0.67A of the 8 (plus 1 bad) atoms in scripts/mlphare.com resolution 1000 2 using FOMDM*F and PHIDM for difference Fouriers fft will use F > 1*sigma(F) with |DANO| < 127.35 and |delta-F| < 102.45 DANOFhr DANOFpeak Fhr-Fpeak 3 difference Fouriers weighting maps... combining maps.. 49 peaks found > 3*sigma, (41 new). making Pattersons (DANOFhr)^2 (DANOFpeak)^2 (Fhr-Fpeak)^2 weighting Pattersons... combining Pattersons.. checking 41 sites against average Patterson all peaks and scores written to ./more_atoms.list top 5 new sites: sigma X Y Z is dist from nearest neighbor 4.6 0.819 0.809 0.839 3.07A ATOM5 in DERIV 1 4.2 0.768 0.202 0.370 3.55A ATOM3 in DERIV 1 3.2 0.766 0.736 0.834 3.29A ATOM3 in DERIV 2 3.5 0.854 0.765 0.841 3.19A ATOM5 in DERIV 1 3.4 0.864 0.715 0.847 5.42A ATOM5 in DERIV 1
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