- phenixbb - phenix-online.org

Reading Rfree Flags from Refmac
by James Fraser 08 Jan '08

08 Jan '08

Hello, Someone in our lab has started a refinement run in REFMAC and wants to continue it in Phenix.refine. Is there an easy way to get phenix to recognize the r-free flag from REFMAC (freeR=0)? Thanks, jf -- James Fraser jamesfraser(a)berkeley.edu Alber Lab 356 Stanley Hall, QB3 UC Berkeley Berkeley, CA 94720 http://ucxray.berkeley.edu/~jfraser/

2 2

Failure when calculating a composite omit map
by Dale Tronrud 07 Jan '08

07 Jan '08

Hi all, I'm trying to calculate a composite omit map so that I can get a clear view of a troublesome region in my structure. I have two copies of everything in the asu so I created some dummy atoms to mask the region in the A chain and called those atoms chain Y and another collection to mask the region in the C chain and created a Z chain for them. I put these atoms in a file name Mask.pdb I attempted to calculate the composite omit map starting from my MR solution but that fails because Autobuild doesn't like being given the Fourier coefficients produced by Phaser. To work around this problem I decided to ask it to create the omit map based on the results of my AutoBuild followed the MR. My script is: phenix.autobuild model=AutoBuild_run_12_/overall_best.pdb data=1M50-2.mtz \ input_refinement_labels="FP SIGFP None None None None None None FreeR_flag" \ seq_file=../fmo-ct.pir \ resolution=2.2 dmax=20 refinement_resolution=2.2 \ cif_def_file_list=/usr/users/dale/geometry/chromophores/bcl_tnt.cif \ input_lig_file_list=AutoMR_run_4_/MR.1-Bchl-a.pdb \ composite_omit_type=iterative_build_omit omit_region_specification=omit_around_pdb omit_box_pdb=Mask.pdb\ omit_res_start_list="1 1" omit_res_end_list="39 30" omit_chain_list="Y Z" \ rebuild_in_place=Yes Mask.pdb is attached. Resolve is unable to create a mask. The log file, omit_box_id.log is also attached. Resolve creates a temp file named TMP.pdb which I would expect to contain the contents of my Mask.pdb. It only contains the first set of dummy atoms; chain Y. Then when Resolve reads this file it appears not to find even those atoms. I know Tom is out of reach for quite a while. Is there someone else who could help me over this hurdle? Dale Tronrud

1 0

Autosol Feedback and questions
by Partha Chakrabarti 03 Jan '08

03 Jan '08

Happy new year everybody, I had quite a bit of difficulty with a SAD dataset which also showed Sulphur. Previously I had tried SHELEX to find sites, MLPHARE to refine, AddSOLVE to find more , and both SOLVE and PHASER to solve but it did not get to a point where I could do manual building. Autosol worked beautifully, the input files were scalepack merged data, ha.pdb (from addsolve step), and the sequence. PHASER to solve and TEXTAL & RESOLVE with through build option. This actually leave me with some confusions / questions: 1. When I compare the other "solutions", they look like the right one, just not good enough. Where exactly is the autosol making a difference? Is it the ability of of TEXTAL to build something more meaningful when the solution is not good or number of iterations? 2. How does PHASER know the different anomalous atoms? Does is use a different scaling factor for SE and S? 3. I see that phenix.refine has been used in the internal runs, I have used phenix.refine earlier. But after playing with the side chains in Coot, when I tried to use the modified pdb file and resolve.mtz, it complained about the good old Free_R flag. However, it ran directly in Refmac. Is it a known problem or maybe I did something stupid? I could do a dry run and change the read mtz and not cns if that would solve the problem. 4. Lastly, is it possible to use multiple processors to run the job? Best regards, Partha -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: pchakra(a)nimr.mrc.ac.uk Phone: + 44 208 816 2515

2 1

Re: [phenixbb] Using the Same Test Set in AutoBuild and Phenix.Refine
by Thomas C. Terwilliger 02 Jan '08

02 Jan '08

Hi Dale, Can you try something else: phenix.refine AutoBuild_run_12_/overall_best.pdb \ refinement.input.xray_data.file_name=\ AutoBuild_run_12/exptl_fobs_freeR_flags.mtz \ refinement.main.high_resolution=2.2 refinement.main.low_resolution=20 \ /usr/users/dale/geometry/chromophores/bcl_tnt.cif This differs from your run only by substituting AutoBuild_run_12/exptl_fobs_freeR_flags.mtz for your 2 refinement data files. This is the exact file that is used in refinement by AutoBuild. I agree that you should be able to use your original data file instead. A possible reason why this has failed is that the original data file has a couple reflections for which there is no data...and which were tossed by AutoBuild before creating exptl_fobs_freeR_flags.mtz . Two files that differ only in reflections with no data will still give different checksums, I think. All the best, Tom T > Hi Dale, > >>> 1) Why you specify reflection MTZ file twice in phenix.refine script? >>> >>> >> I put the mtz in twice because if I put it in once phenix.refine >> complains that I have no free R flags. It seems to want one file with >> the amplitudes and another with the flags. Since I have both in the >> same file I put that file on the line twice and phenix.refine finds >> everything it needs. >> > > phenix.refine looks for free-R flags in your main data file > (1M50-2.mtz). Optionally you can provide a separate file containing > free-R flags (I have to write about this in the manual). However, if > your 1M50-2.mtz contains free-R flags then you don't need to give it > twice. So clearly something is wrong at this step and we need to find > out what is wrong before doing anything else. Could you send the result > of the command "phenix.mtz.dump 1M50-2.mtz" to see what's inside of your > data file? Or I can debug it myself if you send me the data and model. > >> If the MD5 hash of the test set depends on the resolution then >> certainly >> I could be in trouble. > > No. It must always use the original files before any processing. > >> Does the resolution limit affect the MD5 hash of the test set? >> > > No. If it does then it is a very bad bug. I will play with this myself > later tonight. > >> >>> 3) Does this work: >>> >>> (...) >> >> I'll try these but it will take a bit of time. >> > > Don't run it until completion. Just make sure it passed through the > processing step. > > Pavel. > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

3 2

Using the Same Test Set in AutoBuild and Phenix.Refine
by Dale Tronrud 02 Jan '08

02 Jan '08

Hi all, I have another problem, I'm afraid. I have built a model using phenix.autobuild and now want to run some refinement. While in the long run I'll do some manually rebuilding using Coot I just wanted to run a test of phenix.refine to ensure I have the script right and have a baseline to compare against later. My autobuild script is: phenix.autobuild model=AutoMR_run_4_/MR.1-protein.pdb data=1M50-2.mtz \ input_refinement_labels="FP SIGFP None None None None None None FreeR_flag" \ map_file=AutoMR_run_4_/MR.MAP_COEFFS.1.mtz \ seq_file=../fmo-ct.pir \ resolution=2.2 dmax=20 refinement_resolution=2.2 \ cif_def_file_list=/usr/users/dale/geometry/chromophores/bcl_tnt.cif \ input_lig_file_list=AutoMR_run_4_/MR.1-Bchl-a.pdb \ rebuild_in_place=Yes My refine script is phenix.refine AutoBuild_run_12_/overall_best.pdb \ refinement.input.xray_data.file_name=1M50-2.mtz 1M50-2.mtz \ refinement.main.high_resolution=2.2 refinement.main.low_resolution=20 \ /usr/users/dale/geometry/chromophores/bcl_tnt.cif As you can guess, my test set flags are in the same mtz file as the amplitudes. I'm feeding exactly the same file into both runs. Despite this I get in my output ******************************************************************************* ******************************************************************************* The MD5 checksum for the R-free flags array summarized above is: 785fd03f6881898dcd91bc5f8c3e5b26 The corresponding MD5 checksum in the PDB file summarized above is: 6f86ee71dbcd2dc1f5282cf18547c79b These checksums should be identical but are in fact different. This is because the R-free flags used at previous stages of refinement are different from the R-free flags summarized above. As a consequence, the values for R-free will be biased and misleading. It is best to avoid this situation by consistently using the same R-free flags throughout the refinement of a model. If the previously used R-free flags are still available run this command again with the name of the file containing the original flags as an additional input. If the original R-free flags are unrecoverable, remove the REMARK r_free_flags.md5.hexdigest 6f86ee71dbcd2dc1f5282cf18547c79b record from the input PDB file to proceed with the refinement. In this case the values for R-free will become meaningful only after many cycles of refinement. ******************************************************************************* ******************************************************************************* Sorry: Please resolve the R-free flags mismatch. While I'm glad that Phenix is checking to ensure that I haven't goofed and tried to switch test sets, I believe I'm being unjustly accused. Why does phenix.refine think I'm a bad boy? Dale Tronrud

2 5

Re: [phenixbb] Autosol Feedback and questions
by Ralf W. Grosse-Kunstleve 02 Jan '08

02 Jan '08

Hi Partha, > 3. I see that phenix.refine has been used in the internal runs, I have used > phenix.refine earlier. But after playing with the side chains in Coot, when > I tried to use the modified pdb file and resolve.mtz, it complained about > the good old Free_R flag. Is this the MD5 error message? > However, it ran directly in Refmac. Is it a known > problem or maybe I did something stupid? I could do a dry run and change > the read mtz and not cns if that would solve the problem. I'm not sure what's going wrong. To be sure, I'd need a reproducer, or at least an exact description of what happened in which order. > 4. Lastly, is it possible to use multiple processors to run the job? No, sorry. Parallelization is a big, complex project. The Cambridge group has started some work in this direction, but it is still very experimental. Ralf

1 0

Fatal Error: Incomplete libtbx environment!
by Yong-Fu Li 01 Jan '08

01 Jan '08

Hi, I just installed Phenix 1.3b, however got this error message when I tried to run phenix. ******************************************* Fatal Error: Incomplete libtbx environment! ******************************************* Please re-run the libtbx/configure.py command. My system is: 2.6.23.8-34.fc7 i686 Here is what I did: 1) downloaded phenix-installer-1.3b-rc6-intel-linux-2.6.tar 2) tar -xvf ... 3) In directory: phenix-installer-1.3b/, execute ./install 4) moved phenix-1.3b-rc6/ from /usr/local to /usr/local/progs where all of my programs dwell 5) source phenix_env in: /usr/local/progs/Phenix/phenix-1.3b-rc6 6) then run: ./phenix, and got the above message 7) as root go to /libtbx, chmod +x configure.py, and ./configure.py (I don't know about python, and my Python is 2.5), it hangs there for very long (>10 min) with another error: ./configure.py: line 3: syntax error near unexpected token `(' ./configure.py: line 3: `def run():' I checked the bb for help but didn't find any useful info (not finished reading all the messages). I wonder whether someone could help! Thanks and happy new year! Yongfu

3 2

heavy atom sites in autobuild
by Bryan W. Lepore 28 Dec '07

28 Dec '07

i'm confused about treatment of heavy atom sites in autobuild. couple questions : 1. since heavy atom sites can be treated as single atoms, should phenix.autobuild simply refine the positions within a protein model? i.e. heavy atom sites should not need to be treated as ligands, with a .cif -- right? 2. if i want autobuild to build around the heavy atom site, can i just use input_pdb_file=heavy.pdb? input_lig_file_list= is not working. -bryan

2 1

Se SAD data to include Sulphurs?
by Partha Chakrabarti 28 Dec '07

28 Dec '07

Hiya, I have a SAD dataset collected at 0.979A to very good completeness and redundancy, upto 2.1A. Two molecules in AU, each containing 2 Se and the solvent content is 40%. The Signal to noise is more than 1 upto 2.1A , however solve resolve and phaser did not work. I am not an expert but what is getting somewhere is if I use SHELEX (or hyss) to find the sites, pick the best 3 of them, use MLPHARE or so to refine and Addsolve to find the other Se. However, looks like the fourth Se is less ordered. Now, the SHELEX file also finds several others which I guess are Sulphurs. I can see helix like density in the map after Addsolve (& resolve) or SHELEXE but have not been able to place any aromatic residue yet. I guess one problem is lack of proper NCS and low solvent content. Could someone point me to a method in which I can improve the map by including the Sulphurs? For example, using the already found Se as seeds? I am trying the autosol option anyway. Cheers, Partha

2 1

Re: [phenixbb] How do I gather the pieces after AutoBuild?
by Thomas C. Terwilliger 26 Dec '07

26 Dec '07

Hi Dale, If you run AutoBuild with "rebuild_in_place=Yes" then it will keep the pieces that you have, try to rebuild them (in nearby locations), and not reassemble the molecule. Rebuilding in place is supposed to be a way to finish off your structure, and that's why it doesn't move it around. In your case, you are rebuilding in place after Phaser molecular replacement. Usually Phaser will make a compact molecule during MR, so this should not normally be a problem. I gather that in this case it didn't do so, however. With rebuild_in_place=No then AutoBuild should try and make a compact molecule. If you have NCS then it will try to make a compact molecule with NCS. All the best, Tom T > Hi all, > > I have finished my Autobuild but the resulting model has some residues > that are scattered in distant asymmetric units. Coot shows their symmetry > images where they belong, next to the rest of the protein. I could > rebuild these residues by hand in the right place, or collecte together > all the symmetry operators and write a script to gather them, but being > lazy would like a more automated solution. Surely this happens to > other people and there is a tool that solves this problem. I've read > a bunch of the web pages for AutoBuild but didn't find a solution there. > > My AutoBuild command was > > phenix.autobuild model=AutoMR_run_4_/MR.1-protein.pdb data=1M50-2.mtz \ > map_file=AutoMR_run_4_/MR.MAP_COEFFS.1.mtz \ > seq_file=../fmo-ct.pir \ > resolution=2.2 dmax=20 refinement_resolution=2.2 \ > cif_def_file_list=/usr/users/dale/geometry/chromophores/bcl_tnt.cif > \ > input_lig_file_list=AutoMR_run_4_/MR.1-Bchl-a.pdb \ > rebuild_in_place=Yes > > Shouldn't AutoBuild build a compact model by default? > > Dale Tronrud > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

2 1

How do I gather the pieces after AutoBuild?
by Dale Tronrud 23 Dec '07

23 Dec '07

Hi all, I have finished my Autobuild but the resulting model has some residues that are scattered in distant asymmetric units. Coot shows their symmetry images where they belong, next to the rest of the protein. I could rebuild these residues by hand in the right place, or collecte together all the symmetry operators and write a script to gather them, but being lazy would like a more automated solution. Surely this happens to other people and there is a tool that solves this problem. I've read a bunch of the web pages for AutoBuild but didn't find a solution there. My AutoBuild command was phenix.autobuild model=AutoMR_run_4_/MR.1-protein.pdb data=1M50-2.mtz \ map_file=AutoMR_run_4_/MR.MAP_COEFFS.1.mtz \ seq_file=../fmo-ct.pir \ resolution=2.2 dmax=20 refinement_resolution=2.2 \ cif_def_file_list=/usr/users/dale/geometry/chromophores/bcl_tnt.cif \ input_lig_file_list=AutoMR_run_4_/MR.1-Bchl-a.pdb \ rebuild_in_place=Yes Shouldn't AutoBuild build a compact model by default? Dale Tronrud

1 0

Re: [phenixbb] autosol w/ "no merge original index"?
by Tom Terwilliger 19 Dec '07

19 Dec '07

Hi Brian, Thanks for sending me the top of your hkl file....I added some random data after that and it runs on my version just fine. Can you possibly try again with the most recent version of phenix on the web site (rc6)? Thanks! -Tom T At 01:24 PM 12/19/2007, you wrote: >phenix 1.3b of 21-10-2007 > >confusion w/ "no merge original index" data file in phenix.autosol. this >should work, right? > >caveat - the 'nmoi' hkl is actually from scala, but that usually is fine >w/ e.g. solve-2.13. 'nmoi' requires declaration of cell='(numbers)' on >command line. > >phenix.autosol seems to go through all the usual checks fine, then >reports (in AutoSol_run_2_/LAST.LOG): >".... > The error seems to be at line 0 > Here is what the first few lines of this file look like: > 1 > -987 > 86.052 86.052 132.608 90.000 90.000 90.000 p41212 > You have set the keywords readdenzo and unmerged > Please check whether you should have set readformatted or readtrek or >premerged >...." > >... 'readdenzo' and 'unmerged' are just right for 'nmoi' files. etc. > >-bryan >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

1 0

Re: [phenixbb] autosol w/ "no merge original index"?
by Tom Terwilliger 19 Dec '07

19 Dec '07

Hi Bryan, Yes, "No merge original index" files should work fine. This file should be converted by the autosol wizard to premerged scalepack during the run. In your case this seems to be so as the file header that is being read during the middle of the run 1 -987 86.052 86.052 132.608 90.000 90.000 90.000 p41212 is premerged scalepack. Now what does not make sense is the error message "You have set the keywords readdenzo and unmerged". I am not sure where that has come from. I just ran a SAD dataset to test this with an unmerged original index file, and it ran fine for me. If this doesn't help, could you send me (terwilliger(a)lanl.gov) your input script and datafile ( or even the first 1000 lines of the datafile) and I can try to debug it. Thanks! -Tom T At 01:24 PM 12/19/2007, you wrote: >phenix 1.3b of 21-10-2007 > >confusion w/ "no merge original index" data file in phenix.autosol. this >should work, right? > >caveat - the 'nmoi' hkl is actually from scala, but that usually is fine >w/ e.g. solve-2.13. 'nmoi' requires declaration of cell='(numbers)' on >command line. > >phenix.autosol seems to go through all the usual checks fine, then >reports (in AutoSol_run_2_/LAST.LOG): >".... > The error seems to be at line 0 > Here is what the first few lines of this file look like: > 1 > -987 > 86.052 86.052 132.608 90.000 90.000 90.000 p41212 > You have set the keywords readdenzo and unmerged > Please check whether you should have set readformatted or readtrek or >premerged >...." > >... 'readdenzo' and 'unmerged' are just right for 'nmoi' files. etc. > >-bryan >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

1 0

autosol w/ "no merge original index"?
by Bryan W. Lepore 19 Dec '07

19 Dec '07

phenix 1.3b of 21-10-2007 confusion w/ "no merge original index" data file in phenix.autosol. this should work, right? caveat - the 'nmoi' hkl is actually from scala, but that usually is fine w/ e.g. solve-2.13. 'nmoi' requires declaration of cell='(numbers)' on command line. phenix.autosol seems to go through all the usual checks fine, then reports (in AutoSol_run_2_/LAST.LOG): ".... The error seems to be at line 0 Here is what the first few lines of this file look like: 1 -987 86.052 86.052 132.608 90.000 90.000 90.000 p41212 You have set the keywords readdenzo and unmerged Please check whether you should have set readformatted or readtrek or premerged ...." ... 'readdenzo' and 'unmerged' are just right for 'nmoi' files. etc. -bryan

1 0

Re: [phenixbb] MTZ intensities interpreted as amplitudes by autobuild command-line versions up to 1.3b/rc6
by Thomas C. Terwilliger 18 Dec '07

18 Dec '07

Hi again Peter, Yes, the AutoMR wizard (any version) will run correctly with input MTZ data that are intensities. However all versions up to now will pass this MTZ file on to AutoBuild without conversion to amplitudes and it will be incorrectly interpreted by AutoBuild. Note that this only applies to MTZ files. Any other source of amplitudes/intensities doesn't cause any problem. If you run from the GUI, you will have the chance to set the correct columns in AutoBuild, if amplitudes are available in your data file. From the command_line, for existing versions, you would need to say when you run AutoMR: input_labels='F SIGF' (or whatever your amplitudes are in this MTZ file) All the best, Tom T > Hi Tom, > > What about the AutoMR wizard. Can I use intensities there instead of amplitudes? I always get confused. > > Thanks, > > Peter > > 2007/12/18, Tom Terwilliger <terwilliger(a)lanl.gov>: >> Hi phenix.autobuild users, >> I'm sorry to report a serious bug that I have just noticed that applies to MTZ files for autobuild containing intensities. The >> problem is fixed now. I'm very sorry about this mistake. >> All the best, >> -Tom T >> >> >> THE PROBLEM: >> >> In all alpha and beta versions of phenix up to now (up to 1.3b/rc6), there has been a bug in autobuild in which the command >> >> phenix.autobuild data.mtz model.pdb >> >> will misinterpret intensity data as amplitudes if the input file is an mtz file (for example if the mtz file has IMEAN,SIGIMEAN and F,SIGF). (This can also happen in the GUI version, but you will have been presented on screen 3 with a list of data types (FP SIGFP) and columns from the input data file to match them and it is not so likely that you will have chosen to match FP with IMEAN.) >> >> You can tell if this has happened in your case by looking for >> something like (search for the string "Input labels:"): >> >> Input labels: ['IMEAN', 'SIGIMEAN', 'None', 'None', 'None', 'None', 'None', 'None', 'FreeR_flag'] >> >> in your log file (where the None's don't matter, just the first 2 column names. The columns in this list should be >> amplitude-containing columns only. If everything is ok.it should look instead like: >> >> Input labels: ['F', 'SIGF', 'None', 'None', 'None', 'None', 'None', 'None', 'None'] >> >> THE SOLUTION: >> >> In existing versions, the solution to this is to either (1) only have amplitude arrays in your mtz file, or (2) use the GUI and select the correct amplitude arrays, or (3) specify what amplitude columns to use with a command like: >> >> input_labels="F SIGF". >> >> Note that you cannot use intensity data from an mtz file with the existing versions of autobuild, only amplitude data. In the corrected version (1.3b/rc7, not yet out) , you will be able to use an mtz file with intensity data as long as there is no amplitude data in the same mtz file. >> >> Note also that all this applies equally to the refinement_file and hires_file data. Also note that if the file type is not mtz, then this bug does not apply (because the file is always imported and converted from intensities to amplitudes automatically). >> >> >> >> >> >> >> >> >> >> Thomas C. Terwilliger >> Mail Stop M888 >> Los Alamos National Laboratory >> Los Alamos, NM 87545 >> >> Tel: 505-667-0072 email: terwilliger(a)LANL.gov >> Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org >> ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu >> TB Structural Genomics Consortium web site: >> http://www.doe-mbi.ucla.edu/TB >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >> > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

1 0

after_autosol
by Bryan W. Lepore 18 Dec '07

18 Dec '07

using phenix 1.3b of 21-10-2007, trying `phenix.autobuild after_autosol` : how does one identify the "highest-numbered AutoSol run", and that it is completed? what does `phenix.autobuild` want for such a solution e.g. in terms of files/directories? or does `phenix.autobuild after_autosol` need to be included in the command at the time when `phenix.autosol` is submitted? phenix.autobuild reads a lot of params from my AutoSol dir, but apparently no solutions -- even though `phenix.autosol show_runs` shows one. -bryan

2 1

chain definition in phenix
by Kornelius Zeth 18 Dec '07

18 Dec '07

Dear all, I'm trying to refine/rebuild a structure of 48 identical chains. In Refmac the small letters a, b, c and 0 1 2 for the chains work quite well and are distinguished. However that does not apply to Phenix which sees A equal to a. What might be the solution to use? Thanks and best wishes Kornelius ---------------------------------------------- Kornelius Zeth Max Planck Institute for Developmental Biology Dept. Protein Evolution Spemannstr. 35 72076 Tuebingen, Germany kornelius.zeth(a)tuebingen.mpg.de Tel -49 7071 601 323 Fax -49 7071 601 349

5 6

Re: [phenixbb] Resolution Limits in the transition from AutoMR to AutoBuild
by Tom Terwilliger 17 Dec '07

17 Dec '07

Hi Dale, Thanks for the notes! Here is what is supposed to happen: the autobuild wizard keeps all the data you supply. resolution=2.2 will set the resolution of model-building and density modification and refinement refinement_resolution=2.3 will set the resolution for refinement to 2.3 instead of the 2.2 defined by resolution=2.2 There is as you guessed a bug however somewhere in the communication between the autobuild wizard and phenix.refine, so the refinement_resolution did not get passed properly. I will fix that... Thanks! -Tom T . At 01:29 AM 12/17/2007, Dale Tronrud wrote: > The structure factors that I downloaded from the PDB for my >little MR project contains both reflections behind the beam stop >and reflections of higher resolution than even the original authors >would use. When setting up the MR I entered the more restrictive >resolution limits into the Wizard and Phaser appears to have obeyed. > > As near as I can tell from the log files, however, Resolve is >using all the data in the rebuild. I am including a copy of the >log file from the "best" refinement. I would prefer that only >data between 30 and 2.2A were used but it is clear that the >refinement is, at least, monitoring the fit to all the data. I >am presuming that the program is refining against the same data >it is monitoring. > > I would like to suggest that either the log file be clearer >about the resolution limits it is actually refining to, or the >plumbing that passes the resolution limits from the AutoMR wizard >to the AutoBuild wizard be checked. > >Dale Tronrud > >P.S. That's all my problems... For now. The project I'm working >on is cursed and brings out the worst in all the software I have >used. > Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

2 2

A Small Problem with Atom Types in AutoBuild
by Dale Tronrud 17 Dec '07

17 Dec '07

The probe model in my MR project comes from a Shelxl refinement, and the .pdb file does not contain atom types at the end of each ATOM statement as modern .pdb files do. I have magnesium atoms in my model and the atom names for these atoms are "MG" and are properly shifted one space to the left of place where atoms with single letter element symbols lie. Phaser has no problem with this .pdb file. Resolve, however, considers this to be a fatal error. Opening MR.1.pdb and reading coordinates Warning...unknown atom type "M " ...this may indicate characters in columns 77-78 of this PDB file that are not the element ID. This and all similar labels ignored Failed to read line in PDB entry The PDB line is: ATOM 2953 MG BCL B 1 26.429 2.746 -11.155 1.00 12.03 Sorry could not read model file MR.1.pdb Seems a little harsh to me. Especially since the error message doesn't make it back to the log file monitored by the Wizard. I was confused about what was causing the wizard to stop until I dug into the other files in the AutoBuild directory. Earlier in the log file the program worries about my atoms "NA" and "NB" but does conclude that they are nitrogen atoms. In the future I'll work with .pdb files with the extra atom types at the end of the line. Dale Tronrud

2 1

Resolution Limits in the transition from AutoMR to AutoBuild
by Dale Tronrud 17 Dec '07

17 Dec '07

The structure factors that I downloaded from the PDB for my little MR project contains both reflections behind the beam stop and reflections of higher resolution than even the original authors would use. When setting up the MR I entered the more restrictive resolution limits into the Wizard and Phaser appears to have obeyed. As near as I can tell from the log files, however, Resolve is using all the data in the rebuild. I am including a copy of the log file from the "best" refinement. I would prefer that only data between 30 and 2.2A were used but it is clear that the refinement is, at least, monitoring the fit to all the data. I am presuming that the program is refining against the same data it is monitoring. I would like to suggest that either the log file be clearer about the resolution limits it is actually refining to, or the plumbing that passes the resolution limits from the AutoMR wizard to the AutoBuild wizard be checked. Dale Tronrud P.S. That's all my problems... For now. The project I'm working on is cursed and brings out the worst in all the software I have used. AutoBuild_run_3_/TEMP0/LIG_EDITED_EDITED_edit_model.pdb Monomer Library directory: "/usr/local/phenix-1.3b-rc6/ext_ref_files/mon_lib" Total number of atoms: 6255 Number of models: 1 Model: 0 Number of conformers: 1 Conformer: " " Number of atoms: 6255 Number of chains: 4 Number of residues, atoms: 352, 2697 Classifications: {'peptide': 352} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 16, 'TRANS': 333, 'PCIS': 2} Chain breaks: 8 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLN:plan2': 2, 'GLN%COO:plan2': 1, 'GLN%COO:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Number of residues, atoms: 352, 2694 Classifications: {'peptide': 352} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 10} Link IDs: {'PTRANS': 17, 'TRANS': 333, 'PCIS': 1} Chain breaks: 5 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLN:plan2': 2, 'GLN%COO:plan2': 1, 'GLN%COO:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 34 Number of residues, atoms: 7, 432 Unusual residues: {'BCL': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 12 Number of residues, atoms: 7, 432 Unusual residues: {'BCL': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 8.94, per 1000 atoms: 1.43 ================================== X-ray data ================================= F-obs: AutoBuild_run_3_/TEMP0/exptl_fobs_phases_freeR_flags.mtz:FP,SIGFP R-free flags: AutoBuild_run_3_/TEMP0/exptl_fobs_phases_freeR_flags.mtz:FreeR_flag Miller array info: AutoBuild_run_3_/TEMP0/exptl_fobs_phases_freeR_flags.mtz:FP,SIGFP Observation type: xray.amplitude Type of data: double, size=38159 Type of sigmas: double, size=38159 Number of Miller indices: 38159 Anomalous flag: False Unit cell: (169.1, 169.1, 169.1, 90, 90, 90) Space group: P 43 3 2 (No. 212) Systematic absences: 0 Centric reflections: 4505 Resolution range: 75.6238 2.14896 Completeness in resolution range: 0.839637 Completeness with d_max=infinity: 0.8396 Number of F-obs in resolution range: 38159 Number of F-obs <= 0: 0 Refinement resolution range: d_max = 75.6238 d_min = 2.1490 Miller array info: AutoBuild_run_3_/TEMP0/exptl_fobs_phases_freeR_flags.mtz:FreeR_flag Observation type: None Type of data: int, size=38159 Type of sigmas: None Number of Miller indices: 38159 Anomalous flag: False Unit cell: (169.1, 169.1, 169.1, 90, 90, 90) Space group: P 43 3 2 (No. 212) Systematic absences: 0 Centric reflections: 4505 Resolution range: 75.6238 2.14896 Completeness in resolution range: 0.839637 Completeness with d_max=infinity: 0.8396 Test (R-free flags) flag value: 0 Number of work/free reflections by resolution: work free %free bin 1: 75.6707 - 4.6295 [4755/4893] 4536 219 4.6% bin 2: 4.6295 - 3.6746 [4493/4607] 4248 245 5.5% bin 3: 3.6746 - 3.2101 [4414/4577] 4178 236 5.3% bin 4: 3.2101 - 2.9166 [4232/4498] 4007 225 5.3% bin 5: 2.9166 - 2.7075 [4221/4533] 4026 195 4.6% bin 6: 2.7075 - 2.5479 [4005/4483] 3792 213 5.3% bin 7: 2.5479 - 2.4203 [3811/4480] 3637 174 4.6% bin 8: 2.4203 - 2.3149 [3223/4472] 3066 157 4.9% bin 9: 2.3149 - 2.2258 [2846/4459] 2702 144 5.1% bin 10: 2.2258 - 2.1490 [2159/4445] 2042 117 5.4% overall 36234 1925 5.0% No array of experimental phases found. ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ========================== Set up restraints manager ========================== Number of disulfides: simple=0, symmetry=0 Time building geometry restraints manager: 0.40 seconds Histogram of bond lengths: 1.12 - 1.26: 957 1.26 - 1.40: 1621 1.40 - 1.55: 3702 1.55 - 1.69: 131 1.69 - 1.83: 23 Bond restraints sorted by residual: atom i - atom j ideal model delta weight residual " O1A BCL B 6 " - " CGA BCL B 6 " 1.212 1.117 0.095 2.50e+03 2.25e+01 " O1A BCL D 6 " - " CGA BCL D 6 " 1.212 1.118 0.094 2.50e+03 2.22e+01 " C15 BCL D 6 " - " C16 BCL D 6 " 1.540 1.459 0.081 2.50e+03 1.63e+01 " C15 BCL B 6 " - " C16 BCL B 6 " 1.540 1.460 0.080 2.50e+03 1.60e+01 " N PRO A 188 " - " CD PRO A 188 " 1.473 1.418 0.055 5.10e+03 1.56e+01 ... (remaining 6429 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.17: 9 2.17 - 2.85: 1981 2.85 - 3.53: 8408 3.53 - 4.22: 16251 4.22 - 4.90: 27426 Nonbonded interactions sorted by model distance: atom i - atom j model vdw sym.op. j " OG SER A 24 " - " C GLY C 23 " 1.486 3.270 " OG SER A 24 " - " N SER C 24 " 1.747 3.120 " OH TYR A 330 " - " OE1 GLN C 333 " 1.870 3.040 x-1/4,-z-1/4,y+1/4 " C ASN A 121 " - " N LEU A 122 " 1.941 3.350 x+1,y+1,z+1 " OG SER A 24 " - " O GLY C 23 " 1.956 3.040 ... (remaining 54070 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.73: 1959 22.73 - 45.46: 198 45.46 - 68.20: 68 68.20 - 90.93: 27 90.93 - 113.66: 1 Dihedral angle restraints sorted by residual: " CA ALA C 327 " " C ALA C 327 " " N PRO C 328 " " CA PRO C 328 " ideal model delta periodicty weight residual 180.00 -66.34 -113.66 1 4.00e-02 5.17e+02 " C2B BCL D 7 " " C3B BCL D 7 " " CAB BCL D 7 " " OBB BCL D 7 " ideal model delta periodicty weight residual 0.00 147.16 32.84 2 4.00e-02 4.31e+01 " C2B BCL B 7 " " C3B BCL B 7 " " CAB BCL B 7 " " OBB BCL B 7 " ideal model delta periodicty weight residual 0.00 147.20 32.80 2 4.00e-02 4.30e+01 ... (remaining 2250 not shown) ==================== Fixing bad ADP in input model (if any) =================== ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 4 Type Number sf(0) Gaussians S 14 15.96 2 O 1076 7.97 2 N 1007 6.97 2 C 4158 5.97 2 sf(0) = scattering factor at diffraction angle 0. ====================== Modifying start model if requested ===================== atom_attributes_list is modified in-place to define missing element types when possible. ==================== Fixing bad ADP in input model (if any) =================== ================== Extract refinement strategy and selections ================= individual_sites = True rigid_body = False individual_adp = True group_adp = False tls = False individual_occupancies = False group_occupancies = False group_anomalous = False size = 6255 n_use = 6255 n_use_u_iso = 6255 n_use_u_aniso = 0 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 n_anisotropic_flag = 0 total number of scatterers = 6255 ==================== Process input NCS or/and find new NCS ==================== NCS groups found in parameter file: 0 Automatic NCS search: Chains in this PDB file: ['A', 'C'] GROUPS BASED ON QUICK COMPARISON: [] Looking for invariant domains for ...: ['A', 'C'] [[[9, 366]], [[9, 366]]] Updated/new NCS groups: refinement.ncs.restraint_group { reference = chain A and (resseq 9:118 or resseq 128:207 or resseq 215:366 ) selection = chain C and (resseq 9:118 or resseq 128:207 or resseq 215:366 ) } ----------Building NCS restraints---------- NCS restraint group 1: NCS operator 1: Reference selection: "chain A and (resseq 9:118 or resseq 128:207 or resseq 215:366 )" Other selection: "chain C and (resseq 9:118 or resseq 128:207 or resseq 215:366 )" Number of atom pairs: 2603 Rotation={{-0.999509, -0.0190423, 0.0248896}, {0.0243783, 0.0266261, 0.999348}, {-0.0196926, 0.999464, -0.0261488}} Translation={{38.5072}, {-44.0643}, {42.3394}} Histogram of differences: 0.001760 - 0.701888: 2552 0.701888 - 1.402017: 14 1.402017 - 2.102145: 22 2.102145 - 2.802274: 6 2.802274 - 3.502402: 4 3.502402 - 4.202531: 5 RMS difference with respect to the reference: 0.312576 =================== Write initial parameters into .eff file =================== ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { input { pdb { file_name = "/usr/users/dale/structure/fmo-ct/tronrud_2007/AutoBuild_run_3_/TEMP0/LIG_EDITED_EDITED_edit_model.pdb" } xray_data { file_name = "AutoBuild_run_3_/TEMP0/exptl_fobs_phases_freeR_flags.mtz" labels = "FP,SIGFP" high_resolution = 2.2 r_free_flags { file_name = "AutoBuild_run_3_/TEMP0/exptl_fobs_phases_freeR_flags.mtz" label = "FreeR_flag" test_flag_value = 0 } } monomers { file_name = "/usr/users/dale/geometry/chromophores/bcl_tnt.cif" } } output { prefix = "AutoBuild_run_3_/TEMP0/Build_composite_refined_side_3" serial = 1 write_eff_file = False write_geo_file = False write_def_file = False export_final_f_model = *mtz cns write_maps = False } main { ordered_solvent = True ncs = True use_experimental_phases = False random_seed = 516344 } ncs { special_position_warnings_only = True restraint_group { reference = "chain A and (resseq 9:118 or resseq 128:207 or resseq 215:366 )" selection = "chain C and (resseq 9:118 or resseq 128:207 or resseq 215:366 )" } } ordered_solvent { low_resolution = 3 } mask { ignore_zero_occupancy_atoms = False } } #phil __OFF__ ============================= ml refinement start ============================= ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 2.15 - 75.62 A; n_refl. = 38159)------------------------------| | | | r_work= 0.3243 r_free= 0.3131 ksol= 0.00 Bsol= 0.00 scale= 1.698 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | maximum likelihood estimate for coordinate error: 0.40 A | | x-ray target function (ml) for work reflections: 7.754289 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 75.6707 - 5.1788 0.97 3272 159 0.4168 0.3905 8.6988 8.5536| | 2: 5.1788 - 4.1106 0.98 3112 155 0.2200 0.2341 8.4215 8.4968| | 3: 4.1106 - 3.5910 0.97 3000 188 0.2279 0.2321 8.1284 8.1202| | 4: 3.5910 - 3.2627 0.97 2977 168 0.2388 0.2465 7.9459 8.0053| | 5: 3.2627 - 3.0288 0.95 2930 152 0.2747 0.2878 7.8061 7.8021| | 6: 3.0288 - 2.8502 0.93 2844 159 0.2741 0.2804 7.6418 7.6974| | 7: 2.8502 - 2.7075 0.93 2860 139 0.2757 0.3123 7.5349 7.6274| | 8: 2.7075 - 2.5896 0.89 2705 156 0.2878 0.3340 7.453 7.4977| | 9: 2.5896 - 2.4899 0.89 2715 135 0.2982 0.3356 7.3586 7.5621| | 10: 2.4899 - 2.4040 0.81 2488 115 0.3089 0.3543 7.3181 7.3706| | 11: 2.4040 - 2.3288 0.72 2176 109 0.3142 0.3613 7.3041 7.3373| | 12: 2.3288 - 2.2623 0.67 2018 110 0.3096 0.3293 7.3086 7.3357| | 13: 2.2623 - 2.2027 0.58 1742 104 0.3370 0.3823 7.3303 7.508| | 14: 2.2027 - 2.1490 0.46 1395 76 0.3749 0.3710 7.4161 7.4587| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 75.6707 - 5.1788 3272 159 0.64 39.15 1.16 1.12 4689001.73| | 2: 5.1788 - 4.1106 3112 155 0.79 26.44 2.03 1.66 3059064.97| | 3: 4.1106 - 3.5910 3000 188 0.82 24.63 2.13 1.94 1936112.07| | 4: 3.5910 - 3.2627 2977 168 0.81 25.88 2.18 2.02 1377840.11| | 5: 3.2627 - 3.0288 2930 152 0.78 28.52 2.16 2.01 1065329.57| | 6: 3.0288 - 2.8502 2844 159 0.76 30.45 2.06 1.97 856549.95| | 7: 2.8502 - 2.7075 2860 139 0.77 30.05 2.04 1.88 690049.30| | 8: 2.7075 - 2.5896 2705 156 0.75 31.56 1.99 1.78 594991.98| | 9: 2.5896 - 2.4899 2715 135 0.72 34.01 1.90 1.74 528160.82| | 10: 2.4899 - 2.4040 2488 115 0.71 35.26 1.94 1.68 488836.19| | 11: 2.4040 - 2.3288 2176 109 0.72 34.25 1.95 1.68 443633.67| | 12: 2.3288 - 2.2623 2018 110 0.73 33.21 1.92 1.64 434086.87| | 13: 2.2623 - 2.2027 1742 104 0.67 39.14 2.01 1.62 524747.84| | 14: 2.2027 - 2.1490 1395 76 0.56 47.31 2.05 1.54 720558.54| |alpha: min = 1.12 max = 2.02 mean = 1.74| |beta: min = 434086.87 max = 4689001.73 mean = 1388851.17| |figures of merit: min = 0.00 max = 1.00 mean = 0.74| |phase err.(work): min = 0.00 max = 89.94 mean = 31.97| |phase err.(test): min = 0.00 max = 89.63 mean = 32.13| |-----------------------------------------------------------------------------| ============================== Outliers rejection ============================= basic_wilson_outliers = 0 extreme_wilson_outliers = 2 beamstop_shadow_outliers = 6 total = 8 ====================== Target weights (before refinement) ===================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 12.037420 wxc_scale = 0.500 wc = 1.000 | | angle between x-ray and geometry gradient vectors: 96.336 (deg) | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxc = 0.231372 wxc_scale = 1.000 wc = 1.000 | | angle between Xray and ADP gradient vectors: 93.656 (deg) | |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- |-Geometry statistics: start--------------------------------------------------| | Histogram of deviations from ideal values for | | Bonds | Angles | Nonbonded contacts | | 0.000 - 0.009: 4797 | 0.000 - 2.504: 7924 | 1.486 - 1.828: 2 | | 0.009 - 0.019: 1097 | 2.504 - 5.009: 655 | 1.828 - 2.169: 7 | | 0.019 - 0.028: 284 | 5.009 - 7.513: 145 | 2.169 - 2.511: 30 | | 0.028 - 0.038: 144 | 7.513 - 10.018: 40 | 2.511 - 2.852: 1951 | | 0.038 - 0.047: 61 | 10.018 - 12.522: 8 | 2.852 - 3.193: 3550 | | 0.047 - 0.057: 31 | 12.522 - 15.026: 4 | 3.193 - 3.535: 4858 | | 0.057 - 0.066: 13 | 15.026 - 17.531: 2 | 3.535 - 3.876: 8239 | | 0.066 - 0.076: 3 | 17.531 - 20.035: 0 | 3.876 - 4.217: 8012 | | 0.076 - 0.085: 2 | 20.035 - 22.539: 0 | 4.217 - 4.559: 11917 | | 0.085 - 0.095: 2 | 22.539 - 25.044: 1 | 4.559 - 4.900: 15509 | |-----------------------------------------------------------------------------| |-Geometry statistics: start--------------------------------------------------| | Type | Count | Deviation from ideal | Targets | Target (sum) | | | | rmsd max min | | | | bond | 6434 | 0.012 0.095 0.000 | 0.323 | | | angle | 8779 | 1.693 25.044 0.000 | 0.420 | | | chirality | 905 | 0.089 0.406 0.000 | 0.199 | 0.156 | | planarity | 977 | 0.007 0.154 0.000 | 0.242 | | | dihedral | 2253 | 17.723 113.659 0.001 | 1.614 | | | nonbonded | 6434 | 4.142 4.900 1.486 | 0.255 | | |-----------------------------------------------------------------------------| |-ADP statistics (Wilson B = 25.121)------------------------------------------| | Atom | Number of | Isotropic or equivalent| Anisotropy lmin/max | | type |iso aniso | min max mean | min max mean | | - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - - | | all : 6255 0 7.67 118.66 27.52 None None None | | all(noH): 6255 0 7.67 118.66 27.52 None None None | | Sol. : 0 0 None None None None None None | | Mac. : 6255 0 7.67 118.66 27.52 None None None | | Hyd. : 0 0 None None None None None None | | - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | | Distribution of isotropic (or equivalent) ADP for non-H atoms: | | Bin# value range #atoms | Bin# value range #atoms | | 0: 7.670 - 18.769: 1649 | 5: 63.165 - 74.264: 119 | | 1: 18.769 - 29.868: 2973 | 6: 74.264 - 85.363: 80 | | 2: 29.868 - 40.967: 840 | 7: 85.363 - 96.462: 50 | | 3: 40.967 - 52.066: 296 | 8: 96.462 - 107.561: 28 | | 4: 52.066 - 63.165: 198 | 9: 107.561 - 118.660: 22 | | =>continue=> | |-----------------------------------------------------------------------------| |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 2.15 - 75.62 A; n_refl. = 38159)------------------------------| | | | r_work= 0.3243 r_free= 0.3131 ksol= 0.00 Bsol= 0.00 scale= 1.698 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | maximum likelihood estimate for coordinate error: 0.40 A | | x-ray target function (ml) for work reflections: 7.754289 | |-----------------------------------------------------------------------------| ====================== bulk solvent modeling and scaling ====================== |--(resolution: 2.15 - 75.62 A; n_refl. = 38159)------------------------------| | | | r_work= 0.2582 r_free= 0.2742 ksol= 0.35 Bsol= 50.00 scale= 2.164 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (2.32,2.32,2.32,0.00,0.00,-0.00); trace/3= 2.32 | | | | maximum likelihood estimate for coordinate error: 0.39 A | | x-ray target function (ml) for work reflections: 7.690252 | |-----------------------------------------------------------------------------| ========================== Target weights: x-ray data ========================= |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 10.750300 wxc_scale = 0.500 wc = 1.000 | | angle between x-ray and geometry gradient vectors: 96.207 (deg) | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxc = 0.205411 wxc_scale = 1.000 wc = 1.000 | | angle between Xray and ADP gradient vectors: 94.015 (deg) | |-----------------------------------------------------------------------------| ================================ xyz refinement =============================== |-LBFGS minimization----------------------------------------------------------| | start r-factor (work) = 0.2582 final r-factor (work) = 0.2348 | | start r-factor (free) = 0.2742 final r-factor (free) = 0.2713 | |-----------------------------------------------------------------------------| | T_start = wxc * wxc_scale * Exray + wc * Echem | | 42.5209 = 10.75 * 0.50 * 7.7632 + 1.00 * 0.7926 | | | | T_final = wxc * wxc_scale * Exray + wc * Echem | | 41.1803 = 10.75 * 0.50 * 7.6326 + 1.00 * 0.1541 | |-----------------------------------------------------------------------------| | number of iterations = 25 | number of function evaluations = 26 | |-----------------------------------------------------------------------------| ================================ ADP refinement =============================== ----------Individual ADP refinement---------- |-LBFGS minimization----------------------------------------------------------| | start r-factor (work) = 0.2348 final r-factor (work) = 0.2216 | | start r-factor (free) = 0.2713 final r-factor (free) = 0.2676 | |-----------------------------------------------------------------------------| | T_start = wxu * wxu_scale * Exray + wu * Eadp | | 1.5745 = 0.21 * 1.00 * 7.6326 + 1.00 * 0.0067 | | | | T_final = wxu * wxu_scale * Exray + wu * Eadp | | 1.5631 = 0.21 * 1.00 * 7.5874 + 1.00 * 0.0045 | |-----------------------------------------------------------------------------| | number of iterations = 23 | number of function evaluations = 24 | |-----------------------------------------------------------------------------| |-ADP statistics (Wilson B = 25.121)------------------------------------------| | Atom | Number of | Isotropic or equivalent| Anisotropy lmin/max | | type |iso aniso | min max mean | min max mean | | - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - - | | all : 6255 0 0.00 117.10 26.33 None None None | | all(noH): 6255 0 0.00 117.10 26.33 None None None | | Sol. : 0 0 None None None None None None | | Mac. : 6255 0 0.00 117.10 26.33 None None None | | Hyd. : 0 0 None None None None None None | | - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | | Distribution of isotropic (or equivalent) ADP for non-H atoms: | | Bin# value range #atoms | Bin# value range #atoms | | 0: 0.000 - 11.710: 203 | 5: 58.550 - 70.260: 136 | | 1: 11.710 - 23.420: 3284 | 6: 70.260 - 81.969: 72 | | 2: 23.420 - 35.130: 1811 | 7: 81.969 - 93.679: 42 | | 3: 35.130 - 46.840: 395 | 8: 93.679 - 105.389: 25 | | 4: 46.840 - 58.550: 266 | 9: 105.389 - 117.099: 21 | | =>continue=> | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 2.15 - 75.62 A; n_refl. = 38159)------------------------------| | | | r_work= 0.2216 r_free= 0.2676 ksol= 0.35 Bsol= 50.00 scale= 2.155 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (2.32,2.32,2.32,0.00,0.00,-0.00); trace/3= 2.32 | | | | maximum likelihood estimate for coordinate error: 0.37 A | | x-ray target function (ml) for work reflections: 7.578854 | |-----------------------------------------------------------------------------| ================== ordered solvent: location/analysis/update ================== Start model: number = 0 b_iso_min = None (limit = 1.00) b_iso_max = None (limit = 50.00) b_iso_mean = None occupancy_min = None (limit = 0.10) occupancy_max = None (limit = 1.20) dist_sol_mol_min = None (limit = 1.80) dist_sol_mol_max = None (limit = 6.00) Peak search: maximum allowed number of peaks: 6250 number of peaks from mFobs-DFmodel map: 449 number of peaks from 2mFobs-DFmodel map: 2500 number of peaks after clustering: 392 Filter by distance & map next to the model: mapped sites are within: 0.520 - 5.987 number of sites selected in [dist_min= 1.80, dist_max= 6.00]: 291 from: 392 mapped sites are within: 1.816 - 5.987 Peak filtering (peak - peak close contact elimination): peaks rejected: 0 total number of peaks selected: 291 Final model: number = 291 b_iso_min = 26.33 (limit = 1.00) b_iso_max = 26.33 (limit = 50.00) b_iso_mean = 26.33 occupancy_min = 1.00 (limit = 0.10) occupancy_max = 1.00 (limit = 1.20) dist_sol_mol_min = 1.82 (limit = 1.80) dist_sol_mol_max = 5.99 (limit = 6.00) ====================== bulk solvent modeling and scaling ====================== |--(resolution: 2.15 - 75.62 A; n_refl. = 38159)------------------------------| | | | r_work= 0.2037 r_free= 0.2379 ksol= 0.34 Bsol= 50.00 scale= 2.123 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (2.43,2.43,2.43,0.00,0.00,-0.00); trace/3= 2.43 | | | | maximum likelihood estimate for coordinate error: 0.32 A | | x-ray target function (ml) for work reflections: 7.486761 | |-----------------------------------------------------------------------------| ========================== Target weights: x-ray data ========================= |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 6.888030 wxc_scale = 0.500 wc = 1.000 | | angle between x-ray and geometry gradient vectors: 121.803 (deg) | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxc = 0.171233 wxc_scale = 1.000 wc = 1.000 | | angle between Xray and ADP gradient vectors: 117.753 (deg) | |-----------------------------------------------------------------------------| ================================ xyz refinement =============================== |-LBFGS minimization----------------------------------------------------------| | start r-factor (work) = 0.2037 final r-factor (work) = 0.1944 | | start r-factor (free) = 0.2379 final r-factor (free) = 0.2423 | |-----------------------------------------------------------------------------| | T_start = wxc * wxc_scale * Exray + wc * Echem | | 26.1593 = 6.89 * 0.50 * 7.5465 + 1.00 * 0.1690 | | | | T_final = wxc * wxc_scale * Exray + wc * Echem | | 25.8504 = 6.89 * 0.50 * 7.4673 + 1.00 * 0.1330 | |-----------------------------------------------------------------------------| | number of iterations = 25 | number of function evaluations = 27 | |-----------------------------------------------------------------------------| ================================ ADP refinement =============================== ----------Individual ADP refinement---------- |-LBFGS minimization----------------------------------------------------------| | start r-factor (work) = 0.1944 final r-factor (work) = 0.1882 | | start r-factor (free) = 0.2423 final r-factor (free) = 0.2396 | |-----------------------------------------------------------------------------| | T_start = wxu * wxu_scale * Exray + wu * Eadp | | 1.2834 = 0.17 * 1.00 * 7.4673 + 1.00 * 0.0047 | | | | T_final = wxu * wxu_scale * Exray + wu * Eadp | | 1.2813 = 0.17 * 1.00 * 7.4563 + 1.00 * 0.0045 | |-----------------------------------------------------------------------------| | number of iterations = 18 | number of function evaluations = 19 | |-----------------------------------------------------------------------------| |-ADP statistics (Wilson B = 25.121)------------------------------------------| | Atom | Number of | Isotropic or equivalent| Anisotropy lmin/max | | type |iso aniso | min max mean | min max mean | | - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - - | | all : 6546 0 2.33 119.19 25.98 None None None | | all(noH): 6546 0 2.33 119.19 25.98 None None None | | Sol. : 291 0 3.23 59.44 29.93 None None None | | Mac. : 6255 0 2.33 119.19 25.79 None None None | | Hyd. : 0 0 None None None None None None | | - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | | Distribution of isotropic (or equivalent) ADP for non-H atoms: | | Bin# value range #atoms | Bin# value range #atoms | | 0: 2.330 - 14.016: 627 | 5: 60.762 - 72.449: 124 | | 1: 14.016 - 25.703: 3737 | 6: 72.449 - 84.135: 75 | | 2: 25.703 - 37.389: 1297 | 7: 84.135 - 95.822: 35 | | 3: 37.389 - 49.076: 396 | 8: 95.822 - 107.508: 18 | | 4: 49.076 - 60.762: 219 | 9: 107.508 - 119.195: 18 | | =>continue=> | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 2.15 - 75.62 A; n_refl. = 38159)------------------------------| | | | r_work= 0.1882 r_free= 0.2396 ksol= 0.34 Bsol= 50.00 scale= 2.114 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (2.43,2.43,2.43,0.00,0.00,-0.00); trace/3= 2.43 | | | | maximum likelihood estimate for coordinate error: 0.33 A | | x-ray target function (ml) for work reflections: 7.449879 | |-----------------------------------------------------------------------------| ================== ordered solvent: location/analysis/update ================== Start model: number = 291 b_iso_min = 3.23 (limit = 1.00) b_iso_max = 59.44 (limit = 50.00) b_iso_mean = 29.93 occupancy_min = 1.00 (limit = 0.10) occupancy_max = 1.00 (limit = 1.20) dist_sol_mol_min = 2.06 (limit = 1.80) dist_sol_mol_max = 5.96 (limit = 6.00) Peak search: maximum allowed number of peaks: 6250 number of peaks from mFobs-DFmodel map: 420 number of peaks from 2mFobs-DFmodel map: 2405 number of peaks after clustering: 300 Filter by distance & map next to the model: mapped sites are within: 0.214 - 5.940 number of sites selected in [dist_min= 1.80, dist_max= 6.00]: 118 from: 300 mapped sites are within: 1.802 - 5.940 Peak filtering (peak - peak close contact elimination): peaks rejected: 0 total number of peaks selected: 118 Final model: number = 398 b_iso_min = 3.23 (limit = 1.00) b_iso_max = 49.81 (limit = 50.00) b_iso_mean = 28.22 occupancy_min = 1.00 (limit = 0.10) occupancy_max = 1.00 (limit = 1.20) dist_sol_mol_min = 1.80 (limit = 1.80) dist_sol_mol_max = 5.96 (limit = 6.00) ====================== bulk solvent modeling and scaling ====================== |--(resolution: 2.15 - 75.62 A; n_refl. = 38159)------------------------------| | | | r_work= 0.1875 r_free= 0.2312 ksol= 0.33 Bsol= 50.00 scale= 2.126 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (3.18,3.18,3.18,0.00,0.00,-0.00); trace/3= 3.18 | | | | maximum likelihood estimate for coordinate error: 0.31 A | | x-ray target function (ml) for work reflections: 7.433926 | |-----------------------------------------------------------------------------| ========================== Target weights: x-ray data ========================= |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 4.792070 wxc_scale = 0.500 wc = 1.000 | | angle between x-ray and geometry gradient vectors: 137.678 (deg) | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxc = 0.173077 wxc_scale = 1.000 wc = 1.000 | | angle between Xray and ADP gradient vectors: 129.742 (deg) | |-----------------------------------------------------------------------------| ================================ xyz refinement =============================== |-LBFGS minimization----------------------------------------------------------| | start r-factor (work) = 0.1875 final r-factor (work) = 0.1857 | | start r-factor (free) = 0.2312 final r-factor (free) = 0.2341 | |-----------------------------------------------------------------------------| | T_start = wxc * wxc_scale * Exray + wc * Echem | | 18.0062 = 4.79 * 0.50 * 7.4550 + 1.00 * 0.1437 | | | | T_final = wxc * wxc_scale * Exray + wc * Echem | | 17.9146 = 4.79 * 0.50 * 7.4304 + 1.00 * 0.1110 | |-----------------------------------------------------------------------------| | number of iterations = 25 | number of function evaluations = 27 | |-----------------------------------------------------------------------------| ================================ ADP refinement =============================== ----------Individual ADP refinement---------- |-LBFGS minimization----------------------------------------------------------| | start r-factor (work) = 0.1857 final r-factor (work) = 0.1818 | | start r-factor (free) = 0.2341 final r-factor (free) = 0.2331 | |-----------------------------------------------------------------------------| | T_start = wxu * wxu_scale * Exray + wu * Eadp | | 1.2906 = 0.17 * 1.00 * 7.4304 + 1.00 * 0.0046 | | | | T_final = wxu * wxu_scale * Exray + wu * Eadp | | 1.2897 = 0.17 * 1.00 * 7.4228 + 1.00 * 0.0050 | |-----------------------------------------------------------------------------| | number of iterations = 9 | number of function evaluations = 9 | |-----------------------------------------------------------------------------| |-ADP statistics (Wilson B = 25.121)------------------------------------------| | Atom | Number of | Isotropic or equivalent| Anisotropy lmin/max | | type |iso aniso | min max mean | min max mean | | - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - - | | all : 6653 0 0.00 118.91 25.71 None None None | | all(noH): 6653 0 0.00 118.91 25.71 None None None | | Sol. : 398 0 0.00 55.54 31.76 None None None | | Mac. : 6255 0 2.01 118.91 25.32 None None None | | Hyd. : 0 0 None None None None None None | | - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | | Distribution of isotropic (or equivalent) ADP for non-H atoms: | | Bin# value range #atoms | Bin# value range #atoms | | 0: 0.000 - 11.891: 364 | 5: 59.455 - 71.345: 131 | | 1: 11.891 - 23.782: 3643 | 6: 71.345 - 83.236: 75 | | 2: 23.782 - 35.673: 1625 | 7: 83.236 - 95.127: 43 | | 3: 35.673 - 47.564: 492 | 8: 95.127 - 107.018: 20 | | 4: 47.564 - 59.455: 243 | 9: 107.018 - 118.909: 17 | | =>continue=> | |-----------------------------------------------------------------------------| ======================= ordered solvent: final clean up ======================= Start model: number = 398 b_iso_min = 0.00 (limit = 1.00) b_iso_max = 55.54 (limit = 50.00) b_iso_mean = 31.76 occupancy_min = 1.00 (limit = 0.10) occupancy_max = 1.00 (limit = 1.20) dist_sol_mol_min = 2.05 (limit = 1.80) dist_sol_mol_max = 5.96 (limit = 6.00) Final model: number = 388 b_iso_min = 3.51 (limit = 1.00) b_iso_max = 49.97 (limit = 50.00) b_iso_mean = 31.36 occupancy_min = 1.00 (limit = 0.10) occupancy_max = 1.00 (limit = 1.20) dist_sol_mol_min = 2.05 (limit = 1.80) dist_sol_mol_max = 5.96 (limit = 6.00) ----------X-ray data---------- |--(resolution: 2.15 - 75.62 A; n_refl. = 38159)------------------------------| | | | r_work= 0.1831 r_free= 0.2329 ksol= 0.33 Bsol= 50.00 scale= 2.114 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (3.18,3.18,3.18,0.00,0.00,-0.00); trace/3= 3.18 | | | | maximum likelihood estimate for coordinate error: 0.32 A | | x-ray target function (ml) for work reflections: 7.422958 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 75.6707 - 5.1788 0.97 3272 159 0.2130 0.2552 8.1276 8.228| | 2: 5.1788 - 4.1106 0.98 3112 155 0.1356 0.1644 7.8761 8.0672| | 3: 4.1106 - 3.5910 0.97 3000 188 0.1468 0.1750 7.7387 7.8215| | 4: 3.5910 - 3.2627 0.97 2977 168 0.1558 0.1979 7.5865 7.8088| | 5: 3.2627 - 3.0288 0.95 2930 152 0.1709 0.2266 7.4557 7.5858| | 6: 3.0288 - 2.8502 0.93 2844 159 0.1755 0.2362 7.2991 7.4461| | 7: 2.8502 - 2.7075 0.93 2860 139 0.1762 0.2620 7.2285 7.4876| | 8: 2.7075 - 2.5896 0.89 2705 156 0.1910 0.2717 7.1596 7.3038| | 9: 2.5896 - 2.4899 0.89 2715 135 0.2060 0.2556 7.0999 7.3902| | 10: 2.4899 - 2.4040 0.81 2488 115 0.2115 0.3023 7.0774 7.2784| | 11: 2.4040 - 2.3288 0.72 2176 109 0.2299 0.3153 7.0902 7.1912| | 12: 2.3288 - 2.2623 0.67 2018 110 0.2312 0.2806 7.1132 7.2823| | 13: 2.2623 - 2.2027 0.58 1742 104 0.2705 0.3734 7.181 7.532| | 14: 2.2027 - 2.1490 0.46 1395 76 0.3164 0.3752 7.339 7.432| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 75.6707 - 5.1788 3272 159 0.84 21.52 2.03 1.91 1706271.76| | 2: 5.1788 - 4.1106 3112 155 0.92 13.72 2.19 2.12 1119490.86| | 3: 4.1106 - 3.5910 3000 188 0.90 16.33 2.16 2.10 948218.23| | 4: 3.5910 - 3.2627 2977 168 0.88 18.25 2.15 2.06 723060.91| | 5: 3.2627 - 3.0288 2930 152 0.86 20.64 2.12 2.04 602696.08| | 6: 3.0288 - 2.8502 2844 159 0.85 21.95 2.09 2.03 469088.14| | 7: 2.8502 - 2.7075 2860 139 0.84 22.75 2.07 2.01 423879.11| | 8: 2.7075 - 2.5896 2705 156 0.83 23.91 2.02 1.89 364459.47| | 9: 2.5896 - 2.4899 2715 135 0.80 26.95 1.96 1.80 333699.76| | 10: 2.4899 - 2.4040 2488 115 0.80 26.92 1.99 1.83 318772.98| | 11: 2.4040 - 2.3288 2176 109 0.80 27.04 2.01 1.79 305463.63| | 12: 2.3288 - 2.2623 2018 110 0.81 26.41 2.04 1.78 298736.36| | 13: 2.2623 - 2.2027 1742 104 0.76 30.75 2.14 1.86 366985.74| | 14: 2.2027 - 2.1490 1395 76 0.63 41.90 2.25 1.80 624233.56| |alpha: min = 1.78 max = 2.12 mean = 1.95| |beta: min = 298736.36 max = 1706271.76 mean = 657914.19| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 90.00 mean = 23.00| |phase err.(test): min = 0.00 max = 89.39 mean = 23.30| |-----------------------------------------------------------------------------| ====================== bulk solvent modeling and scaling ====================== |--(resolution: 2.15 - 75.62 A; n_refl. = 38159)------------------------------| | | | r_work= 0.1826 r_free= 0.2324 ksol= 0.34 Bsol= 65.65 scale= 2.111 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,-0.00); trace/3= 0.00 | | | | maximum likelihood estimate for coordinate error: 0.32 A | | x-ray target function (ml) for work reflections: 7.421608 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.15 - 75.62 A; n_refl. = 38159)------------------------------| | | | r_work= 0.1826 r_free= 0.2324 ksol= 0.34 Bsol= 65.65 scale= 2.111 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,-0.00); trace/3= 0.00 | | | | maximum likelihood estimate for coordinate error: 0.32 A | | x-ray target function (ml) for work reflections: 7.421608 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 75.6707 - 5.1788 0.97 3272 159 0.2125 0.2562 8.1276 8.23| | 2: 5.1788 - 4.1106 0.98 3112 155 0.1356 0.1646 7.8765 8.0679| | 3: 4.1106 - 3.5910 0.97 3000 188 0.1471 0.1753 7.7395 7.8223| | 4: 3.5910 - 3.2627 0.97 2977 168 0.1557 0.1975 7.5862 7.8097| | 5: 3.2627 - 3.0288 0.95 2930 152 0.1700 0.2270 7.4544 7.5859| | 6: 3.0288 - 2.8502 0.93 2844 159 0.1744 0.2359 7.2964 7.4451| | 7: 2.8502 - 2.7075 0.93 2860 139 0.1754 0.2619 7.227 7.4839| | 8: 2.7075 - 2.5896 0.89 2705 156 0.1902 0.2712 7.1561 7.3014| | 9: 2.5896 - 2.4899 0.89 2715 135 0.2054 0.2548 7.0962 7.3838| | 10: 2.4899 - 2.4040 0.81 2488 115 0.2109 0.3026 7.0744 7.2786| | 11: 2.4040 - 2.3288 0.72 2176 109 0.2295 0.3132 7.088 7.1878| | 12: 2.3288 - 2.2623 0.67 2018 110 0.2309 0.2813 7.112 7.2824| | 13: 2.2623 - 2.2027 0.58 1742 104 0.2704 0.3724 7.1801 7.5313| | 14: 2.2027 - 2.1490 0.46 1395 76 0.3163 0.3749 7.3386 7.432| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 75.6707 - 5.1788 3272 159 0.83 21.68 2.02 1.90 1729678.56| | 2: 5.1788 - 4.1106 3112 155 0.92 13.76 2.19 2.11 1122862.76| | 3: 4.1106 - 3.5910 3000 188 0.90 16.38 2.16 2.10 950321.91| | 4: 3.5910 - 3.2627 2977 168 0.88 18.29 2.16 2.07 725331.21| | 5: 3.2627 - 3.0288 2930 152 0.86 20.71 2.13 2.04 606450.12| | 6: 3.0288 - 2.8502 2844 159 0.85 22.01 2.10 2.04 469766.50| | 7: 2.8502 - 2.7075 2860 139 0.84 22.78 2.08 2.02 424394.38| | 8: 2.7075 - 2.5896 2705 156 0.83 23.83 2.03 1.89 361907.39| | 9: 2.5896 - 2.4899 2715 135 0.80 26.81 1.97 1.81 330530.78| | 10: 2.4899 - 2.4040 2488 115 0.80 26.80 1.99 1.84 316100.00| | 11: 2.4040 - 2.3288 2176 109 0.80 26.93 2.01 1.80 303267.90| | 12: 2.3288 - 2.2623 2018 110 0.81 26.36 2.05 1.79 297871.94| | 13: 2.2623 - 2.2027 1742 104 0.76 30.68 2.15 1.87 365788.30| | 14: 2.2027 - 2.1490 1395 76 0.63 41.83 2.25 1.81 622797.66| |alpha: min = 1.79 max = 2.11 mean = 1.95| |beta: min = 297871.94 max = 1729678.56 mean = 660171.29| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.91 mean = 23.00| |phase err.(test): min = 0.00 max = 89.92 mean = 23.31| |-----------------------------------------------------------------------------| |-ADP statistics (Wilson B = 25.121)------------------------------------------| | Atom | Number of | Isotropic or equivalent| Anisotropy lmin/max | | type |iso aniso | min max mean | min max mean | | - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - - | | all : 6643 0 5.23 122.12 28.89 None None None | | all(noH): 6643 0 5.23 122.12 28.89 None None None | | Sol. : 388 0 6.73 53.19 34.57 None None None | | Mac. : 6255 0 5.23 122.12 28.54 None None None | | Hyd. : 0 0 None None None None None None | | - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | | Distribution of isotropic (or equivalent) ADP for non-H atoms: | | Bin# value range #atoms | Bin# value range #atoms | | 0: 5.229 - 16.918: 693 | 5: 63.676 - 75.366: 120 | | 1: 16.918 - 28.608: 3694 | 6: 75.366 - 87.055: 73 | | 2: 28.608 - 40.297: 1313 | 7: 87.055 - 98.744: 43 | | 3: 40.297 - 51.987: 450 | 8: 98.744 - 110.434: 19 | | 4: 51.987 - 63.676: 221 | 9: 110.434 - 122.123: 17 | | =>continue=> | |-----------------------------------------------------------------------------| ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) ------------------------------------------------------------------------ R-factors, x-ray target values and norm of gradient of x-ray target stage r-work r-free xray_target_w xray_target_t 0 : 0.3243 0.3131 7.754289e+00 7.797944e+00 1_bss: 0.2582 0.2742 7.690252e+00 7.754360e+00 1_xyz: 0.2348 0.2713 7.623999e+00 7.734510e+00 1_adp: 0.2216 0.2676 7.578854e+00 7.714267e+00 2_bss: 0.2037 0.2379 7.486761e+00 7.615026e+00 2_xyz: 0.1944 0.2423 7.473436e+00 7.629683e+00 2_adp: 0.1882 0.2396 7.449879e+00 7.620893e+00 3_bss: 0.1875 0.2312 7.433926e+00 7.596287e+00 3_xyz: 0.1857 0.2341 7.435421e+00 7.607941e+00 3_adp: 0.1818 0.2331 7.418785e+00 7.599553e+00 3_bss: 0.1826 0.2324 7.421608e+00 7.597030e+00 ------------------------------------------------------------------------ stage k_sol b_sol b11 b22 b33 b12 b13 b23 0 : 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1_bss: 0.347 50.000 2.318 2.318 2.318 0.000 0.000 -0.000 1_xyz: 0.347 50.000 2.318 2.318 2.318 0.000 0.000 -0.000 1_adp: 0.347 50.000 2.318 2.318 2.318 0.000 0.000 -0.000 2_bss: 0.337 50.000 2.425 2.425 2.425 0.000 0.000 -0.000 2_xyz: 0.337 50.000 2.425 2.425 2.425 0.000 0.000 -0.000 2_adp: 0.337 50.000 2.425 2.425 2.425 0.000 0.000 -0.000 3_bss: 0.335 50.000 3.181 3.181 3.181 0.000 0.000 -0.000 3_xyz: 0.335 50.000 3.181 3.181 3.181 0.000 0.000 -0.000 3_adp: 0.335 50.000 3.181 3.181 3.181 0.000 0.000 -0.000 3_bss: 0.337 65.653 0.000 0.000 0.000 0.000 0.000 -0.000 ------------------------------------------------------------------------ stage <pher> fom alpha beta 0 : 31.982 0.7396 1.7443 1387840.945 1_bss: 29.194 0.7699 1.9599 974799.679 1_xyz: 28.118 0.7819 1.9866 928279.367 1_adp: 27.348 0.7902 1.9633 892955.282 2_bss: 24.199 0.8225 1.9720 689127.593 2_xyz: 24.569 0.8186 1.9572 710017.017 2_adp: 23.913 0.8260 1.9393 697946.465 3_bss: 23.043 0.8347 1.9776 647848.901 3_xyz: 23.264 0.8326 1.9689 664228.536 3_adp: 22.951 0.8359 1.9502 655975.202 3_bss: 23.013 0.8352 1.9517 659994.149 ------------------------------------------------------------------------ stage angl bond chir dihe plan repu geom_target 0 : 1.693 0.012 0.089 17.723 0.007 4.142 1.5608e-01 1_bss: 1.693 0.012 0.089 17.723 0.007 4.142 1.5608e-01 1_xyz: 1.635 0.010 0.087 18.407 0.008 4.141 1.4451e-01 1_adp: 1.635 0.010 0.087 18.407 0.008 4.141 1.4451e-01 2_bss: 1.635 0.010 0.087 18.407 0.008 4.135 1.6105e-01 2_xyz: 1.421 0.009 0.083 18.369 0.007 4.141 1.2821e-01 2_adp: 1.421 0.009 0.083 18.369 0.007 4.141 1.2821e-01 3_bss: 1.421 0.009 0.083 18.369 0.007 4.136 1.3974e-01 3_xyz: 1.283 0.007 0.075 17.946 0.007 4.138 1.0907e-01 3_adp: 1.283 0.007 0.075 17.946 0.007 4.138 1.0907e-01 3_bss: 1.283 0.007 0.075 17.946 0.007 4.138 1.0822e-01 ------------------------------------------------------------------------ Maximal deviations: stage angl bond chir dihe plan repu |grad| 0 : 25.044 0.095 0.406113.659 0.154 1.486 1.5120e-01 1_bss: 25.044 0.095 0.406113.659 0.154 1.486 1.5120e-01 1_xyz: 25.658 0.089 0.312115.970 0.157 1.921 6.5351e-02 1_adp: 25.658 0.089 0.312115.970 0.157 1.921 6.5351e-02 2_bss: 25.658 0.089 0.312115.970 0.157 1.816 6.3368e-02 2_xyz: 23.516 0.082 0.391119.400 0.155 1.926 4.8056e-02 2_adp: 23.516 0.082 0.391119.400 0.155 1.926 4.8056e-02 3_bss: 23.516 0.082 0.391119.400 0.155 1.802 4.8972e-02 3_xyz: 23.841 0.048 0.338113.663 0.152 1.976 3.4188e-02 3_adp: 23.841 0.048 0.338113.663 0.152 1.976 3.4188e-02 3_bss: 23.841 0.048 0.338113.663 0.152 1.976 3.4255e-02 ------------------------------------------------------------------------ |-----overall-----|---macromolecule----|------solvent-------| stage b_max b_min b_ave b_max b_min b_ave b_max b_min b_ave 0 : 118.66 7.67 27.52 117.10 0.00 26.33 26.33 26.33 26.33 1_bss: 118.66 7.67 27.52 117.10 0.00 26.33 26.33 26.33 26.33 1_xyz: 118.66 7.67 27.52 119.19 2.33 25.79 59.44 3.23 29.93 1_adp: 117.10 0.00 26.33 119.19 2.33 25.79 49.81 3.23 28.22 2_bss: 117.10 0.00 26.33 119.19 2.33 25.79 49.81 3.23 28.22 2_xyz: 117.10 0.00 26.33 118.91 2.01 25.32 55.54 0.00 31.76 2_adp: 119.19 2.33 25.98 122.12 5.23 28.54 53.19 6.73 34.57 ------------------------------------------------------------------------ stage Deviation of refined model from start model max min mean 0 : 0.000 0.000 0.000 1_bss: 0.000 0.000 0.000 1_xyz: 2.308 0.002 0.111 1_adp: 2.308 0.002 0.111 2_bss: 2.308 0.002 0.111 2_xyz: 2.461 0.002 0.117 2_adp: 2.461 0.002 0.117 3_bss: 2.461 0.002 0.117 3_xyz: 2.748 0.003 0.122 3_adp: 2.748 0.003 0.122 3_bss: 2.748 0.003 0.122 ------------------------------------------------------------------------ stage number of ordered solvent 0 : 0 1_bss: 0 1_xyz: 0 1_adp: 0 2_bss: 291 2_xyz: 291 2_adp: 291 3_bss: 398 3_xyz: 398 3_adp: 398 3_bss: 388 ------------------------------------------------------------------------ ===================== NCS restraints at end of refinement ===================== NCS restraint group 1: NCS operator 1: Reference selection: "chain A and (resseq 9:118 or resseq 128:207 or resseq 215:366 )" Other selection: "chain C and (resseq 9:118 or resseq 128:207 or resseq 215:366 )" Number of atom pairs: 2603 Rotation={{-0.999497, -0.0191321, 0.0252909}, {0.0247831, 0.0263321, 0.999346}, {-0.0197855, 0.99947, -0.0258447}} Translation={{38.4881}, {-44.0747}, {42.34}} Histogram of differences: 0.002570 - 0.054938: 2350 0.054938 - 0.107305: 233 0.107305 - 0.159673: 16 0.159673 - 0.212040: 2 0.212040 - 0.264408: 1 0.264408 - 0.316775: 1 RMS difference with respect to the reference: 0.037521 Writing refined structure to PDB file: AutoBuild_run_3_/TEMP0/Build_composite_refined_side_3.pdb n_use = 6643 n_use_u_iso = 6643 n_use_u_aniso = 0 n_grad_site = 0 n_grad_u_iso = 6643 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 n_anisotropic_flag = 0 total number of scatterers = 6643 Writing map coefficients to MTZ file: /usr/users/dale/structure/fmo-ct/tronrud_2007/AutoBuild_run_3_/TEMP0/Build_composite_refined_side_3_001_map_coeffs.mtz Writing refined fmodel to MTZ file: /usr/users/dale/structure/fmo-ct/tronrud_2007/AutoBuild_run_3_/TEMP0/Build_composite_refined_side_3_001_f_model.mtz # Date 2007/12/14 11:38:03 Final R(work) = 0.1826, R(free) = 0.2324

1 0

Re: [phenixbb] Problem with AutoBuild and Alternative Conformations
by Thomas C. Terwilliger 16 Dec '07

16 Dec '07

Hi again Dale, I spoke too quickly...it is not so easy to change the code as I hoped. However here is a work-around that may be preferable anyhow: 1. Remove your ligand from the PDB file to be rebuilt and put it in "lig.pdb" 2. add to your commands for autobuild: input_lig_file_list=lig.pdb This will put all the contents of lig.pdb at the end of all PDB files just before refinement. All the best, Tom T Hi Dale, Your hypothesis: "I suspect that the coder assumed that all alternative conformations mutually exclusive and involve the same subset of the residue." is quite correct. (I am the coder in question). I think that I may be able to fix this particular problem and take care of the cases you have in this structure by simply allowing all conformations of ligands in the input file to be kept during rebuilding. With luck, this will work and will be in the final 1.3b version due out very shortly. The autobuild wizard still will not know how to build multiple conformations into a structure. For the time being it will have to stick with building one conformation. Thanks very much for the suggestion! -Tom T > Hi, > > I desire to resolve a crystal, who's structure factors I've downloaded > from the PDB, using my new high resolution model of this protein from a different species. I have decided to use the AutoMR wizard from Phenix for the chore. The MR seems to work just find, but I've run into a problem with the follow-up AutoBuild. > > This protein has a peptide chain that I would like rebuilt with the > proper amino acid sequence and seven Bchl-a molecules that I would like to be carried through to the end. Since the probe is from a high res refinement it contains quite a few groups with alternative conformations. This is not a problem in the protein part as it is being rebuilt and comes back with a single conformation for each residue. The Bchl-a molecules, however, are being horribly mutilated. > > In the Bchl-a groups, the "A" conformation is being promoted to > be the "main" (and only) conformation and the "B", "C", "D", "E", and, yes, the "F" conformations are lost. A Bchl-a molecule is much larger than an amino acid so it is quite possible, and reasonable, for one part to have a "A" and "B" pair of conformations, another part to have a "C" and "D" pair, and somewhere else for there to be a "E" and "F" pair. When conformation "C", "D", "E", and "F" are discarded whole sections of the Bchl-a molecule disappear > completely. This is bad. > > I suspect that the coder assumed that all alternative conformations > mutually exclusive and involve the same subset of the residue. I would prefer a more careful analysis to uncover the fact that "A" and "B" go together, and "C" and "D" go together. If there is a need to reduce the complexity of the model, (and I would prefer that all the alternatives make it through to the end) could the program keep "A", "C", and "E", or whatever makes sense for any particular residue? Better yet, instead of always keeping the first alternative of a set, could it keep the one with the highest occupancy? > > I'm using phenix-1.3b-rc6 on a Fedora 6 PC. > > Thanks, > Dale Tronrud >

2 1

Re: [phenixbb] Problem with AutoBuild and Alternative Conformations
by Thomas C. Terwilliger 16 Dec '07

16 Dec '07

Hi Dale, Your hypothesis: "I suspect that the coder assumed that all alternative conformations mutually exclusive and involve the same subset of the residue." is quite correct. (I am the coder in question). I think that I may be able to fix this particular problem and take care of the cases you have in this structure by simply allowing all conformations of ligands in the input file to be kept during rebuilding. With luck, this will work and will be in the final 1.3b version due out very shortly. The autobuild wizard still will not know how to build multiple conformations into a structure. For the time being it will have to stick with building one conformation. Thanks very much for the suggestion! -Tom T > Hi, > > I desire to resolve a crystal, who's structure factors I've downloaded > from the PDB, using my new high resolution model of this protein from a > different species. I have decided to use the AutoMR wizard from Phenix > for the chore. The MR seems to work just find, but I've run into a > problem with the follow-up AutoBuild. > > This protein has a peptide chain that I would like rebuilt with the > proper amino acid sequence and seven Bchl-a molecules that I would like > to be carried through to the end. Since the probe is from a high res > refinement it contains quite a few groups with alternative conformations. > This is not a problem in the protein part as it is being rebuilt and > comes back with a single conformation for each residue. The Bchl-a > molecules, however, are being horribly mutilated. > > In the Bchl-a groups, the "A" conformation is being promoted to > be the "main" (and only) conformation and the "B", "C", "D", "E", > and, yes, the "F" conformations are lost. A Bchl-a molecule is much > larger than an amino acid so it is quite possible, and reasonable, > for one part to have a "A" and "B" pair of conformations, another > part to have a "C" and "D" pair, and somewhere else for there to > be a "E" and "F" pair. When conformation "C", "D", "E", and "F" > are discarded whole sections of the Bchl-a molecule disappear > completely. This is bad. > > I suspect that the coder assumed that all alternative conformations > mutually exclusive and involve the same subset of the residue. I > would prefer a more careful analysis to uncover the fact that "A" and > "B" go together, and "C" and "D" go together. If there is a need to > reduce the complexity of the model, (and I would prefer that all the > alternatives make it through to the end) could the program keep "A", > "C", and "E", or whatever makes sense for any particular residue? > Better yet, instead of always keeping the first alternative of a set, > could it keep the one with the highest occupancy? > > I'm using phenix-1.3b-rc6 on a Fedora 6 PC. > > Thanks, > Dale Tronrud >

1 0

[Fwd: Auto-discard notification]
by Paul Adams 16 Dec '07

16 Dec '07

-- Paul Adams Deputy Division Director, Physical Biosciences Division, LBL Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road, BLDG 64R0121 Berkeley, CA 94720, USA. --

1 0

relative pathnames in .def or .eff files for phenix.refine?
by Schubert, Carsten [PRDUS] 14 Dec '07

14 Dec '07

Hi, would it be possible to add the option of using relative pathnames instead of full pathnames when .def and .eff files are written by phenix.refine? Would make transfer of files/projects easier. Cheers Carsten

1 0

Re: [phenixbb] Very very small Phaser Bug
by Tom Terwilliger 11 Dec '07

11 Dec '07

Hi James, Yes this sounds like a bug to me. I think it is a mis-communication between the automr wizard and phaser. We'll check it out. Thank you! -Tom T At 10:05 PM 12/10/2007, you wrote: >This is a fairly trivial bug, but I thought I'd report it anyway (I'm >not sure whether the problem is with the phenix.automr (rc6 build) or >with all phaser implementations (the one included is: 2.1.1 so I've >emailed both lists): > >when running phaser in data that was scaled in P 31 2 1, I used >phenix.automr to automate MR searches in all spacegroups that are >indistinguishable by systematic absences with: > >phenix.automr template.pdb final_P3121.sca RMS=1 mass=17000 >rebuild_after_mr=False copies=1 use_all_plausible_sg=True > >The program correctly finds the solution in P3221 with a log >likelihood gain of 1000 vs 20 for P3121, everything is fine in the >outputted PDB CRYST1 line and MTZ; however the log file annoyingly >mentions the spacegroup for the last time with "Final space group:P 31 >2 1" even though elsewhere in the log file it correctly lists >"SpaceGroup of Solution: P 32 2 1". I've excerpted the log file >below. If this is the intended behaviour and not a bug, then I >apologize but find it quite counterintuitive. > >Just a small bug, haven't seen if this behaviour occurs in other >systematic absence-equivalent space groups. > >Best, > >jf > >**BEGIN LOG > > SpaceGroup of Solution: P 32 2 1 > > SINGLE solution > > Solution written to PDB file: /Users/jfraser/data/AutoMR_run_7_/MR.1.pd >b > Solution written to MTZ file: /Users/jfraser/data/AutoMR_run_7_/MR.1.mt >z > Solution log-likelihood gain: 1056.73 > Solution annotation (history): RFZ=11.9 TFZ=27.5 PAK=0 LLG=850 LLG=1057 > > > >AUTOMR RUN: 7 > >Files in directory : AutoMR_run_7_ > > > >CRITERIA FOR PHASER MR RUN: >selection_criteria_rot : Percent_of_best >selection_criteria_rot_value : 75 >use_all_plausible_sg : Yes >overlap_allowed : > >List of space groups tested: >['P 3 2 1', 'P 31 2 1', 'P 32 2 1'] > >Final space group:P 31 2 1 > >CURRENT ENSEMBLES: > >ENSEMBLE ID: ensemble_1 >FILE: template.pdb RMS = 1.0 >ENSEMBLES USED IN SEARCH: ensemble_1 > >**************** SOLUTION MR ******* > > Log likelihood gain for solution MR: 1056.7344 > Output PDB files for solution MR: MR.1.pdb > Output MTZ files for solution MR: MR.1.mtz > >**END LOG > > >-- >James Fraser >jamesfraser(a)berkeley.edu >Alber Lab >356 Stanley Hall, QB3 >UC Berkeley >Berkeley, CA 94720 >http://ucxray.berkeley.edu/~jfraser/ >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

1 0