[phenixbb] Iterative build omit map error

Wed Nov 27 09:03:30 PST 2013

Hi Heather,

It looks as though something happened in phenix.refine during that omit map calculation.  I am guessing that the individual runs have not finished and so it might be necessary to do it over, however you can check the log files for some of the runs to see if some finished and others didn't, in which case you will only need to repeat the ones that did not finish.  Also if it turns out that the refinement that failed was the very last re-refinement against original data you may not need to rerun it.

So first we need to figure out what happened.  The basic error message here is:

Refining model:  edit_model.pdb
approx_equal eps: 1e-06
approx_equal multiplier: 10000000000.0
0.0197876048373 approx_equal ERROR
0.0197856373852 approx_equal ERROR

Hopefully if you go to the subdirectory where the failed run is located (/Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/AutoBuild_run_32_/TEMP0/) the last file written there will be some kind of refinement log file and that may have a clue.  You may also find the parameters for that refinement run and then you can just rerun it and see if it fails.

If that doesn't work, send me the full log file for the failed run and the listing of that TEMP0 directory and any log files near the end of the listing and I'll try to figure it out.

All the best,
Tom T

On Nov 27, 2013, at 8:33 AM, Heather L Condurso wrote:

> SO just as my omit map run should have finished, it gave an error instead.  I'm running 1.8.4-1496 on a Mac with OSX 10.6.8 and 8GB of memory.  Here is the end of the log file:
> 
> Splitting work into 32 jobs and running with 1 processors using sh 
> background=False in /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0
> Final job will be run with sh  with background=True
> Starting job 1...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_1.log
> Starting job 2...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_2.log
> Starting job 3...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_3.log
> Starting job 4...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_4.log
> Starting job 5...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_5.log
> Starting job 6...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_6.log
> Starting job 7...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_7.log
> Starting job 8...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_8.log
> Starting job 9...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_9.log
> Starting job 10...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_10.log
> Starting job 11...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_11.log
> Starting job 12...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_12.log
> Starting job 13...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_13.log
> Starting job 14...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_14.log
> Starting job 15...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_15.log
> Starting job 16...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_16.log
> Starting job 17...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_17.log
> Starting job 18...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_18.log
> Starting job 19...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_19.log
> Starting job 20...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_20.log
> Starting job 21...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_21.log
> Starting job 22...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_22.log
> Starting job 23...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_23.log
> Starting job 24...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_24.log
> Starting job 25...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_25.log
> Starting job 26...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_26.log
> Starting job 27...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_27.log
> Starting job 28...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_28.log
> Starting job 29...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_29.log
> Starting job 30...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_30.log
> Starting job 31...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_31.log
> Starting job 32...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_32.log
> 
> 
> ********************************************************************************
> Sorry, a subprocess has failed...
> 
> END OF LOG FILE /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_32.log :
> 
> /TEMP0/Build_composite_refined_3.pdb  R/Rfree=0.32/0.39
> 
> Maps from refinement will be filled (2FOFCWT PH2FOFCWT)
> Set refine map coeffs file  pdb_file_refine_map_coeffs  to  refine_map_coeffs_3.mtz
> Rebuilding side chains from  Build_composite_refined_3.pdb
> Refining model:  edit_model.pdb
> approx_equal eps: 1e-06
> approx_equal multiplier: 10000000000.0
> 0.0197876048373 approx_equal ERROR
> 0.0197856373852 approx_equal ERROR
> 
> Refinement strategy:  ['individual_sites', 'individual_adp', 'occupancies']
> Moving refinement file AutoBuild_run_32_/TEMP0/Build_composite_refined_side_3_001_f_model.mtz to AutoBuild_run_32_/TEMP0/refine_fmodel.mtz
> Moving refinement file AutoBuild_run_32_/TEMP0/Build_composite_refined_side_3_001.mtz to AutoBuild_run_32_/TEMP0/refine_map_coeffs_3.mtz
> Model: AutoBuild_run_32_/TEMP0/Build_composite_refined_side_3.pdb  R/Rfree=0.33/0.38
> 
> Maps from refinement will be filled (2FOFCWT PH2FOFCWT)
> Set refine map coeffs file  pdb_file_refine_map_coeffs  to  refine_map_coeffs_3.mtz
> 
> 
> 
> 
> 
> 
> ********************************************************************************
> Failed to carry out AutoBuild_parallel_omit:
> 
> 
> ********************************************************************************
> Sorry, a subprocess has failed...
> 
> END OF LOG FILE /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_32.log :
> 
> /TEMP0/Build_composite_refined_3.pdb  R/Rfree=0.32/0.39
> 
> Maps from refinement will be filled (2FOFCWT PH2FOFCWT)
> Set refine map coeffs file  pdb_file_refine_map_coeffs  to  refine_map_coeffs_3.mtz
> Rebuilding side chains from  Build_composite_refined_3.pdb
> Refining model:  edit_model.pdb
> approx_equal eps: 1e-06
> approx_equal multiplier: 10000000000.0
> 0.0197876048373 approx_equal ERROR
> 0.0197856373852 approx_equal ERROR
> 
> Refinement strategy:  ['individual_sites', 'individual_adp', 'occupancies']
> Moving refinement file AutoBuild_run_32_/TEMP0/Build_composite_refined_side_3_001_f_model.mtz to AutoBuild_run_32_/TEMP0/refine_fmodel.mtz
> Moving refinement file AutoBuild_run_32_/TEMP0/Build_composite_refined_side_3_001.mtz to AutoBuild_run_32_/TEMP0/refine_map_coeffs_3.mtz
> Model: AutoBuild_run_32_/TEMP0/Build_composite_refined_side_3.pdb  R/Rfree=0.33/0.38
> 
> Maps from refinement will be filled (2FOFCWT PH2FOFCWT)
> Set refine map coeffs file  pdb_file_refine_map_coeffs  to  refine_map_coeffs_3.mtz
> 
> 
> 
> ********************************************************************************
> 
> Can this be salvaged?  It took 5 days to run.  I found a section about this in the documentation, but I can't find the maps for each region overall_best_denmod_map_coeffs.mtz_OMIT_REGION_1 etc.
> 
> I can only find working_best_denmod_map_coeffs.mtz_OMIT_REGION_1 etc. 
> 
> Will these maps work?  Can you tell what the error means so that I can avoid this problem in the future?
> 
> Thanks,
> Heather
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb