[phenixbb] Iterative build omit map error

Heather L Condurso condurso at bc.edu
Wed Nov 27 07:33:35 PST 2013 

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
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