<div dir="ltr"><div><div><div>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:<br><br>Splitting work into 32 jobs and running with 1 processors using sh <br>
background=False in /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0<br>Final job will be run with sh with background=True<br>Starting job 1...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_1.log<br>
Starting job 2...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_2.log<br>Starting job 3...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_3.log<br>
Starting job 4...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_4.log<br>Starting job 5...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_5.log<br>
Starting job 6...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_6.log<br>Starting job 7...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_7.log<br>
Starting job 8...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_8.log<br>Starting job 9...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_9.log<br>
Starting job 10...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_10.log<br>Starting job 11...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_11.log<br>
Starting job 12...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_12.log<br>Starting job 13...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_13.log<br>
Starting job 14...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_14.log<br>Starting job 15...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_15.log<br>
Starting job 16...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_16.log<br>Starting job 17...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_17.log<br>
Starting job 18...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_18.log<br>Starting job 19...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_19.log<br>
Starting job 20...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_20.log<br>Starting job 21...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_21.log<br>
Starting job 22...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_22.log<br>Starting job 23...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_23.log<br>
Starting job 24...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_24.log<br>Starting job 25...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_25.log<br>
Starting job 26...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_26.log<br>Starting job 27...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_27.log<br>
Starting job 28...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_28.log<br>Starting job 29...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_29.log<br>
Starting job 30...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_30.log<br>Starting job 31...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_31.log<br>
Starting job 32...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_32.log<br><br><br>********************************************************************************<br>Sorry, a subprocess has failed...<br>
<br>END OF LOG FILE /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_32.log :<br><br>/TEMP0/Build_composite_refined_3.pdb R/Rfree=0.32/0.39<br><br>Maps from refinement will be filled (2FOFCWT PH2FOFCWT)<br>
Set refine map coeffs file pdb_file_refine_map_coeffs to refine_map_coeffs_3.mtz<br>Rebuilding side chains from Build_composite_refined_3.pdb<br>Refining model: edit_model.pdb<br>approx_equal eps: 1e-06<br>approx_equal multiplier: 10000000000.0<br>
0.0197876048373 approx_equal ERROR<br>0.0197856373852 approx_equal ERROR<br><br>Refinement strategy: ['individual_sites', 'individual_adp', 'occupancies']<br>Moving refinement file AutoBuild_run_32_/TEMP0/Build_composite_refined_side_3_001_f_model.mtz to AutoBuild_run_32_/TEMP0/refine_fmodel.mtz<br>
Moving refinement file AutoBuild_run_32_/TEMP0/Build_composite_refined_side_3_001.mtz to AutoBuild_run_32_/TEMP0/refine_map_coeffs_3.mtz<br>Model: AutoBuild_run_32_/TEMP0/Build_composite_refined_side_3.pdb R/Rfree=0.33/0.38<br>
<br>Maps from refinement will be filled (2FOFCWT PH2FOFCWT)<br>Set refine map coeffs file pdb_file_refine_map_coeffs to refine_map_coeffs_3.mtz<br><br><br><br><br><br><br>********************************************************************************<br>
Failed to carry out AutoBuild_parallel_omit:<br><br><br>********************************************************************************<br>Sorry, a subprocess has failed...<br><br>END OF LOG FILE /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_32.log :<br>
<br>/TEMP0/Build_composite_refined_3.pdb R/Rfree=0.32/0.39<br><br>Maps from refinement will be filled (2FOFCWT PH2FOFCWT)<br>Set refine map coeffs file pdb_file_refine_map_coeffs to refine_map_coeffs_3.mtz<br>Rebuilding side chains from Build_composite_refined_3.pdb<br>
Refining model: edit_model.pdb<br>approx_equal eps: 1e-06<br>approx_equal multiplier: 10000000000.0<br>0.0197876048373 approx_equal ERROR<br>0.0197856373852 approx_equal ERROR<br><br>Refinement strategy: ['individual_sites', 'individual_adp', 'occupancies']<br>
Moving refinement file AutoBuild_run_32_/TEMP0/Build_composite_refined_side_3_001_f_model.mtz to AutoBuild_run_32_/TEMP0/refine_fmodel.mtz<br>Moving refinement file AutoBuild_run_32_/TEMP0/Build_composite_refined_side_3_001.mtz to AutoBuild_run_32_/TEMP0/refine_map_coeffs_3.mtz<br>
Model: AutoBuild_run_32_/TEMP0/Build_composite_refined_side_3.pdb R/Rfree=0.33/0.38<br><br>Maps from refinement will be filled (2FOFCWT PH2FOFCWT)<br>Set refine map coeffs file pdb_file_refine_map_coeffs to refine_map_coeffs_3.mtz<br>
<br><br><br>********************************************************************************<br><br></div>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.<br>
<br></div>I can only find working_best_denmod_map_coeffs.mtz_OMIT_REGION_1 etc. <br><br></div>Will these maps work? Can you tell what the error means so that I can avoid this problem in the future?<br><div><pre><br></pre>
<pre>Thanks,<br></pre><pre>Heather<br></pre></div></div>