[mcdbx-horowsah:120813/1to8p4122fromqinping/phenix_refine] horowsah% phenix.rosetta_refine zn-ref2_noalt2.pdb 1to8p4122znfromqingping_refine_data.mtz protocol=hires
Output directory:
/Users/horowsah/Documents/Bardwell Lab Work/spy/xtalstrucs/120813/1to8p4122fromqinping/phenix_refine/rosetta_9
=========================== Importing data and flags ==========================
----------Scaling input intensities via French-Wilson Method----------
Trying 60 bins...
Number of bins = 60
** Calculating bin mean intensity values for each intensity **
** Total # rejected intensities: 0 **
----------Setting up input files for Rosetta----------
Warning: temporarily removing residue X 227 IMD
Warning: temporarily removing residue X 228 IMD
Warning: temporarily removing residue X 229 IMD
/rosetta/rosetta_2013wk49_bundle/main/source
----------Loading model and data----------
=========================== ROSETTA X-ray refinement ==========================
|-starting model--------------------------------------------------------------|
| target_work(ml) = 5.09382 r_work = 0.2295 r_free = 0.2807 |
|-----------------------------------------------------------------------------|
Validation statistics (starting model):
Ramachandran outliers = 0.00 %
favored = 98.22 %
Rotamer outliers = 2.10 %
C-beta deviations = 0
Clashscore = 1.78
Molprobity score = 1.18
Generating 5 models on 1 processors...
DEBUG dumping error message
ERROR: Rosetta exited with status 1
stderr output:
ERROR: ERROR: Unused "free" argument specified: Lab
Traceback (most recent call last):
File "//Applications/PHENIX-1.8.4-1496/Contents/phenix-1.8.4-1496/build/mac-intel-osx-x86_64/../../phenix/phenix/command_line/rosetta_refine.py", line 330, in <module>
run(sys.argv[1:], create_dir=True)
File "//Applications/PHENIX-1.8.4-1496/Contents/phenix-1.8.4-1496/build/mac-intel-osx-x86_64/../../phenix/phenix/command_line/rosetta_refine.py", line 327, in run
create_dir=create_dir)
File "//Applications/PHENIX-1.8.4-1496/Contents/phenix-1.8.4-1496/build/mac-intel-osx-x86_64/../../phenix/phenix/command_line/rosetta_refine.py", line 127, in __init__
self.run_rosetta_scripts()
File "//Applications/PHENIX-1.8.4-1496/Contents/phenix-1.8.4-1496/build/mac-intel-osx-x86_64/../../phenix/phenix/command_line/rosetta_refine.py", line 181, in run_rosetta_scripts
debug=self.params.runtime.debug)
File "//Applications/PHENIX-1.8.4-1496/Contents/phenix-1.8.4-1496/phenix/phenix/rosetta/refine.py", line 307, in __init__
self.run_jobs()
File "//Applications/PHENIX-1.8.4-1496/Contents/phenix-1.8.4-1496/phenix/phenix/rosetta/refine.py", line 372, in run_jobs
check_result(result)
File "//Applications/PHENIX-1.8.4-1496/Contents/phenix-1.8.4-1496/phenix/phenix/rosetta/refine.py", line 363, in check_result
raise RuntimeError("Aborted due to error in job %d." % result.job_id)
RuntimeError: Aborted due to error in job 1.