Hi Carlos, The first error looks to be a problem with rotamer correction when using torsion NCS restraints. I'm not sure what is causing this crash in your case, but if you would send me your input pdb, mtz, and .eff file direct to my email, I will have a look. The second crash looks like you've run out of memory on that particular machine. Perhaps one of the other developers would have an idea on that, but my guess is that the NCS crash is a problem either way. Thanks, Jeff On Wed, Jul 31, 2013 at 2:20 PM, Carlos Frazao wrote:

Hi,

After the last model building of my protein I am not succeeding to further refine its structure, because phenix.refine crashes.

However, if I set "main.number_of_macro_cycles=**0" the job reaches its expected end and outputs a .pdb file.

If I set "main.number_of_macro_cycles=**1" the job crashes a few lines after the log-file indication " ============================== Exporting results ==============================**" and produces an incomplete .pdb file with part of the header.

Alternatively, If I set "main.number_of_macro_cycles=**2" the job crashes during "MACRO_CYCLE 2 OF 2" after log-file indication " ----------Correcting NCS rotamer outliers---------- Set U 69 GLU to tp10 rotamer"

followed by the error message : "Traceback (most recent call last): File "/usr/local/phenix/phenix-dev-**1391/build/intel-linux-2.6-** x86_64/../../phenix/phenix/**command_line/refine.py", line 11, in <module> command_line.run(command_name=**"phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix/phenix-dev-**1391/phenix/phenix/refinement/**command_line.py", line 161, in run call_back_handler=call_back_**handler) File "/usr/local/phenix/phenix-dev-**1391/phenix/phenix/refinement/**driver.py", line 1659, in run ncs_manager = self.ncs_manager).result File "/usr/local/phenix/phenix-dev-**1391/phenix/phenix/refinement/**strategies.py", line 170, in __init__ ion_placement_manager = ion_placement_manager) File "/usr/local/phenix/phenix-dev-**1391/phenix/phenix/refinement/**macro_cycle.py", line 66, in __init__ self.call(self.ncsrot, "NCS rotamer correction") File "/usr/local/phenix/phenix-dev-**1391/phenix/phenix/refinement/**macro_cycle.py", line 101, in call func(prefix = prefix) File "/usr/local/phenix/phenix-dev-**1391/phenix/phenix/refinement/**macro_cycle.py", line 146, in ncsrot log = self.log) File "/usr/local/phenix/phenix-dev-**1391/phenix/phenix/refinement/**misc.py", line 89, in ncs_rotamer_update log=log) File "/usr/local/phenix/phenix-dev-**1391/cctbx_project/mmtbx/** torsion_restraints/torsion_**ncs.py", line 1111, in fix_rotamer_outliers key=key) File "/usr/local/phenix/phenix-dev-**1391/cctbx_project/mmtbx/** torsion_restraints/rotamer_**search.py", line 178, in search assert rotamer == cur_rotamer AssertionError"

I have been using built phenix-dev-1391 (I also checked phenix version 1.8.2-1309 or built dev-1436, they crashed as well) x86_64-fc3, in a machine running Ubuntu 10.04.4 LTS with Python 2.6.5.

I tried another machine, running Ubuntu 12.04 LTS with Python 2.7.3, and using built phenix-dev-1391 x86_64-fc3 I got at the end of the log-file: " ----------Correcting NCS rotamer outliers----------

Traceback (most recent call last): File "/usr/local/phenix/phenix-dev-**1391/build/intel-linux-2.6/../** ../phenix/phenix/command_line/**refine.py", line 11, in <module> command_line.run(command_name=**"phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix/phenix-dev-**1391/phenix/phenix/refinement/**command_line.py", line 161, in run call_back_handler=call_back_**handler) File "/usr/local/phenix/phenix-dev-**1391/phenix/phenix/refinement/**driver.py", line 1659, in run ncs_manager = self.ncs_manager).result File "/usr/local/phenix/phenix-dev-**1391/phenix/phenix/refinement/**strategies.py", line 170, in __init__ ion_placement_manager = ion_placement_manager) File "/usr/local/phenix/phenix-dev-**1391/phenix/phenix/refinement/**macro_cycle.py", line 66, in __init__ self.call(self.ncsrot, "NCS rotamer correction") File "/usr/local/phenix/phenix-dev-**1391/phenix/phenix/refinement/**macro_cycle.py", line 101, in call func(prefix = prefix) File "/usr/local/phenix/phenix-dev-**1391/phenix/phenix/refinement/**macro_cycle.py", line 146, in ncsrot log = self.log) File "/usr/local/phenix/phenix-dev-**1391/phenix/phenix/refinement/**misc.py", line 89, in ncs_rotamer_update log=log) File "/usr/local/phenix/phenix-dev-**1391/cctbx_project/mmtbx/** torsion_restraints/torsion_**ncs.py", line 1044, in fix_rotamer_outliers self.rotamer_search_manager.**prepare_map(fmodel=fmodel) File "/usr/local/phenix/phenix-dev-**1391/cctbx_project/mmtbx/** torsion_restraints/rotamer_**search.py", line 57, in prepare_map torsion_utils.prepare_map(**fmodel=fmodel) File "/usr/local/phenix/phenix-dev-**1391/cctbx_project/mmtbx/**torsion_restraints/utils.py", line 771, in prepare_map not exclude_free_r_reflections)) File "/usr/local/phenix/phenix-dev-**1391/cctbx_project/mmtbx/map_**tools.py", line 242, in fft_map symmetry_flags = symmetry_flags) File "/usr/local/phenix/phenix-dev-**1391/cctbx_project/cctbx/**miller/__init__.py", line 3420, in fft_map f_000=f_000) File "/usr/local/phenix/phenix-dev-**1391/cctbx_project/cctbx/**miller/__init__.py", line 4236, in __init__ conjugate_flag=True) MemoryError"-

I did not succeed to find out what may I have done wrong with the model and/or params files Any help is highly appreciated,

Carlos

-- **************************************** Dr. Carlos Frazao Structural Biology Laboratory - Macromolecular Crystallography Unit ITQB-UNL, Av Republica, Apartado 127 2781-901 Oeiras, P

Phone: (351)-214469666 FAX: (351)-214433644 e-mail: [email protected] www.itqb.unl.pt

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