Hi,
I'm refining a huge structure with ~13,000 residues in the asymmetric unit.
I started a massive job with the following inputs:
phenix.refine data.mtz model.pdb
ordered_solvent=true
strategy=individual_sites+group_adp+tls
tls_group_selections.params
main.ncs=true
main.number_of_macro_cycles=10
After >24 h the Rfree had dropped from 45% to 33%, but at the very end,
just before outputting the refined pdb model, Phenix died with the following
error message:
############################################################
Hello all========== residual map mFobs-DFmodel: highest peaks and deepst
holes =========
----------peaks----------
Traceback (most recent call last):
File "/usr/local/phenix-1.3-final/phenix/phenix/command_line/refine.py",
line 5, in <module>
command_line.run(command_name="phenix.refine", args=sys.argv[1:])
File
"/usr/local/phenix-1.3-final/phenix/phenix/refinement/command_line.py", line
89, in run
call_back_after_monitor_collect=call_back_after_monitor_collect)
File "/usr/local/phenix-1.3-final/phenix/phenix/refinement/driver.py",
line 1081, in run
call_back_after_monitor_collect = call_back_after_monitor_collect)
File "/usr/local/phenix-1.3-final/phenix/phenix/refinement/strategies.py",
line 724, in refinement_machine
fmodels=fmodels, model=model, log=log)
File "/usr/local/phenix-1.3-final/phenix/phenix/refinement/strategies.py",
line 752, in highest_peaks_and_deepest_holes_in_residual_map
log = log)
File "/usr/local/phenix-1.3-final/mmtbx/mmtbx/find_peaks.py", line 210, in
show_highest_peaks_and_deepest_holes
log = log)
File "/usr/local/phenix-1.3-final/mmtbx/mmtbx/find_peaks.py", line 117, in
__init__
map = fft_map_data).all(max_clusters = max_number_of_peaks)
File "/usr/local/phenix-1.3-final/cctbx/cctbx/maptbx/__init__.py", line
196, in peak_search
max_clusters=parameters.max_clusters())
File "/usr/local/phenix-1.3-final/cctbx/cctbx/maptbx/__init__.py", line
303, in __init__
general_positions_only=self._general_positions_only)
File "/usr/local/phenix-1.3-final/cctbx/cctbx/crystal/__init__.py", line
477, in site_cluster_analysis
cubicle_epsilon=cubicle_epsilon)
RuntimeError: Not enough memory for cubicles:
This may be due to unreasonable parameters:
cubicle_edge=0.7
space_span=(293.298,92.903,214.527)
n_cubicles=(419,133,307)
max_number_of_bytes=1724676096
######################################################
Any suggestion on what to do?
As invididual refinement modules (e.g. regular rigid body refinemnet, SA,
energy minimization, TLS, etc)
run OK, is the problem coming from the "ordered_solvent=true" command?
Thanks in advance!
Gino Cingolani, Ph.D.
***********************************************************
Gino Cingolani, Ph.D.
Assistant Professor
Dept. of Biochemistry and Molecular Biology
SUNY Upstate Medical University
750 E. Adams Street, Syracuse, NY, 13210
Tel. (315) 464 8744
Fax. (315) 464 8750
Email: cingolag(a)upstate.edu
***********************************************************
"Nati non foste per viver come bruti, ma per seguir virtute e conoscenza"
("You were not born to live like brutes, but to follow virtue and
knowledge")
Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120)
