Dear Phenix community, I am still having problems to refine a large unit cell (~13,500 residues/asymmetric unit). The refinement goes well but at the very last cycle, immediately prior to outputting the refined model, phenix stops with the following error message: $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ ========== residual map mFobs-DFmodel: highest peaks and deepst holes ========= ----------peaks---------- Traceback (most recent call last): File "/usr/local/phenix-1.4-3/phenix/phenix/command_line/refine.py", line 9, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/command_line.py", line 89, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/driver.py", line 1098, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/strategies.py", line 710, in refinement_machine fmodels=fmodels, model=model, log=log) File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/strategies.py", line 738, in highest_peaks_and_deepest_holes_in_residual_map log = log) File "/usr/local/phenix-1.4-3/mmtbx/find_peaks.py", line 212, in show_highest_peaks_and_deepest_holes log = log) File "/usr/local/phenix-1.4-3/mmtbx/find_peaks.py", line 117, in __init__ map = fft_map_data).all(max_clusters = max_number_of_peaks) File "/usr/local/phenix-1.4-3/cctbx/maptbx/__init__.py", line 196, in peak_search max_clusters=parameters.max_clusters()) File "/usr/local/phenix-1.4-3/cctbx/maptbx/__init__.py", line 303, in __init__ general_positions_only=self._general_positions_only) File "/usr/local/phenix-1.4-3/cctbx/crystal/__init__.py", line 479, 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 Traceback (most recent call last): File "/usr/local/phenix-1.4-3/phenix/phenix/command_line/refine.py", line 9, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/command_line.py", line 89, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/driver.py", line 1098, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/strategies.py", line 710, in refinement_machine fmodels=fmodels, model=model, log=log) File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/strategies.py", line 738, in highest_peaks_and_deepest_holes_in_residual_map log = log) File "/usr/local/phenix-1.4-3/mmtbx/find_peaks.py", line 212, in show_highest_peaks_and_deepest_holes log = log) File "/usr/local/phenix-1.4-3/mmtbx/find_peaks.py", line 117, in __init__ map = fft_map_data).all(max_clusters = max_number_of_peaks) File "/usr/local/phenix-1.4-3/cctbx/maptbx/__init__.py", line 196, in peak_search max_clusters=parameters.max_clusters()) File "/usr/local/phenix-1.4-3/cctbx/maptbx/__init__.py", line 303, in __init__ general_positions_only=self._general_positions_only) File "/usr/local/phenix-1.4-3/cctbx/crystal/__init__.py", line 479, 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 $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ Following the various suggestions received after my previous email (~2 weeks ago), I have tried the following: --> Using phenix 1.4-3, which gave exactly the same problem as phenix 1.3 --> Using MACRO_CYCLE=0 before refinement to see if phenix can write out such a large asymmetric unit, and that works. Phenix does write out the model at a starting Rfree ~35.5%. --> Removing ordered_solvent=true Right now the refinement scheme I am using is as follows: phenix.refine XX.mtz model.pdb simulated_annealing=true elbow.XX_pdb.cif strategy=individual_sites+group_adp+tls tls_group_selections.params main.number_of_macro_cycles=5 main.ncs=true refinement.ncs.excessive_distance_limit=None refinement.pdb_interpretation.clash_guard.nonbonded_distance_threshold=No Once again, the refinement proceeds smoothly for 2-3 days; the Rfree drops nearly 3 points, and right at the very end, the programs stops without outputting a refined model. Does anybody have any idea what's going on? Thanks, Gino *********************************************************** 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: [email protected] *********************************************************** "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)