[phenixbb] RuntimeError: Not enough memory for cubicles:

[Gino Cingolani]

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:  cingolag at 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)