On Thu, Jun 14, 2012 at 7:10 AM, CPMAS Chen
I thought I am the only one have this problem. I have encountered the same problem with the newest version of phenix. RuntimeError: Estimated memory allocation for cubicles exceeds max_number_of_bytes: This may be due to unreasonable parameters: cubicle_edge=5 space_span=(2696.14,2555.98,2650.54) n_cubicles=(540,512,531) max_number_of_bytes=1073741824
Several other users have reported the same problem. Pavel thinks the underlying cause (which should be fixable) is that the minimizer is exploding the structure during real-space refinement, and throwing atoms several unit cells away. The part that's crashing is trying to divide the atoms into boxes for calculating the nonbonded interactions more efficiently. If the structure covers too much physical space, it ends up with too many boxes. (Regarding Kay's posting, I think I was confused about the expected size of "unsigned long" on a 64-bit platform - which does not in fact change. Presumably I was confusing this with "size_t", which should change.) Those of you who encounter this problem, it seems to be associated with these two parameters: refinement.ncs.torsion.fix_outliers = Auto refinement.ncs.torison.check_rotamer_consistency = Auto If you set these to False, it should run okay. -Nat