[phenixbb] phenix.real_space_refine crashes for very large pdb files

#AHMED TOFAYEL# TOFAYEL001 at e.ntu.edu.sg
Thu Dec 1 21:24:01 PST 2016

Hi Pavel,

Thanks so much for your reply ! Disabling the b-factor refinement solved my problem.

Best regards,


From: Pavel Afonine <pafonine at lbl.gov>
Sent: Thursday, December 1, 2016 11:22 PM
To: #AHMED TOFAYEL#; PHENIX user mailing list
Subject: Re: [phenixbb] phenix.real_space_refine crashes for very large pdb files

Hi Tofayel,

My phenix.real_space_refine run crashes with the error mentioned below when I have used following command to run it on a complete ribosome (containing coordinates for small subunit and large subunit in a single pdb file):

phenix.real_space_refine model.pdb map.mrc resolution=4.5 reference_coordinate_restraints.enabled=true reference_coordinate_restraints.selection="chain A and resseq 2:700" reference_coordinate_restraints.sigma=0.05 secondary_structure.enabled=True res.eff > out.out

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