[phenixbb] Refinement going wild in latest versions

Hugues Nury hugues.nury at ibs.fr
Fri Oct 4 01:14:18 PDT 2013

Hello everyone,

I am experiencing differences with phenix.refine versions 1.8.3 or 1.8.4 compared to 1.8.2. Performing comparable runs, Rs are rising several percents with the latest versions, while marginally decreasing using version 1.8.2. I am a very recent convert to Phenix, so maybe I'm missing something obvious, but here are the details:

Refinement strategy is xyz+real space+tls+individual Bs at 3.5 A, using NCS and secondary structure restraints, and weight optimization.
Starting R/Rfree are around 24.5/28.5

Part of the problem seems to come from secondary structure restraints, with (many) messages in the log file of the refinement going wild looking like
WARNING: could not process nonbonded pair
    Original error:
      cctbx Internal Error: /net/clover/scratch1/phenix/phenix-1.8.4-1496/cctbx_project/cctbx/crystal/pair_tables.h(663): CCTBX_ASSERT(j_sym >= 0) failure.
    pdb=" N   GLN B 130 " segid="B   "  pdb=" O   VAL B 115 " segid="B   "
In log files of refinement with version 1.8.2, there are no such messages, and in either case the definition of beta strands were done automatically by Phenix

But even secondary structure restraints are switched off, it starts ok but goes wrong at the beginning of cycle 2, during local real space refinement
start: r_work=0.2271 r_free=0.2785
final: r_work=0.2418 r_free=0.2937
And then continue to worsen.

Any help appreciated!


Hugues Nury

Institut de Biologie Structurale
41 rue Jules Horowitz, F-38027 Grenoble Cedex 1, France
+33 6 52 45 17 79

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