This is not at all expected; it sounds like there is something specific in your structure that the current code isn't handling properly, but it's impossible to guess based on your description alone.  Can you please send all input files plus the log file for a representative run to bugs@phenix-online.org so we can try to reproduce the problem?  (They will of course be kept confidential within our group.)

thanks,

Nat

On Fri, Oct 4, 2013 at 1:14 AM, Hugues Nury <hugues.nury@ibs.fr> wrote:

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!

Cheers,

Hugues

--
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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