Re: [phenixbb] Refinement going wild in latest versions

Whoops, Pavel beat me to it - I guess GMail is also a little buggy this morning. On Fri, Oct 4, 2013 at 7:40 AM, Nathaniel Echols wrote:

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 [email protected] 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 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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