[phenixbb] Refinement going wild in latest versions
nechols at lbl.gov
Fri Oct 4 07:40:34 PDT 2013
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 at phenix-online.org so we can try to reproduce the problem? (They will
of course be kept confidential within our group.)
On Fri, Oct 4, 2013 at 1:14 AM, Hugues Nury <hugues.nury at 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
> WARNING: could not process nonbonded pair
> Original error:
> cctbx Internal Error:
> 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
> phenixbb mailing list
> phenixbb at phenix-online.org
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