[phenixbb] Refinement going wild in latest versions
nechols at lbl.gov
Fri Oct 4 07:41:17 PDT 2013
Whoops, Pavel beat me to it - I guess GMail is also a little buggy this
On Fri, Oct 4, 2013 at 7:40 AM, Nathaniel Echols <nechols at lbl.gov> 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
> 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
>> 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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