[phenixbb] Refinement going wild in latest versions
pafonine at lbl.gov
Fri Oct 4 07:23:45 PDT 2013
could you please send me data and model files so I can have a closer
look at what's happening?
On 10/4/13 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:
> 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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