[phenixbb] Refinement going wild in latest versions

Pavel Afonine pafonine at lbl.gov
Fri Oct 4 07:23:45 PDT 2013


Hi Hugues,

could you please send me data and model files so I can have a closer 
look at what's happening?

Thanks,
Pavel


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: 
> /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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