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<div class="moz-cite-prefix">Hi Hugues,<br>
<br>
could you please send me data and model files so I can have a
closer look at what's happening?<br>
<br>
Thanks,<br>
Pavel<br>
<br>
<br>
On 10/4/13 1:14 AM, Hugues Nury wrote:<br>
</div>
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Hello everyone,
<div><br>
</div>
<div>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:</div>
<div><br>
</div>
<div>Refinement strategy is xyz+real space+tls+individual Bs at
3.5 A, using NCS and secondary structure restraints, and weight
optimization.</div>
<div>Starting R/Rfree are around 24.5/28.5</div>
<div><br>
</div>
<div>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</div>
<div>
<div><font face="Courier">WARNING: could not process nonbonded
pair</font></div>
<div><font face="Courier"> Original error:</font></div>
<div><font face="Courier"> 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.</font></div>
<div><font face="Courier"> pdb=" N GLN B 130 " segid="B "
pdb=" O VAL B 115 " segid="B "</font></div>
</div>
<div>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</div>
<div><br>
</div>
<div>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</div>
<div>
<div><font face="Courier">start: r_work=0.2271 r_free=0.2785</font></div>
<div><font face="Courier">final: r_work=0.2418 r_free=0.2937</font></div>
</div>
<div><font face="Courier">And then continue to worsen.</font></div>
<div><font face="Courier"><br>
</font></div>
<div>Any help appreciated!</div>
<div><br>
</div>
<div>Cheers,</div>
<div>Hugues</div>
<div><br>
</div>
<div><br>
</div>
<br>
<div>
<div>--<br>
Hugues Nury<br>
<br>
Institut de Biologie Structurale<br>
41 rue Jules Horowitz, F-38027 Grenoble Cedex 1, France<br>
+33 6 52 45 17 79</div>
</div>
<div><br>
</div>
<br>
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