<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">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></body></html>