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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Hi Nat,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>I have found that phenix.model_vs_data does not deal well with a perfect twin data set. The refined data is:<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> r_work=0.2013 r_free=0.2298 (in PDB file)<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> r_work=0.2815 r_free=0.3006 (from phenix.model_vs_data)<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>There is one merohedral twin operator: -h-k,k,-l (48%) and 6 very small (<1.0%) pseudo-merohedral twin operators. <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Ryan Spencer<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> phenixbb-bounces@phenix-online.org [mailto:phenixbb-bounces@phenix-online.org] <b>On Behalf Of </b>Nathaniel Echols<br><b>Sent:</b> Thursday, November 07, 2013 2:52 PM<br><b>To:</b> PHENIX user mailing list<br><b>Subject:</b> Re: [phenixbb] structure factor labels in phenix.refine<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>On Thu, Nov 7, 2013 at 12:57 PM, Pavel Afonine <<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>> wrote:<o:p></o:p></p><div><div><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in'><p class=MsoNormal>Depending which kind of differences you mean (magnitude). Ideally, R-factors should be identical. If it's like 0.1856 vs 0.1858, then it's fine, if larger then some of us here need to investigate what's going on.<o:p></o:p></p></blockquote><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Agreed, since the Table 1 program is using phenix.model_vs_data internally, which was designed to reproduce the R-factors from phenix.refine, any major discrepancy is cause for concern. We have seen a handful of cases where they deviate significantly, but it's been very difficult to isolate the cause, so data is always helpful. (Of course this doesn't rule out the possibility that there's simply a bug in my code somewhere, but I don't think the program is doing anything fancy.)<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>-Nat<o:p></o:p></p></div></div></div></div></div></body></html>