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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoPlainText><a name="_MailEndCompose">Dear All,<o:p></o:p></a></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>Kay helped me reprocess the data set with XDS, the program pick up I422 as space group. It turned out that when I originally used XDS, I used spindle axis -1, 0, 0 for the APS ID22 detector, it should be 1, 0, 0. The output from XDS:<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText><span style='font-size:8.0pt;font-family:"Courier New"'>SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF RESOLUTION<o:p></o:p></span></p><p class=MsoPlainText><span style='font-size:8.0pt;font-family:"Courier New"'> RESOLUTION NUMBER OF REFLECTIONS COMPLETENESS R-FACTOR R-FACTOR COMPARED I/SIGMA R-meas CC(1/2) Anomal SigAno Nano<o:p></o:p></span></p><p class=MsoPlainText><span style='font-size:8.0pt;font-family:"Courier New"'> LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected Corr<o:p></o:p></span></p><p class=MsoPlainText><span style='font-size:8.0pt;font-family:"Courier New"'><o:p> </o:p></span></p><p class=MsoPlainText><span style='font-size:8.0pt;font-family:"Courier New"'> 8.87 4414 841 858 98.0% 2.7% 3.2% 4402 45.77 3.0% 99.9* -18 0.664 577<o:p></o:p></span></p><p class=MsoPlainText><span style='font-size:8.0pt;font-family:"Courier New"'> 6.33 7883 1374 1385 99.2% 3.7% 3.9% 7872 35.76 4.1% 99.9* -17 0.687 1108<o:p></o:p></span></p><p class=MsoPlainText><span style='font-size:8.0pt;font-family:"Courier New"'> 5.18 10205 1724 1734 99.4% 5.1% 4.9% 10195 29.38 5.6% 99.8* -15 0.748 1468<o:p></o:p></span></p><p class=MsoPlainText><span style='font-size:8.0pt;font-family:"Courier New"'> 4.49 12194 2042 2055 99.4% 5.0% 4.7% 12185 30.77 5.4% 99.8* -20 0.727 1764<o:p></o:p></span></p><p class=MsoPlainText><span style='font-size:8.0pt;font-family:"Courier New"'> 4.02 13830 2284 2297 99.4% 6.2% 5.9% 13822 24.55 6.7% 99.8* -15 0.736 2019<o:p></o:p></span></p><p class=MsoPlainText><span style='font-size:8.0pt;font-family:"Courier New"'> 3.67 15377 2501 2530 98.9% 9.4% 9.3% 15368 16.77 10.3% 99.6* -12 0.752 2245<o:p></o:p></span></p><p class=MsoPlainText><span style='font-size:8.0pt;font-family:"Courier New"'> 3.40 16709 2702 2724 99.2% 14.3% 14.5% 16700 11.31 15.6% 99.2* -5 0.761 2430<o:p></o:p></span></p><p class=MsoPlainText><span style='font-size:8.0pt;font-family:"Courier New"'> 3.18 18091 2904 2934 99.0% 23.3% 24.6% 18084 7.14 25.4% 98.4* -3 0.726 2635<o:p></o:p></span></p><p class=MsoPlainText><span style='font-size:8.0pt;font-family:"Courier New"'> 3.00 18105 2972 3107 95.7% 37.3% 40.4% 18071 4.42 40.7% 96.4* -6 0.665 2624<o:p></o:p></span></p><p class=MsoPlainText><span style='font-size:8.0pt;font-family:"Courier New"'> total 116808 19344 19624 98.6% 8.2% 8.4% 116699 18.79 9.0% 99.8* -10 0.724 16870<o:p></o:p></span></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>Attached please also find the xtriage log for data processed with XDS.<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>Final model with I422 data set at 3 A resolution looked fine to me, r-free went down from ~0.32 to 0.298, the map even let me correctly fitted one place that supposed to have a Cis-Pro. The final numbers for the model is:<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>r_work = 0.2611<o:p></o:p></p><p class=MsoPlainText>r_free = 0.2983<o:p></o:p></p><p class=MsoPlainText>bonds = 0.002<o:p></o:p></p><p class=MsoPlainText>angles = 0.568 <o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>Thank you all for all the help!<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>Regards,<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>Tongqing<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>Tongqing Zhou, Ph.D.<o:p></o:p></p><p class=MsoPlainText>Staff Scientist<o:p></o:p></p><p class=MsoPlainText>Structural Biology Section<o:p></o:p></p><p class=MsoPlainText>Vaccine Research Center, NIAID/NIH<o:p></o:p></p><p class=MsoPlainText>Building 40, Room 4609B<o:p></o:p></p><p class=MsoPlainText>40 Convent Drive, MSC3027<o:p></o:p></p><p class=MsoPlainText>Bethesda, MD 20892<o:p></o:p></p><p class=MsoPlainText>(301) 594-8710 (Tel)<o:p></o:p></p><p class=MsoPlainText>(301) 793-0794 (Cell)<o:p></o:p></p><p class=MsoPlainText>(301) 480-2658 (Fax)<o:p></o:p></p><p class=MsoPlainText>******************************************************************************<o:p></o:p></p><p class=MsoPlainText>The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.<o:p></o:p></p><p class=MsoPlainText>******************************************************************<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>-----Original Message-----<br>From: Pavel Afonine [mailto:pafonine@lbl.gov] <br>Sent: Tuesday, May 08, 2012 2:07 PM<br>To: phenixbb@phenix-online.org<br>Subject: Re: [phenixbb] UPDATE-- Difficult dataset and refinement--P422? I422?Twinning?</p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>Hi,<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>>> 1. Is it really twinned since including twin-law in refinment gave much<o:p></o:p></p><p class=MsoPlainText>>> better numbers?<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>R-factors may not be directly comparable:<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>G.Murshudov, Appl. Comput. Math., V.10, N.2, 2011, pp.250-261.<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>The strategy is:<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>- check to see if Xtriage tells it's twinned (based on reflection statistics, not just predicted twin laws based on geometry);<o:p></o:p></p><p class=MsoPlainText>- use phenix.model_vs_data to see if it's worth using it.<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>Pavel<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>_______________________________________________<o:p></o:p></p><p class=MsoPlainText>phenixbb mailing list<o:p></o:p></p><p class=MsoPlainText><a href="mailto:phenixbb@phenix-online.org"><span style='color:windowtext;text-decoration:none'>phenixbb@phenix-online.org</span></a><o:p></o:p></p><p class=MsoPlainText><a href="http://phenix-online.org/mailman/listinfo/phenixbb"><span style='color:windowtext;text-decoration:none'>http://phenix-online.org/mailman/listinfo/phenixbb</span></a><o:p></o:p></p></div></body></html>