<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Yes, yes. But before one admits the model with the higher Rfree is the more accurate model, one must make sure the refinement protocol is correct.<DIV><BR class="khtml-block-placeholder"></DIV><DIV>Jianghai</DIV><DIV><BR><DIV> <SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><DIV>+++++++++++++++++++++++++++++++</DIV><DIV>Jianghai Zhu, Ph.D</DIV><DIV>CBR Institute for Biomedical Research</DIV><DIV>Department of Pathology</DIV><DIV>Harvard Medical School</DIV><DIV>200 Longwood Ave., Boston, MA 02115</DIV><DIV>Ph: 617-278-3211</DIV><DIV>Fx: 618-278-3232</DIV><DIV>+++++++++++++++++++++++++++++++</DIV><DIV><BR class="khtml-block-placeholder"></DIV><BR class="Apple-interchange-newline"></SPAN></SPAN></SPAN></SPAN></SPAN></SPAN></SPAN> </DIV><BR><DIV><DIV>On Aug 4, 2007, at 10:06 PM, Mayer, Mark (NIH/NICHD) [E] wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Forgive me for saying this but the object of refinement is to build the most accurate model, not to obtain the lowest Rvalue,</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">which will vary with weights applied to diffraction data versus constraints. There have been multiple posts about this on</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">crystallographic BBs in the last few months ...</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">-----Original Message-----</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">From: Jianghai Zhu [<A href="mailto:jzhu@cbr.med.harvard.edu">mailto:jzhu@cbr.med.harvard.edu</A>]</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Sent: Sat 8/4/2007 9:19 PM</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">To: PHENIX user mailing list</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Subject: [phenixbb] R, Rfree, and wxu_scale</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Hi,</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Just finished a round of refinement.<SPAN class="Apple-converted-space"> </SPAN>Rfree went up about 1% and R <SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">went down a bit.<SPAN class="Apple-converted-space"> </SPAN>I am wondering what happened here.<SPAN class="Apple-converted-space"> </SPAN>Also Rfree <SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">always went down after TLS refinement but always went up a lot more <SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">after the individual ADP refinement.<SPAN class="Apple-converted-space"> </SPAN>Is there anything I can do <SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">here?<SPAN class="Apple-converted-space"> </SPAN>Should I use weaker B restraints?<SPAN class="Apple-converted-space"> </SPAN>I tried to assign a <SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">wxu_scale value.<SPAN class="Apple-converted-space"> </SPAN>But phenix.refine automatically adjust it to 1.81 <SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">every time.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">------------------------------------------------------------------------</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">R-factors, x-ray target values and norm of gradient of x-ray target</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">stage <SPAN class="Apple-converted-space"> </SPAN>r-work r-free<SPAN class="Apple-converted-space"> </SPAN>xray_target_w<SPAN class="Apple-converted-space"> </SPAN>xray_target_t</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>0<SPAN class="Apple-converted-space"> </SPAN>:<SPAN class="Apple-converted-space"> </SPAN>0.3982 0.5701 <SPAN class="Apple-converted-space"> </SPAN>6.156859e+00 <SPAN class="Apple-converted-space"> </SPAN>6.238509e+00</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>1_bss:<SPAN class="Apple-converted-space"> </SPAN>0.2008 0.2494 <SPAN class="Apple-converted-space"> </SPAN>5.949117e+00 <SPAN class="Apple-converted-space"> </SPAN>6.088855e+00</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>1_xyz:<SPAN class="Apple-converted-space"> </SPAN>0.2030 0.2497 <SPAN class="Apple-converted-space"> </SPAN>5.953829e+00 <SPAN class="Apple-converted-space"> </SPAN>6.091696e+00</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>1_adp:<SPAN class="Apple-converted-space"> </SPAN>0.1998 0.2559 <SPAN class="Apple-converted-space"> </SPAN>5.952833e+00 <SPAN class="Apple-converted-space"> </SPAN>6.099340e+00</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>2_bss:<SPAN class="Apple-converted-space"> </SPAN>0.1996 0.2557 <SPAN class="Apple-converted-space"> </SPAN>5.952517e+00 <SPAN class="Apple-converted-space"> </SPAN>6.099196e+00</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>2_xyz:<SPAN class="Apple-converted-space"> </SPAN>0.1984 0.2576 <SPAN class="Apple-converted-space"> </SPAN>5.953246e+00 <SPAN class="Apple-converted-space"> </SPAN>6.104085e+00</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>2_adp:<SPAN class="Apple-converted-space"> </SPAN>0.1974 0.2578 <SPAN class="Apple-converted-space"> </SPAN>5.950434e+00 <SPAN class="Apple-converted-space"> </SPAN>6.102336e+00</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>3_bss:<SPAN class="Apple-converted-space"> </SPAN>0.1972 0.2574 <SPAN class="Apple-converted-space"> </SPAN>5.950333e+00 <SPAN class="Apple-converted-space"> </SPAN>6.102222e+00</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>3_xyz:<SPAN class="Apple-converted-space"> </SPAN>0.1997 0.2576 <SPAN class="Apple-converted-space"> </SPAN>5.956524e+00 <SPAN class="Apple-converted-space"> </SPAN>6.103647e+00</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>3_adp:<SPAN class="Apple-converted-space"> </SPAN>0.1987 0.2590 <SPAN class="Apple-converted-space"> </SPAN>5.955554e+00 <SPAN class="Apple-converted-space"> </SPAN>6.104434e+00</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>3_bss:<SPAN class="Apple-converted-space"> </SPAN>0.1986 0.2588 <SPAN class="Apple-converted-space"> </SPAN>5.955445e+00 <SPAN class="Apple-converted-space"> </SPAN>6.104227e+00</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">------------------------------------------------------------------------</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Weights for target T = Exray * wxc * wxc_scale + Echem * wc and</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">angles between gradient vectors, eg. (d_Exray/d_sites, d_Echem/d_sites)</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">stage<SPAN class="Apple-converted-space"> </SPAN>wxc<SPAN class="Apple-converted-space"> </SPAN>wxu<SPAN class="Apple-converted-space"> </SPAN>wxc_sc<SPAN class="Apple-converted-space"> </SPAN>wxu_sc /_gxc,gc /_gxu,gu</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>0<SPAN class="Apple-converted-space"> </SPAN>:<SPAN class="Apple-converted-space"> </SPAN>5.5611e-01 <SPAN class="Apple-converted-space"> </SPAN>7.2249e-01 <SPAN class="Apple-converted-space"> </SPAN>0.050 <SPAN class="Apple-converted-space"> </SPAN>1.810 <SPAN class="Apple-converted-space"> </SPAN>96.334<SPAN class="Apple-converted-space"> </SPAN>101.736</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>1_bss:<SPAN class="Apple-converted-space"> </SPAN>5.5611e-01 <SPAN class="Apple-converted-space"> </SPAN>7.2249e-01 <SPAN class="Apple-converted-space"> </SPAN>0.050 <SPAN class="Apple-converted-space"> </SPAN>1.810 <SPAN class="Apple-converted-space"> </SPAN>96.334<SPAN class="Apple-converted-space"> </SPAN>101.736</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>1_xyz:<SPAN class="Apple-converted-space"> </SPAN>4.5001e-01 <SPAN class="Apple-converted-space"> </SPAN>6.1023e-01 <SPAN class="Apple-converted-space"> </SPAN>0.050 <SPAN class="Apple-converted-space"> </SPAN>1.810 <SPAN class="Apple-converted-space"> </SPAN>96.591<SPAN class="Apple-converted-space"> </SPAN>102.016</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>1_adp:<SPAN class="Apple-converted-space"> </SPAN>4.5001e-01 <SPAN class="Apple-converted-space"> </SPAN>6.1023e-01 <SPAN class="Apple-converted-space"> </SPAN>0.050 <SPAN class="Apple-converted-space"> </SPAN>1.810 <SPAN class="Apple-converted-space"> </SPAN>96.591<SPAN class="Apple-converted-space"> </SPAN>102.016</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>2_bss:<SPAN class="Apple-converted-space"> </SPAN>4.5001e-01 <SPAN class="Apple-converted-space"> </SPAN>6.1023e-01 <SPAN class="Apple-converted-space"> </SPAN>0.050 <SPAN class="Apple-converted-space"> </SPAN>1.810 <SPAN class="Apple-converted-space"> </SPAN>96.591<SPAN class="Apple-converted-space"> </SPAN>102.016</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>2_xyz:<SPAN class="Apple-converted-space"> </SPAN>5.1326e-01 <SPAN class="Apple-converted-space"> </SPAN>6.5356e-01 <SPAN class="Apple-converted-space"> </SPAN>0.050 <SPAN class="Apple-converted-space"> </SPAN>1.810<SPAN class="Apple-converted-space"> </SPAN>112.802<SPAN class="Apple-converted-space"> </SPAN>141.393</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>2_adp:<SPAN class="Apple-converted-space"> </SPAN>5.1326e-01 <SPAN class="Apple-converted-space"> </SPAN>6.5356e-01 <SPAN class="Apple-converted-space"> </SPAN>0.050 <SPAN class="Apple-converted-space"> </SPAN>1.810<SPAN class="Apple-converted-space"> </SPAN>112.802<SPAN class="Apple-converted-space"> </SPAN>141.393</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>3_bss:<SPAN class="Apple-converted-space"> </SPAN>5.1326e-01 <SPAN class="Apple-converted-space"> </SPAN>6.5356e-01 <SPAN class="Apple-converted-space"> </SPAN>0.050 <SPAN class="Apple-converted-space"> </SPAN>1.810<SPAN class="Apple-converted-space"> </SPAN>112.802<SPAN class="Apple-converted-space"> </SPAN>141.393</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>3_xyz:<SPAN class="Apple-converted-space"> </SPAN>3.3568e-01 <SPAN class="Apple-converted-space"> </SPAN>7.0695e-01 <SPAN class="Apple-converted-space"> </SPAN>0.050 <SPAN class="Apple-converted-space"> </SPAN>1.810<SPAN class="Apple-converted-space"> </SPAN>111.975<SPAN class="Apple-converted-space"> </SPAN>135.760</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>3_adp:<SPAN class="Apple-converted-space"> </SPAN>3.3568e-01 <SPAN class="Apple-converted-space"> </SPAN>7.0695e-01 <SPAN class="Apple-converted-space"> </SPAN>0.050 <SPAN class="Apple-converted-space"> </SPAN>1.810<SPAN class="Apple-converted-space"> </SPAN>111.975<SPAN class="Apple-converted-space"> </SPAN>135.760</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>3_bss:<SPAN class="Apple-converted-space"> </SPAN>3.3568e-01 <SPAN class="Apple-converted-space"> </SPAN>7.0695e-01 <SPAN class="Apple-converted-space"> </SPAN>0.050 <SPAN class="Apple-converted-space"> </SPAN>1.810<SPAN class="Apple-converted-space"> </SPAN>111.975<SPAN class="Apple-converted-space"> </SPAN>135.760</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">------------------------------------------------------------------------</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Jianghai</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">+++++++++++++++++++++++++++++++</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Jianghai Zhu, Ph.D</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">CBR Institute for Biomedical Research</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Department of Pathology</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Harvard Medical School</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">200 Longwood Ave., Boston, MA 02115</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Ph: 617-278-3211</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Fx: 618-278-3232</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">+++++++++++++++++++++++++++++++</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR><SPAN><DIV><winmail.dat></DIV></SPAN>_______________________________________________</DIV><DIV style="margin-top: 0px; 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