<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Hi:</div><div>We noticed that in some of our refinements, real space refinement was performed even though we chose not to do this.</div><div><div>I tried to opt out of real space refinement as follows:</div><div>" refine {</div><div> strategy = *individual_sites individual_sites_real_space rigid_body \</div><div> *individual_adp group_adp *tls *occupancies group_anomalous ..."</div></div><div><br></div><div>however, the R-free is identical whether we select real space refinement or not, and the logfile shows</div><div><div><br></div><div>" Validate:</div><div> |--------START--------| |--------FINAL--------|</div><div> residue map_cc 2mFo-DFc mFo-DFc map_cc 2mFo-DFc mFo-DFc</div><div> "LYS A 18 " 0.9359 16.78 0.00 0.9107 17.60 0.00 </div><div> "ARG A 19 " 0.9513 21.82 0.00 0.9470 20.97 -6.52 <<<</div><div> "ARG A 26 " 0.9440 26.72 0.00 0.9474 27.33 -2.43 </div><div> "ARG A 69 " 0.9685 31.36 0.00 0.9659 32.58 0.00 </div><div> "GLN A 86 " 0.9681 23.57 -5.81 0.8850 19.29 -18.27 <<<</div><div> "GLU A 89 " 0.9689 26.30 -4.43 0.8977 23.67 -11.59 <<<</div><div> "LYS A 93 " 0.9746 25.19 0.00 0.9682 26.47 2.90 </div></div><div> ... "</div><div>and suggesting that real space refinement was performed.</div><div>Is there a way to correct this, or to ensure that real space refinement is not performed during refinement? </div><div><br></div><div>Thank you,</div><div>-Jerome</div><div><br class="webkit-block-placeholder"></div><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: 'Lucida Grande'; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: 'Lucida Grande'; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: 'Lucida Grande'; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Optima; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Optima; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Optima; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><font class="Apple-style-span" face="'Lucida Grande'" size="3"><span class="Apple-style-span" style="font-size: 12px; ">Jerome C. Nwachukwu, PhD<br>Dept. of Cancer Biology<br>The Scripps Research Institute-Florida<br></span></font></div></span></div></span></div></span></span></div></span></span>
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