<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><blockquote type="cite"><div bgcolor="#ffffff" text="#000000"><br> the answer - I don't know. Optimizing the weight you can use different things, like Rfree, divinations from ideal stereochemistry, LLG, or combination Rfree and divinations from ideal stereochemistry, etc... Rfree seemed to me the most obvious and easy, but again, I have no strong feelings or experience what is better (and what "better" actually means in this context).</div></blockquote><div><br class="webkit-block-placeholder"></div><div>Based on Ian Tickle's paper <a href="http://journals.iucr.org/d/issues/2007/12/00/gx5119/gx5119.pdf">http://journals.iucr.org/d/issues/2007/12/00/gx5119/gx5119.pdf</a>, -LLG is slightly more stable and better than Rfree as a refinement indicator. </div><div><br></div><blockquote type="cite"><div bgcolor="#ffffff" text="#000000"><br> <br> What do you mean by "less stable/reliable" ?<br> <br> The procedure that phenix.refine uses is very simple... The overall target is (for xyz refinement; similar for B-factors):<br> <br> Etotal = wxc * wxc_scale * Exray + wc * Egeom<br> <br> wxc is determined as in CNS (ratio of gradient norms), wc = 1.0, wxc_scale is adjustable parameter which is by default set to 0.5 or so. In most of cases at "normal" resolutions the automatic weight is good. If not, then you need to either play with wxc_scale manually or have phenix.refine do it for you automatically by using optimize_wxc. And what "optimize_wxc=true" does is just a grid search: it tries different wxc_scale values and chooses the one that produces the lowest Rfree. I don't see why it could be unstable or not reliable. Obviously, one can use any other criterion instead of Rfree. <br> <br></div></blockquote><br></div><div>I do have a problem with the default wxc_scale and the optimize_wxc = true. But my structure is at low resolution 3.5 A. The default wxc_scale really couldn't hold up the geometry and the optimize_wxc = true just made it worse. I have to manually set the wxc_scale = 0.1.</div><div><br class="webkit-block-placeholder"></div><div>Jianghai</div></body></html>