<html><body><div style="color:#000; background-color:#fff; font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:16px"><div dir="ltr" id="yui_3_16_0_1_1422344596813_4208"><span>Dear Pavel,</span></div><div dir="ltr" id="yui_3_16_0_1_1422344596813_4209"><span><br></span></div><div dir="ltr" id="yui_3_16_0_1_1422344596813_4194"><span id="yui_3_16_0_1_1422344596813_4193">Once the Ramachandran outliers (and the rotamer outliers) was corrected by coot, another round of Phenix refine usually cause the rising of the Rwork and Rfree. Is any way to avoid this rising? After this Rwork and Rfree rising, can I continue the refinement with the Rwork and Rfree rising PDB and MTZ files to try to lower the Rwork and Rfree?</span></div><div dir="ltr" id="yui_3_16_0_1_1422344596813_4194"><span><br></span></div><div dir="ltr" id="yui_3_16_0_1_1422344596813_4194"><span>Smith</span></div><div dir="ltr" id="yui_3_16_0_1_1422344596813_4194"><span><br></span></div><div dir="ltr" id="yui_3_16_0_1_1422344596813_4194"><span><br></span></div> <div class="qtdSeparateBR"><br><br></div><div class="yahoo_quoted" style="display: block;"> <div style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 16px;"> <div style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 16px;"> <div dir="ltr"> <font size="2" face="Arial"> On Tuesday, January 27, 2015 3:28 PM, Pavel Afonine <pafonine@lbl.gov> wrote:<br> </font> </div> <br><br> <div class="y_msg_container"><div id="yiv9683718427"><div>
George,<br clear="none">
<br clear="none">
what exactly you are trying to achieve by making sense of Rfree and
its relation to Rwork in resolution shells? Just curious..<br clear="none">
<br clear="none">
Pavel<br clear="none">
<br clear="none">
<div class="yiv9683718427yqt1501108413" id="yiv9683718427yqt69101"><div class="yiv9683718427moz-cite-prefix">On 1/26/15 1:50 PM, George Devaniranjan
wrote:<br clear="none">
</div>
<blockquote type="cite">
<div dir="ltr">Thank you Tim and Pavel.
<div><br clear="none">
</div>
<div>Sorry, just to follow up:
<div><br clear="none">
</div>
<div>For the example I gave R /Rfree difference seems high.
Can this still be down to statistical fluctuations?</div>
<div><br clear="none">
</div>
</div>
<div>I am just trying to get a feel when we can simply put it
down to statistical fluctuations and when its a concern.</div>
<div><br clear="none">
</div>
</div>
<div class="yiv9683718427gmail_extra"><br clear="none">
<div class="yiv9683718427gmail_quote">On Mon, Jan 26, 2015 at 4:26 PM, Tim
Gruene <span dir="ltr"><<a rel="nofollow" shape="rect" ymailto="mailto:tg@shelx.uni-ac.gwdg.de" target="_blank" href="mailto:tg@shelx.uni-ac.gwdg.de">tg@shelx.uni-ac.gwdg.de</a>></span>
wrote:<br clear="none">
<blockquote class="yiv9683718427gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Dear
George,<br clear="none">
<br clear="none">
you may also want to take into account that the variation of
Rfree is<br clear="none">
estimated as Rfree^2/k, where k is the number of reflections
in the<br clear="none">
shell. If you only have e.g. 100 reflections there, this
might simply a<br clear="none">
statistical fluctuation, as far as I understand.<br clear="none">
<br clear="none">
Cheers,<br clear="none">
Tim<br clear="none">
<span class="yiv9683718427"><br clear="none">
On 01/26/2015 10:05 PM, George Devaniranjan wrote:<br clear="none">
> Hi,<br clear="none">
><br clear="none">
> I calculated/validated several PDB structures in
Phenix.Validation (GUI)<br clear="none">
><br clear="none">
> The R/R-free (overall) is<br clear="none">
><br clear="none">
> 0.1271/0.1348<br clear="none">
><br clear="none">
> Further down I looked at the R/R-free for the highest
resolution shell.<br clear="none">
><br clear="none">
> Its 0.2538/0.2446<br clear="none">
><br clear="none">
</span>> I am curious why the R-free for the *highest
resolution shell* seems to be<br clear="none">
<span class="yiv9683718427im yiv9683718427HOEnZb">> LOWER than R (work).<br clear="none">
><br clear="none">
><br clear="none">
> Am I reading the information wrong?<br clear="none">
><br clear="none">
> PDB: 3QL9<br clear="none">
><br clear="none">
> Thank you,<br clear="none">
> George<br clear="none">
><br clear="none">
><br clear="none">
><br clear="none">
</span>
<div class="yiv9683718427HOEnZb">
<div class="yiv9683718427h5">>
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<span class="yiv9683718427HOEnZb"><font color="#888888">--<br clear="none">
Dr Tim Gruene<br clear="none">
Institut fuer anorganische Chemie<br clear="none">
Tammannstr. 4<br clear="none">
D-37077 Goettingen<br clear="none">
<br clear="none">
GPG Key ID = A46BEE1A<br clear="none">
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</blockquote>
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</blockquote></div>
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