<div dir="ltr"><div><div><div>Hi Dr <span name="Nathaniel Echols" class="">Echols, <br></span></div><span name="Nathaniel Echols" class="">Thank you for the suggestions. I ran the refinement again with default settings + Rigid body+ Simulated annealing (Cartesian) + Optimize </span>X-ray/stereochemistry weight. And the statistics improved! See below:<br>
</div>R-work=0.2348, R-free=0.2855, Bonds=0.003, Angles=0.919. <br>
Ramachandran outliers: 2.5%, Ramachandran favored: 88.1%.<br>
Rotamer outliers: 10%, c-beta outliers: 0<br>
clashscore: 9.06, overall score: 2.84<br><br></div>Now, I am wondering whether there is any suggestion about what to try and check next to further refine the structure. Thank you so much!<br><br>Best,<br>Wei <br></div><div class="gmail_extra">
<br><br><div class="gmail_quote">On Sun, Jul 28, 2013 at 4:00 PM, Nathaniel Echols <span dir="ltr"><<a href="mailto:nechols@lbl.gov" target="_blank">nechols@lbl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im">On Sun, Jul 28, 2013 at 12:44 PM, Wei Shi <<a href="mailto:wei.shi118@gmail.com">wei.shi118@gmail.com</a>> wrote:<br>
> I have a refined structure with phenix. The resolution=3.2 Å. After<br>
> refinement, the R-work=0.2186, R-free=0.2864, Bonds=0.010, Angles=1.515.<br>
><br>
> Ramachandran outliers: 4.8%, Ramachandran favored: 80.8%.<br>
><br>
> Rotamer outliers: 14.5%, c-beta outliers: 2<br>
><br>
> clashscore: 16.28, overall score: 3.32<br>
><br>
> To fix the Ramanchandran outliers, in coot, by changing the phi-psi of the<br>
> outliers, I could manage to move most of them to the allowed positions. But,<br>
> after another refinement in phenix, those outliers come back.<br>
><br>
> I am wondering whether any of you have any suggestions for me on how to fix<br>
> these outliers.<br>
<br>
</div>Turn on X-ray/stereochemistry weight optimization (for non-GUI users,<br>
optimize_xyz_weight=True). That usually fixes the problem.<br>
<br>
-Nat<br>
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</blockquote></div><br></div>