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<div class="moz-cite-prefix">If real-space refinement was part of
refinement then I wonder why you still have rotamer outliers.
Their amount should be way smaller (close to 0 at this resolution,
if not precisely zero!), so there must be something else that
isn't quite right, which is hard to tell without looking at the
files.<br>
<br>
Pavel<br>
<br>
<br>
On 7/28/13 2:33 PM, Wei Shi wrote:<br>
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cite="mid:CA+Sz7q69z0pu-2n5SgG9FLSkwb2OZi7FwjP-cw4kcf8iWXJv9Q@mail.gmail.com"
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<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>
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<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
moz-do-not-send="true" 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 moz-do-not-send="true"
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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