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Hi George,<br>
<br>
the target function implemented for real-space refinement is such
that it moves atoms towards closest map peaks (the target is the
negative sum of map values calculated at atomic centers). Obviously,
this target is not very similar to R-factor function or reciprocal
space targets that are more or less quadratic near the minimum. All
in all this means that real-space refinement does not guarantee
R-factor decrease and a following round of reciprocal space
refinement is necessary if you plan to look at R-factors. The reason
why this target is use is because it is fastest to calculate.<br>
<br>
Pavel<br>
<br>
<br>
<div class="moz-cite-prefix">On 9/19/14 1:22 PM, Nathaniel Echols
wrote:<br>
</div>
<blockquote
cite="mid:CALeAa1OqCsZ-FBnhe6WwgxWWsupvs1v=-orFarVp=sq-mc2sOg@mail.gmail.com"
type="cite">
<div dir="ltr">Global real-space refinement simply isn't very
useful at high resolution, and you shouldn't need a large radius
of convergence when the R-free is already 13%. �I'm a big fan of
automating everything possible, but this is one case where
fixing the sidechains manually in Coot (which should do an
excellent job) is by far the easiest option. �Once you fix the
sidechains the C-beta outliers will probably disappear.
<div><br>
</div>
<div>PS. A common reason for C-beta deviations at high
resolution is residues with alternate conformations being
split at C-beta rather than splitting the entire residue,
which allows the backbone to move to accommodate the optimal
placement of the sidechain (rather than straining the geometry
to get the sidechain atoms to fit the density). �Always split
the entire residue - the backbone is almost never rigid in
disordered regions.</div>
<div><br>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Fri, Sep 19, 2014 at 1:11 PM, George
Devaniranjan <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:devaniranjan@gmail.com" target="_blank">devaniranjan@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hi,
<div><br>
</div>
<div>I refined (phenix.refine) �a 1.0� structure but it
had a few CB outliers and some rotamer outliers.</div>
<div><br>
</div>
<div>I decided to try real_space_refine, to check if they
could be fixed (given that it has a higher radius of
convergence).</div>
<div>(using run=local_grid_search+minimization_global in
real_space_refine)<br>
</div>
<div><br>
</div>
<div>But, the R/R(free) increased from 11.39/13.24( for
the refine model) to 16.51/17.55 (real_space_refine
model).</div>
<div><br>
</div>
<div>It seemed a big increase, when I looked at the map
against the structure the protein itself seemed fine.</div>
<div>The rotamers outliers had decreased, the CB outliers
were fixed..etc</div>
<div><br>
</div>
<div>The solvent fit to the density had worsened in COOT.</div>
<div><br>
</div>
<div>What am I doing wrong? Any suggestions, advice would
be much appreciated.</div>
<div><br>
</div>
<div>Thank you,</div>
<div>George</div>
</div>
<br>
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</blockquote>
</div>
<br>
</div>
<br>
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