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Hi Yarrow,<br>
<br>
I can have a look if you send me all inputs: data, model and CIF
files, as well as any parameter files (if used).<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 6/23/14, 5:42 PM, Yarrow Madrona
wrote:<br>
</div>
<blockquote
cite="mid:CAMHjG6ZdmEXFmNq6XP-einJCY5TQsFt_6VPjn-g_arNcmXZ9aw@mail.gmail.com"
type="cite">Hello again,
<div><br>
</div>
<div>have fixed the CIF and I still get a large overall bond
deviation > 0.03, even when using wxc_scale = 0.02. It does
not change much even though the angle sigmas move from 1.4 to
about 0.7.<br>
<div><br>
</div>
<div>Is there anyway to set a target of say, .0015 and optimize
the R/Rfree around this? My resolution is 2.5 A. Is it
possible I am over parametizing using isotropic B factor
refinement and individual coordinate refinement? I estitmate
my parameter/obs ratio to be ~ 1.5. I have an unusuallyl large
solvent content, about 65%.<br>
<br>
On Monday, June 23, 2014, Yarrow Madrona <<a
moz-do-not-send="true" href="mailto:amadrona@uci.edu">amadrona@uci.edu</a>>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<span
style="font-family:arial,sans-serif;font-size:15.555556297302246px">Hello,</span>
<div
style="font-family:arial,sans-serif;font-size:15.555556297302246px"><br>
</div>
<div
style="font-family:arial,sans-serif;font-size:15.555556297302246px">
I have a ligand bound to a heme and I have supplied a
CIF for phenix in refinement. I did not include all
atoms just, those close to the iron. Unfortunately, I am
getting very large reported bond deviations for other
atoms. For example I get:</div>
<div
style="font-family:arial,sans-serif;font-size:15.555556297302246px"><br>
</div>
<div
style="font-family:arial,sans-serif;font-size:15.555556297302246px">
<div>bond pdb="FE HEM A 410 "</div>
<div> pdb=" N3 CPZ A 500 "</div>
<div> ideal model delta sigma weight residual</div>
<div> 2.100 4.054 -1.954 2.00e-01 2.50e+01 9.54e+01</div>
</div>
<div
style="font-family:arial,sans-serif;font-size:15.555556297302246px"><br>
</div>
<div
style="font-family:arial,sans-serif;font-size:15.555556297302246px">
N3 and FE are not bonded and not expected to be close to
one another. it is not supported by the structure. I
suspect that this is causing my overall bonds deviations
to be ~0.03 even if I greatly reduce the weight of wxc.</div>
<div
style="font-family:arial,sans-serif;font-size:15.555556297302246px"><br>
</div>
<div
style="font-family:arial,sans-serif;font-size:15.555556297302246px">Is
it necessary to enter all of these outliers into the
.cif file or is there an easier way? Thank you.</div>
</div>
</blockquote>
</div>
</div>
<br>
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</blockquote>
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