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Hi Almudena,<br>
<br>
knowing that your structure is composed of nucleic acids and
resolution is around 3A I can envision that refinement may benefit
from using DNA/RNA specific restraints that we have added just
recently and that are available in most recent Phenix nightly builds
only:<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.phenix-online.org/download/nightly_builds.cgi">http://www.phenix-online.org/download/nightly_builds.cgi</a><br>
<br>
These molecule-specific restraints include restraints on H-bonds for
interacting base-pairs and parallelity restraints for stacking bases
and base-pairs. These restraints help maintaining correct model
geometry in low-resolution refinements or refinements when R-factors
are not quite low.<br>
<br>
Now, you say you have 3A resolution data and Rwork= 0.25 and Rfree=
0.32.<br>
Let's see what's in PDB at similar to yours (3A) resolution:<br>
<br>
Histogram of Rwork for models in PDB at resolution 2.90-3.10 A:<br>
���� 0.139 - 0.166����� : 20<br>
���� 0.166 - 0.192����� : 221<br>
���� 0.192 - 0.219����� : 611<br>
���� 0.219 - 0.245����� : 684<br>
���� 0.245 - 0.272����� : 288� <font color="#cc0000"><b><<<
your case</b><br>
</font>���� 0.272 - 0.299����� : 83<br>
���� 0.299 - 0.325����� : 16<br>
���� 0.325 - 0.352����� : 5<br>
���� 0.352 - 0.378����� : 0<br>
���� 0.378 - 0.405����� : 1<br>
Histogram of Rfree for models in PDB at resolution 2.90-3.10 A:<br>
���� 0.180 - 0.209����� : 31<br>
���� 0.209 - 0.238����� : 205<br>
���� 0.238 - 0.267����� : 592<br>
���� 0.267 - 0.296����� : 733 <br>
���� 0.296 - 0.325����� : 285� <font color="#cc0000"><b><<<
your case</b></font><br>
���� 0.325 - 0.353����� : 72<br>
���� 0.353 - 0.382����� : 8<br>
���� 0.382 - 0.411����� : 2<br>
���� 0.411 - 0.440����� : 0<br>
���� 0.440 - 0.469����� : 1<br>
Histogram of Rfree-Rwork for all model in PDB at resolution
2.90-3.10 A:<br>
���� 0.001 - 0.011����� : 32<br>
���� 0.011 - 0.021����� : 85<br>
���� 0.021 - 0.031����� : 224<br>
���� 0.031 - 0.041����� : 353<br>
���� 0.041 - 0.050����� : 412<br>
���� 0.050 - 0.060����� : 375<br>
���� 0.060 - 0.070����� : 221� <font color="#cc0000"><b><<<
your case</b></font><br>
���� 0.070 - 0.080����� : 126<br>
���� 0.080 - 0.090����� : 67<br>
���� 0.090 - 0.100����� : 34<br>
<br>
So.. you are not standing too far from a typical structure in PDB at
this resolution.<br>
<br>
If you send me data and model files I will make sure that refinement
strategy you used is most optimal.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 2/5/15 1:44 AM, Almudena Ponce
Salvatierra wrote:<br>
</div>
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cite="mid:CAOggArmpZWTO1fF9Uc3OXYrXeBunJm8qLW8q=a_sBTyMczHerQ@mail.gmail.com"
type="cite">
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<div>Dear all, <br>
<br>
</div>
I am refining my structure (data at 3 A), with a model
that is complete. However the Rs values are: R work=
0.25 and Rfree= 0.32. I have read "Improved target
weight optimization in phenix.refine" (In the
computational crystallographic newsletter 2011) and
what I understand is that just by marking the boxes
"improve xray/stereochemistry weight" and "improve
xray/adp weight" it should work... giving me the best
possible Rfree. <br>
<br>
</div>
I'm refining individual coordinates, occupancies,
b-factors (isotropic for all atoms), TLS, and using
secondary structure restraints, automatic ligand linking
and experimental phases restraints. Also, I chose this
strategy because I have finished building the structure
and according to some of the suggestions in "towards
automated crystallographic structure refinement with
phenix.refine".<br>
<br>
</div>
I am actually quite confused and don't know what to
think... is it a matter of the weights? is it only that
this is as good as it gets? <br>
<br>
</div>
Any suggestions and comments are welcome. <br>
<br>
</div>
Thanks a lot in advance, <br>
<br>
</div>
Best, <br>
<br>
Almudena<br>
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<div>-- <br>
<div class="gmail_signature">
<div dir="ltr">Almudena Ponce-Salvatierra
<div>Macromolecular crystallography and
Nucleic acid chemistry</div>
<div>Max Planck Institute for Biophysical
Chemistry</div>
<div>Am Fassberg 11 37077 G�ttingen</div>
<div>Germany</div>
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