<div dir="ltr">As pointed out by a phenixbb reader (thanks!), point 3 was misleading:<div>TLS group cannot be refined with individual <b>anisotropic</b> B-factors (due to technical limitations).</div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, May 24, 2019 at 11:38 AM Dorothee Liebschner <<a href="mailto:dcliebschner@lbl.gov">dcliebschner@lbl.gov</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Hi,<div><br></div><div>A high Rfree can indicate that the refinement strategy is not appropriate.</div><div><br></div><div>Several suggestions:</div><div>1) At 2.5 A resolution, you probably don't need reference model restraints. </div><div><span style="color:rgb(0,0,0)"><font face="arial, sans-serif">2 ) Simulated annealing (SA) is most useful early in refinement, when the model is far from convergence. Manually built models, or MR solutions involving significant local conformational changes, are common inputs where SA can improve over simple gradient-driven refinement. It is generally less helpful later in refinement, and/or at high resolution.</font></span><br></div><div>3) Individual B-factors and TLS are mutually exclusive, so did you define different strategies for different areas? If yes, you could try to revisit the parameterization. </div><div>4) It might be also worthwhile to double check the secondary structure assignment for secondary structure restraints.</div><div><br></div><div>Weight optimization is typically done at the end of refinement. So while you are trying to figure out the strategy, you might want to disable it, as it is time-consuming.</div><div><br></div><div>Best wishes,</div><div><br></div><div>Dorothee</div><div><br></div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, May 23, 2019 at 5:54 PM Pham, Hang <<a href="mailto:Hang.Pham@iaf.inrs.ca" target="_blank">Hang.Pham@iaf.inrs.ca</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<div>Dear all,</div>
<div><br>
</div>
<div>I am refining my structures at 2.5 A. The model is well fitting in the electron density. I already add water and ligands. </div>
<div>I’m trying these options (XYZ coordinates, real-space, TLS parameters, Individual B-factors, Optimize X-ray/stereochemistry weight, Optimize X-ray/ ADP weight, Reference model restraints, Use secondary structure restraints, Simulated annealing
(Cartesian), Automatically correct N/Q/H errors) to refine the structure but the R-free still be high.</div>
<div>The reference model is 98% identity with the structure that I’m building. After refining, the R-work always decrease while R-free increase. My last values for R-work is 0.2501 and for R-free is 0.3246.</div>
<div><br>
</div>
<div>I’m lost and don’t know what to try more.</div>
<div>Can anyone could explain me what happens here ? What others options that I could use to optimize R-free value ?</div>
<div><br>
</div>
<div>Thank you in advance !</div>
<div><br>
</div>
<div>Hang Pham</div>
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------------------------------------------------------<br>
Hang Pham, Ph.D Student,<br>
The Doucet Lab<br>
Centre Armand-Frappier Santé Biotechnologie<br>
Institut National de la Recherche Scientifique (INRS)<br>
Université du Québec<br>
Réseau International des Instituts Pasteur<br>
531 Boulevard des Prairies<br>
Laval (Québec) H7V 1B7 CANADA<br>
Téléphone : (450) 687-5010, poste 4210<br>
Site web: <a href="http://www.profs.inrs.ca/ndoucet/" target="_blank">http://www.profs.inrs.ca/ndoucet/</a></div>
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Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org" target="_blank">phenixbb-leave@phenix-online.org</a></blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail-m_7886392969999355143gmail_signature"><div dir="ltr"><div>Project Scientist, Molecular Biophysics and Integrated Bioimaging<br></div><div>Lawrence Berkeley National Laboratory</div><div>1 Cyclotron Road, M/S 33R0345</div><div>Berkeley, CA 94720</div><div>Tel: (510) 486-5709</div><div>Fax: (510) 486-5909</div><div>Web: <a href="https://phenix-online.org/" style="color:rgb(17,85,204)" target="_blank">https://phenix-online.org</a></div></div></div>
</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div>Project Scientist, Molecular Biophysics and Integrated Bioimaging<br></div><div>Lawrence Berkeley National Laboratory</div><div>1 Cyclotron Road, M/S 33R0345</div><div>Berkeley, CA 94720</div><div>Tel: (510) 486-5709</div><div>Fax: (510) 486-5909</div><div>Web: <a href="https://phenix-online.org/" style="color:rgb(17,85,204)" target="_blank">https://phenix-online.org</a></div></div></div>