<div dir="ltr">Try turning off real space refinement:<div><br></div><div>refine.strategy=individual_sites+individual_adp+occupancies</div><div><br></div><div>(and at this resolution, anomalous_group refinement of the seleniums would probably also be useful, but you'd have to use the anomalous data as input.)</div>
<div><br></div><div>-Nat</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Nov 7, 2013 at 1:12 PM, Mark Wilson <span dir="ltr"><<a href="mailto:mwilson13@unl.edu" target="_blank">mwilson13@unl.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear PHENIX users and developers,<br>
I am refining a structure containing SeMet residues at atomic (1.05 �)<br>
resolution. �The model was initially refined in Refmac5 and behaved as<br>
expected (i.e. reasonable R factors and agreement with maps). �I've used<br>
this final Refmac5 model as a starting point for refinement in PHENIX<br>
1.8.4 with standard settings, as below.<br>
<br>
phenix.refine data.mtz \<br>
refinement.input.xray_data.labels="F, SIGF" model.pdb \<br>
�main.use_experimental_phases=false �\<br>
�refinement.main.number_of_macro_cycles=5 output.prefix="model_refine"><br>
phenix_refine_1.log<br>
<br>
<br>
Strangely, the conformations of the MSE residues are changed quite<br>
significantly after refinement in PHENIX, departing both from electron<br>
density and from the prior model. Any help would be appreciated.<br>
Best regards,<br>
Mark<br>
<br>
Mark A. Wilson<br>
Associate Professor<br>
Department of Biochemistry/Redox Biology Center<br>
University of Nebraska<br>
N118 Beadle Center<br>
1901 Vine Street<br>
Lincoln, NE 68588<br>
<a href="tel:%28402%29%20472-3626" value="+14024723626">(402) 472-3626</a><br>
<a href="mailto:mwilson13@unl.edu">mwilson13@unl.edu</a><br>
<br>
<br>
<br>
<br>
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</blockquote></div><br></div>