Hi,<br><br>I'm refining a 2.88
Angstrom structure and am getting a difference of greater than 6%
between the R-work and R-free. The best result (I think) is what I
have from minimization alone:<br>
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<p style="margin-bottom: 0in; margin-left: 40px;">Start R-work =
0.3219, R-free = 0.3505 (no bulk solvent and anisotropic scale)
</p>
<p style="margin-bottom: 0in; margin-left: 40px;">Final R-work =
0.2424, R-free = 0.3174 (no bulk solvent and anisotropic scale)
</p>
<p style="margin-bottom: 0in; margin-left: 40px;"><br>
</p>
<p style="margin-bottom: 0in; margin-left: 40px;">Start R-work =
0.3220, R-free = 0.3500
</p>
<p style="margin-bottom: 0in; margin-left: 40px;">Final R-work =
0.2411, R-free = 0.3176
</p>
<p style="margin-bottom: 0in; margin-left: 40px;"><br></p>The results from simulated annealing are the following:<br><br>
<p style="margin-bottom: 0in; margin-left: 40px;">Start R-work = 0.3219, R-free = 0.3505
(no bulk solvent and anisotropic scale)
</p>
<p style="margin-bottom: 0in; margin-left: 40px;">Final R-work = 0.2454, R-free = 0.3322
(no bulk solvent and anisotropic scale)
</p>
<p style="margin-bottom: 0in; margin-left: 40px;"><br>
</p>
<p style="margin-bottom: 0in; margin-left: 40px;">Start R-work = 0.3220, R-free = 0.3500
</p>
<p style="margin-bottom: 0in; margin-left: 40px;">Final R-work = 0.2403, R-free = 0.3333</p><p style="margin-bottom: 0in; margin-left: 40px;"><br></p>I have also done the refinement with ncs but ncs is probably not appropriate for my structure. The final R-free ends up being higher (though the difference between R-free and R-work ends up being 6-7%)<br>
<br>My PI (who is on vacation until next week) said that it was a
problem if R-work was more than 0.06 lower than R-free. Any
recommendations for me? Is it possible to reduce this difference? Is it worth it to rebuild the refined pdb if the R-work is this different from the R-free?<br><br>My refinement script is:<br><br><div style="margin-left: 40px;">
phenix.refine ss46_p3_cv.mtz ss46_rebuilt.pdb \<br>
output.prefix=results/ss46_rebuilt_sa \<br> strategy=individual_sites+group_adp cif_link.params nag-nag.cif \<br> twin_law="h,-h-k,-l" \<br> simulated_annealing=true<br><br>(the cif_link.params and nag-nag.cif files are made to handle the N-glycosylation sites, I think).<br>
</div><br>Thanks for your help!<br><font color="#888888">-Sam</font>