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Yes, I also saw this… a solution is to manually edit the PDB file output by phenix.read_set to get rid of HD22 of N-linked Asn residues - then phenix.refine works.
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<div>HTH,</div>
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<div>Luca</div>
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Luca Jovine, Ph.D.<br>
Professor of Structural Biology & EMBO Young Investigator<br>
Karolinska Institutet<br>
Department of Biosciences and Nutrition & Center for Innovative Medicine<br>
Halsovagen 7, SE-141 83 Huddinge, Sweden<br>
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W3: <a href="http://jovinelab.org">http://jovinelab.org</a><br>
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<div>On 27 Apr 2015, at 10:52, Tristan Croll <<a href="mailto:tristan.croll@qut.edu.au">tristan.croll@qut.edu.au</a>> wrote:</div>
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<div style="margin-top: 0px; margin-bottom: 0px;">Hi,</div>
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<div style="margin-top: 0px; margin-bottom: 0px;">I'm currently using the dev 2000 version of Phenix, and noticed an issue with the automatic linking of N-linked (and presumably O-linked) glycans. If you feed a glycosylated structure<span class="Apple-converted-space"> </span><em>sans</em> hydrogens
to Phenix and allow ReadySet to add hydrogens prior to refinement, it adds hydrogens as if the glycans are unlinked. Then, the automatic linking script rejects them due to valence issues.</div>
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<div style="margin-top: 0px; margin-bottom: 0px;">Cheers,</div>
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<div style="margin-top: 0px; margin-bottom: 0px;">Tristan<br>
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