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Hi Cristiano,<br>
<br>
if Molybdenum site isn't disordered, it should have a very prominent
peak at 1.9A resolution, which in turn means metal coordination
restraints may not be necessary. So have you tried to refine without
these restraints?<br>
<br>
You may try to refined occupancy of Mo in case it is partially
occupied. Also, it's heavy enough to warrant refinement of its
anisotropic ADP.<br>
<br>
Finally, clashes may also be false alarms because Molprobity clash
evaluators are unaware of non-standard geometries and bonds.<br>
<br>
I can have a closer look if you send me files (off mailing list).<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 11/20/19 07:24, Cristiano Mota
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CABzUK2x42wciOj8Hg4_GNBtxHw11e+KUeZqitzmTUutcUz9rPw@mail.gmail.com">
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<div dir="ltr"><span style="color:rgb(0,0,0)">Hi all,</span><br>
<div style="color:rgb(0,0,0)"><br>
</div>
<div style="color:rgb(0,0,0)">I'm using phenix.refine to
refine a structure of a Molybo-protein at 1.9Å.</div>
<div style="color:rgb(0,0,0)">The MGD cofactors (molybdopterin
guanine dinucleotide) are being refined with a weird
distorted geometry causing some clashes. The Fo-Fc maps show
that something is going wrong in the aromatic rings
interatomic distances.</div>
<div style="color:rgb(0,0,0)"><br>
</div>
<div style="color:rgb(0,0,0)">I'm using the readyset to pick
up MGD and metal restraints.</div>
<div style="color:rgb(0,0,0)">Am I using the right protocol? </div>
<div style="color:rgb(0,0,0)"><br>
</div>
<div style="color:rgb(0,0,0)">Best regards,</div>
<div style="color:rgb(0,0,0)">Cristiano Mota</div>
<br>
</div>
</div>
</blockquote>
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