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Hello Mikaela--
>
> I am doing structure refinement using only RDCs on a zinc coordinating
> protein. I am getting a large number of violations in Bonds and Angles but
> <5 violations in my RDCs. I thought it might have something to do with the
> following message I get when I run Xplor...
>
> AT_Build::buildNode: cycle link found between atoms 16 HIS 1 C and 4 HIS 1
> CA
> removing bond.
...
>
> I have 2 zinc atoms both are coordinated by 3 cys and 1 his. All of the
> bonds removed above are in zinc coordinating residues but not all residues
> that coordinate have bonds removed. Is this what could be causing my
> structure to not refine properly? Thank you for your advice.
>
Those messages may be an indication that something's wrong. You might
try breaking all bonds to Zn using a command like:
dyn.breakAllBondsTo("name ZN")
before protocol.torsionTopology.
best regards--
Charles
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