[phenixbb] target bond/angle RMS deviations from ideal
pafonine at lbl.gov
Wed Dec 13 17:02:18 PST 2017
> Hello all,
> the documentation
> <https://www.phenix-online.org/documentation/faqs/refine.html> states that
> This is somewhat controversial, but absolute upper limits for a
> well-refined protein structure at high resolution are typically
> 0.02 for RMS(bonds) and 2.0 for RMS(angles); usually they will be
> significantly lower.
> I understand that exceedingly high RMSDs from ideal could indicate
> On the other hand, local deviations from ideal geometry may point to
> correctable modeling errors, and I am concerned that overly tight
> restraints may cause that diagnostic tool to become less sensitive, or
> local errors to be spread in to the model.
Do you have an example? I've heard this many times but so far nobody
could show me a convincing example that demonstrates how tighter
bond/angle restraints mask "other problems".
Also, looking at just bond/angles rmsds from ideal library values isn't
comprehensive and may indeed lead to some problems being overlooked.
Using all arsenal of validation tools, global and local, should find
> For what bond and angle rms deviations from ideal do my colleagues on
> the BB aim and how have they arrived at those targets?
See Jaskolski et al., 2007; Wlodawer et al., 2008; Stec, 2007; Tickle,
2007; Karplus et al., 2008 and references inside.
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