[phenixbb] target bond/angle RMS deviations from ideal

Pavel Afonine pafonine at lbl.gov
Wed Dec 13 17:02:18 PST 2017

Hi Wolfram,

> 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 
> overfitting.
> 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 
most problems.
> 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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