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. Pavel