A lot of the bumps are main-chain CHalpha to main-chain carbonyl O H-bonds, but there are also some CH...O side-chain H-bonds, again with clear density.  The C...O distances are in the range 3.0 to 3.2 Ang., so too short for a vdW contact.  The H...O distances are ~ 2.2 Ang. which is definitely shorter than the sum of the vdW radii ( H: 1.2 + O: 1.5 = 2.7).

I found this survey of CH...O H-bonds but it's restricted to CH...O bonds at the end of helices and I see them mostly in sheets.

This reports 11 examples (i.e. H-bonds, not structures) in the 3.0-3.2 range for the whole of the PDB (admittedly as it was in 2001 when the article appears to have been written).  I have about the same number in one structure!

One possibility I considered was that the unit cells had all somehow 'shrunk'.  This can be tested with WhatCheck: however it only reports a very small shrinkage which translates to an error of ~ 0.02 Ang. in a 3 Ang. distance, which is nowhere near enough to explain a discrepancy of 0.5 Ang.

So I guess my question is has anyone else noticed this in their MP dot-plots; also does anyone know what criteria does MP uses for testing bumps and specifically what value is it using for CH...O H-bonds?  And of course I'd like to know whether this will affect my percentile ranking in the clashscore from the PDB validation!

Cheers

-- Ian