I noticed that analysis seems to miscalculate distances between degenerate methyl-protons. The attached example is only one of a few I came about. In this case the actual distance is calculated to be 5.96 A, which can't be true. Using pymol and measuring only heavy-atom distances I think the true distance is somewhere around 10-11 A.
What could be the reason for this?
I am still using 2.1.5, since a repeated attempt to update did not work.