And the flat counts before the %.
Meaning, with:
40 flat pen (assuming something like MPen boots and abyssal scepter [which isn't actually entry but is pretty much similar], or a haunting guize, also no runes or masteries)
40% pen
vs 200 MR (reduce 66.67% damage)
=
96 MR (reduce 48.98% damage)
So in total, that's a 17.69% damage increase towards people with 200 MR.