Nemesis' Ult's Damage

So, Nemesis' Ult is fairly straightforwards. % damage and protections stolen. What might not be immediately obvious is whether or not the ult is cutting 50% of your targets health as true damage, or merely dealing that number as physical damage, and whether or not the protections theft comes before or after the damage is dealt.

A few helpful notes:
At level 20, Ra has:
1685 health
60 Physical Protection (37.5% of all physical damage is mitigated)
Flat penetration is calculated by simply removing the same amount of protections from the equation. (eg 15 pen on a 30 protection target has damage calculated with 15 protection)

Have a quick look at this webm. It's a tad on the faster side so watch it a few times.
http://a.pomf.se/aqcmwz.webm

In the first ult, Nemesis is built with no Penetration. The ult deals 545, which is 32.5% of Ra's health, which is about what you'd expect. About 35% of the physical damage was mitigated.
In the second ult, Nemesis is built with 61 Penetration. The ult deals 793 damage, which is ~47.5% of Ra's health. In theory I've exceeded Ra's protections and should have dealt a full 842 points of damage. Why about 5% of the damage was mitigated I don't know.
In the 3rd ult, I've built Nemesis with 30 penetration. If the ult steals protections before dealing damage, we should see damage similar to the 2nd test. If it steals after, somewhere in between the 2 tests. As it does 671 damage, we can conclude that Nemesis' ult deals physical damage, after which it then steals protections.