If you are tuning using that method, without a tuner, unless you have perfect pitch it will be next to impossible to make the low E exactly in tune.

Your guitar will be in tune with itself, but that doesn't mean it will be in tune (EADGBe).

If you have tuned it the way you tabbed out, you are in tune more than likely.

If the low E is too low, just raise it some more, and then tune your strings again using the same method.

You should be tuning like this:

E----------------------------------------------------0
B----------------------------------------0-----5------
G--------------------------0------4-------------------
D---------------0-----5-------------------------------
A-----0-----5-----------------------------------------
E--5--------------------------------------------------