The book says to use 90% of your 1RM, but that your 3RM is the same thing as 90% of your 1RM. On my previous program, I had been squatting 240 for 3 reps for a couple weeks, so I used 240 as my number.
The 5 week (week 1), calls for 5 reps at 65%, 75% and 85%. 85% of 240 is 205, and I managed 8 reps.
The 3 week (week 2) calls for 3 reps at 80%, 80% and 90%. I managed 6 reps at 215.
The 5/3/1 week (week 3) had me at 95%, and I only managed 2 reps at 228 (I actually failed on the third rep).
In fact, if you use the rep comparison formula, you can see how my calculated ORM actually drops from 259 in week 1, to 257 in week 2, to 243 in week 3. Its a similar story with bench and deadlift.
My program is
monday: squats, pullups, shrugs
wednesday: bench, barbell curl
friday: deadlift, T-bar rows, incline curl
Side note: from trying several different programs, it seems to me that I often "peak" rather than "plateau". I'll hit a PR and then not be able to duplicate it. Another thing I notice, anytime I take weight off the bar (say, to increase volume), I can't lift the heavier weight anymore.