Even though you may not actually be paid by the minute, it's not a bad way to calculate how much you should be paid overall.
So, if you're in negotiations about compensation, firstly, ask a lot of questions :
1) what's the total budget of the film (then calculate the 1% to 3% figure)
2) then ask how many minutes of music they expect you to score (then calculate an amount that you'd be comfortable with....$1000/minute..etc...)
3) live musicians ? sweetening, is there any expectation and budget for it ? what about AFof M musicians/contracts etc...?
Somewhere in there will be the figure that you can live with.
Get it all in writing ! Get 50% up-front ! 50% upon delivery.