Right now, with the current roster set, we are only $1.985M under the cap. But that will increase a bit with McDonald's redo. He either did a redo with a $2.645M bonus prorated over 3 yrs(savings are $1,763,334) or over 5 years(savings of $2.116M), the 5yr would require extra voidable years to maximize cap savings.
But we will lose $1.017M for our Practice Squad, 10 players will make $107,100 each at minimum. Some teams do overpay for PS players, like NE Bit I doubt we will.
Here's an article I did for NinersNation.com, http://www.ninersnation.com/2014/8/29/6084515/aldon-smith-suspension-navorro-bowman-injury-49ers-salary-cap
, shows possible cap relief we can get for players with roster bonuses, and also Boone's holdout, and Aldon's suspension.