It is okay to file your 2016 tax return. Then, it is a good idea to contact the IRS to get everything straightened out for the prior years. They will send out written notification about any money you owed from prior years. If you didn't receive it, they may not have had your correct address or you are fine. Either way, it's best to know if they require anything further from you and take care of it sooner rather than later.
IRS
Telephone Assistance for Individuals:
Toll-Free, 1-800-829-1040
Expect long wait
times.
Alternatively, this link has the local IRS offices.
Contact Your Local
IRS Office