That's hard to say. IRS states this:
"We hold income tax refunds in cases where our records show that one or more income tax returns are past due. We hold them until we get the past due return or receive an acceptable reason for not filing a past due return." [https://www.irs.gov/businesses/small-businesses-self-employed/filing-past-due-tax-returns]
Once they make sure you don't owe anything for 2013, they'll release your 2016 refund. You should probably figure on at least a month for that to happen, unfortunately.