The IRA custodian will send you a 2016 Form 1099-R for the amount you took out in 2016. You will enter that on your 2016 tax return and the tax on the withdrawal will be included in your 2016 tax. There is no penalty, but you have to pay tax on your 2016 tax return on the amount that you withdrew in 2016.
In addition to taking the remainder of your 2016 RMD in 2017, you will also have to take your RMD for 2017 (your second RMD) in 2017. You will get a 2017 Form 1099-R next year for the total amount that you take out in 2017 - the balance of your 2016 RMD plus your 2017 RMD. You will enter that 1099-R on your 2017 tax return and the tax on the total amount of the withdrawals will be included in your 2017 tax.
