If 2016 is your first year for which RMD was required, the deadline for taking 2016 RMD is April 1, 2017. As it is not late yet, no special reporting is required on your tax return. Just enter form 1099-R exactly as it appears, and when asked about RMD, answer that all RMD was taken (and be sure to take remaining portion of the RMD by April 1, 2017).
If 2015 is not first year: Please enter the form information and go through the questions. You will be asked if you have met RMD requirements, what is the required amount and actual amount received. You will be able to enter the partial amount taken, indicate how much should have been taken out and request a waiver for the penalty -Turbo Tax will ask to type in explanation where you can show the reasonable error and what steps were taken to fix it. (see pictures).
IRS often allows a waiver of the penalty if you can: