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If you have an IP PIN, that goes in a special place.......and yes, since you filed 2016 late, you will use zero for 2016 AGI.

The IP PIN goes in first in the Federal section....on the "Other Tax Situations" page....you get to it there either by going thru the interview (if you haven't already)......or if you see the full menu of items on that page it's under the "Other Return Info" subsection.

...then when you go to file, use a zero for the AGI and leave then regular PIN field blank
____________*Answers are correct to the best of my knowledge when posted, but should not be considered to be legal or official tax advice.*