IF you are getting pension payments, and you were 70.5 or older in 2016, then the software always asks that question.
....you just say YES for that 1099-R and that all of it was an RMD.
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We've asked TTX repeatedly for a third choice to indicate it was you regular annuitized pension, but they haven't so far.
Technically, your regular pension payments are an RMD, you just have no control over them....whatever the pension administration has determined to be your payout is the RMD.......you may not like it, but get used to it.