The IRS does not respond specifically to a 5329 unless you have taken the waiver of penalty in error. Line 55 applies only if you did not take the required minimum distribution (RMD) and are paying the penalty for not doing so. That should be fairly straight forward, as the RMD is given on your Form 5498. Part I , line 2 is where you enter the amount and reason for the penalty waiver. If you are fining a return, you should send it in with your return, not separately.