once you complete 2021 Form 5329 to determine the penalty, you can file 2021 Form 1040-X prepared manually.
With Form 1040-X you attach only the new or changed Forms or Schedules, namely Form 5329.
do not include the old 1040 nor the revised 1040, since 1040-X becomes your new tax return.
get Form 1040-X from IRS website and mail it in with your 5329, which you can also get in fillable PDF.
The amount you owe, 1040-X line 20 should be the amount of the 6% penalty.
@rewashp
