Underpayment penalties are calculated on a per-tax-quarter basis because the US tax system is a pay-as-you-go system. Even if your tax return shows a refund you can still have an underpayment penalty if you have an insufficient amount of tax withholding and quarterly estimated tax payments made throughout the year.
If taking IRA distributions and not moving the money to another retirement account will be a regular, ongoing occurrence, you should have taxes withheld either from the IRA distributions or from some other income source sufficient to cover the increase in tax liability resulting from the IRA distributions.
