The clock stops when the IRS receives your payment of the amount due on the amended return. Mail it by certified mail with a return receipt so you will have tracking and confirmation of delivery.
TurboTax cannot calculate the penalty and interest. One reason is that it has no way of knowing when the IRS will receive your payment. Also, there is no place for the penalty and interest on the amended return form (Form 1040-X), so even if TurboTax could calculate it, it would have no place to put it.
The IRS will send you a bill for the penalty and interest. Just make sure you pay it by the due date on the bill. If the amount is small, they might not bother to bill you.
