Yes.
Your 1099-R will show $50,000 in income, and $10,000 in tax payments. After entering the 1099-R, you are asked if you rolled the money into another plan. When you indicate that you rolled $50,000 into a Traditional IRA, your tax liability is $0 and you have a payment of $10,000.
The $10,000 is a federal tax payment on your return along with all of your withholding and estimated payments, and you are adding no additional income.
Do you have the 1099-R? This situation is accounted for with the entry of the 1099-R and just a few questions after that. The $10,000 should be shown in Box 4. That's the only place you need to enter it.
