I withdrew from a IRA and have an extra tax bill that is due....will this be deducted from my refund or do I need to pay this on my own

[MargaretL]

The extra penalty tax will be deduct from your refund  (if you have one) since IRA distribution is reported on your return. You don't have to pay this on your own, separately from the tax return. Otherwise it will be included in your tax bill if your tax return will result in a liability and not in the refund. 

[katherineann93]

I am getting a return, I filed and printed it but I did not see where the penalty came out, or is it something the IRS does before depositing the refund?

[MargaretL]

The penalty is calculated on your return, nothing additional is done by the IRS or you. You may look at Form 1040, line 59... it will show penalty./ since you are getting a refund, it simply means that your tax withheld and your deductions/credits covered the penalty...