What did you do with the $501.37 check? The $1 25.34 was just an estimated amount for taxes.
You didn't actually pay the tax or 10% penalty (you pay a 10% early withdrawal penalty if you are under 59 ½). You had taxes withheld like from your paycheck. You still have to enter the whole amount (before taxes were withheld) with your other income to figure out the total tax (and it may put you into a higher tax bracket) and then the withholding is subtracted from the total tax to figure your refund or tax due. It has to break out and list the 10% early withdrawal penalty separately on your return. It's on 1040 Schedule 2 line 6. Then you will get credit for the withholding on 1040 line 17.
