On my 1099 R box 4 should have paid my tax penalty. It shows a bigger tax cut than should have occurred. What's the problem here?

On box 2 I withdrew the amount of $3,035. on Box 4 I held 303.50 for the IRS to eliminate this penalty, yet it still shows around $460 dollars being taken out from my return because of all this. I'm confused. I thought the penalty was 10%?