There are certainly situations where disallowing an entire traditional IRA deduction could legitimately result in a tax bill of over $3,000. Perhaps you were not eligible to make any of the traditional IRA contribution, making you ineligible for a deduction for the entire contribution (and subject to an excess contribution penalty), or you actually did not make *any* contribution to a traditional IRA for 2015. Check your 2015 Form(s) 5498 from your IRA(s) that report to the IRS the amount you contributed for 2015.
As Critter#2 has suggested, examine the IRS notice carefully.
