My Refund Says:

you should contact your bank. Banking system can either reject or accept any direct deposit. There is nothing to do with IRS. 

As @lionrockspirit stated, you should contact your bank directly. As long as your bank account is open, they will most likely deduct the amount overdrawn from the deposit to have the remainder left in your account. However, we cannot speak on behalf of your bank, so you should contact them for the best answer.