you can no longer efile it. it must be mailed. follow the TT filing instructions. Mail by a method where you get proof of delivery. to file, you'll also need to attach all federal withholding forms.
you have several options for payment.
1) send a check with return and 1040-V. make sure the check has your SSN, email address, address and "2016 form 1040"
2) go to IRS website and click on make a payment. - can use direct pay (direct withdrawal from checking or savings account, debit card or credit card. afterwards print a copy of the proof of payment page.
3) same day wire
4) money order - retain all documentation in case you need to prove payment.
5) cash at certain retail partners
don't include penalties for late filing and late payment at this tine. let the IRS bill you. if you have a reasonable cause for not realizing return wasn't accepted, when you get the bill for penalties, you may be able to request abatement which is much more difficult if you pay them up front because your sort of acknowledging you had no reasonable cause. good luck
