CP14 after I already paid

There is a TurboTax Help article on the CP14 notice.

See https://ttlc.intuit.com/community/irs/help/i-got-a-cp14-notice-from-the-irs/00/27160

You are not alone.  Seems to be a glitch they are having this year.  Get a copy of the front and back of the processed check , write your name and Social Security number at the top of the page, and send it back with the paperwork they sent you.

I did not pay by check.  I paid with TurboTax making a direct payment from my bank account.  How shall I respond to IRS to prove that the bank statement shows the payment has cleared?  Can TurboTax provide me with documentation of this payment transaction?

When utilizing direct debit through TurboTax, your payment information is submitted to the IRS with your return and then the IRS processes the payment.  TurboTax cannot provide information for this transaction, you will need to contact your bank and obtain proof of payment through them. 

Please see this TurboTax Help Article for more information on Direct Debit: What is direct debit and how does it work?

@mortganeles