First off, if you're trying to amend a 2016 tax return, you should not be working in TurboTax Online. The online version is specific for the 2017 tax year (it's updated every year).
Instead, you need to purchase and install the desktop version of TurboTax 2016 from this link: TurboTax Prior Year Products If you need to amend your State return, you'll need to install that module as well.
Once you enter your cost basis for the stock sale, your tax liability (what you owe) may be reduced.
The "payments" listed in the IRS letter could be the amount of tax the IRS shows that you paid for 2016. Interest accrues on unpaid taxes, which you may need to negotiate once you complete your amended return.
You may wish to visit the Audit Support Center to be sure you're calling the correct phone number.
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