Look at this link:
https://support.turbotax.intuit.com/irs-notice/audit-support/
That will help, with the IRS think about this:
1) timely respond.
2) in your case look over the letter from IRS in great detail as if they are questioning stock sales and say you owe some money ($3K) there may have been some sales dates missing (and then the IRS will tax as Short-term versus Long Term) and the cost basis may be missing and IRS will enter $0 for cost basis.
So do this before you Amend the return to see if you can correct it this way. See link below:
If you need to Amend you will need the TurboTax Premier which is best for stock sales.
https://turbotax.intuit.com/personal-taxes/past-years-products/
