PTO does the reconciliation pretty well but it depends on whether you made the underlying entries for income, losses, and expenses correctly.  Take a look at the Worksheets and you'll find how the numbers tie to F.1116 and F.1040.

One of the key things to remember that deductions are mostly allocated based on gross instead of net income.  If you have capital gains and losses, you'll see that losses are not taken into account in that computation.