i paid $503 to IRA directly, in Turbotax is showing only the w2 federal withhold taxes. When is going to sum up to my return?

I believe you mean you had $503 taken out of your IRA pension withdrawal in federal income tax withheld. If so, that would be reported on the Form 1099-R you would receive from the pension plan, in box 4. You need to make sure you entered that where you enter the Form 1099-R.

To enter a Form 1099-R in TurboTax:

1. From the federal menu in TurboTax navigate to Wages and Income
2. Find the Retirements and Investments or IRA, 401(k), Pension Plan Withdrawals (1099-R) section 
3. Select Start, Revisit or Edit/Add next to IRA, 401(k), Pension Plan Withdrawals
4. Indicate that you did get a 1099-R statement if necessary
5. Select how you want to enter your 1099-R statement (import or type in yourself) and enter your 1099-R information in TurboTax