You will need to enter a 1099R for the money distributed from the 401k. The tax withheld was an estimate, just like when your employer withholds tax from your paychecks. All of your income and all of the tax withheld has to be entered, and then the software calculates whether you owe more or get a refund.
Check with the custodian of the plan --- you can likely get the 1099R from their website.
To enter your retirement income, Go to Federal> Wages and Income>Retirement Plans and Social Security>IRA 401 k) Pension Plan Withdrawals to enter your 1099R.