The "present value of the loan" figure is the cost of all tax adjusted payments plus tax adjusted points, fees and down payment, discounted back to the start of the loan at the savings rate you entered. You may also think of it as the amount you would have to invest today (e.g., in a savings account) to cover the points, fees, down payment, and all monthly payments for as long as you keep this property.

In this calculation, points are deducted up front as opposed to being amortized over the life of the loan. This is most consistent with new primary residence purchases. The deduction on loan points for refinances and income properties are usually amortized over the life of the loan.