Capitalization rate is net operating income divided by price. Net operating income on this page is the rent you enter minus the operating costs you enter. The mortgage payment is not subtracted. A cap rate answers what the building yields before financing.
Rent of $36,000 a year and operating costs of $12,000 leave $24,000 of net operating income. On a $400,000 price the cap rate is 6%. The same income on a higher price is a lower cap rate.
Vacancy, repairs, and management are in the result only to the extent you typed them into operating costs. Debt service, income tax, and future rent growth are not in the cap rate.