A method of calculating an angle of an alignment beam of an alignment system in, for example, a lithographic projection apparatus includes measuring the position of at least two alignment marks. These two alignment marks are manufactured on a measurement substrate or they can be arranged on a reference on a substrate table of the lithographic apparatus itself. The second mark is covered by a transparent plate. Then, the position of the two marks is measured using the alignment system. Due to refraction of the alignment beam in the transparent plate, the alignment beam is shifted when returning to the alignment system. The shift of the alignment beam results in a deviated measured position of the second mark. This shift can be calculated because the distance between the two marks is known. The shift is used to calculate the angle of the alignment beam. The angle can be used to improve a FTBA error verification method.