A method of operating a center pivot irrigation system (10) having a main boom assembly (14) with an end tower (26) and an extension arm (16) pivotally supported to the end tower (26). The method determines an actual position of the end tower (26) while the irrigation system is in operation； determines an actual angular orientation of the extension arm (16) relative to the end tower (26)； accesses memory and determines the desired angular orientation of the extension arm (16)； and compares the actual angular orientation to the desired angular orientation. If the actual angular orientation deviates from the desired angular orientation by more than a threshold amount, the method shuts down the irrigation system.
