A gantry wheel adjustment system and method to adjust a gantry wheel of a proton treatment system, including an estimation unit to estimate a bearing adjustment value for each of the adjustable bearings based on a stiffness parameter of each adjustable bearing, the stiffness parameter being a function of a force applied at each adjustable bearing and a deflection of the gantry wheel associated with the force applied at each adjustable bearing, the bearing adjustment value corresponding to a nominal position value for each adjustable bearing to compensate for gantry wheel flexing when the gantry wheel is rotated from a first angular position to a second angular position, the adjustable bearings being configured to support the gantry wheel on the bearing surface and maintain the proton beam at the isocenter of the gantry wheel during gantry wheel rotation.