You must properly measure three base targets before starting a robot calibration if you want to align the axis 1 with the real robot base frame. These base targets must be chosen so that the reference frame can be found with respect to the robot.
The “home” position of axis 1 directly depends on the three base targets as well as the robot base setup. The robot base setup is the first calibration step, where the base frame of the measurement system is placed with respect to the robot base frame by moving and measuring axis 1 and 2.
The base targets of the measurement system can be set by pressing “Set base targets” (see following image). These are 3 measurements that will define the desired robot reference frame (the first 2 measurements define the X axis and the third point the positive Y axis). You should use appropriate reference points related to the robot base so that this procedure is repeatable.
The correction angle for joint 1 will be the angle between the X axis of the base reference measured through 3 points and the base reference measured by moving the robot axes 1 and 2. Of course, both vectors are previously projected to the XY plane of the base reference obtained by touching the tree points.