You must use a reference target to properly set the “home” position of axis 6. The angle offset will be the rotation around the Z axis of the tool flange needed to best fit the measured TCP (X,Y,Z) with the known TCP reference. The measured TCP (see the following image) is one of the TCPs that were measured in the step two of the calibration procedure. The reference TCP is a known reference that corresponds to one of the TCP for the calibration tool being used.
Ideally, the reference TCP must be measured by the CMM with respect to the tool flange (a replica of the robot tool flange would be best). Alternatively, you can use a new robot to measure (step two of the calibration procedure) the TCP for the first time and use one measured TCP as the reference. It is important to use a dowel pin and/or appropriate tool flange referencing to make sure that the end effector is always placed at the same position.