To add, w/r/t AF-D:
The Nikon motor-in-body autofocus system, being mechanical, has inherent backlash throughout its chain of components to drive the focusing elements to a solution.
Without backlash, nothing moves. With backlash, the system will err.
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This is a key reason why the D300 (and up) bodies have AF Fine Tune capability, which has the ability to adjust for the system backlash inherent in AF-D screw-drive lenses.
Taking this a step further, this is but one reason why AF Fine Tune will usually wreak havoc on the focus ability of AF-S lenses; i.e., AF-S lenses have only the backlash in the AF-S motor which is corrected by the AF module solution calculated by the body.
[As an aside, ALL zoom lenses, Af-D or AF-S, should NEVER be AF-Fine-Tuned, unless you glue the zoom at ONE focal length - - after which, you might consider buying a prime at that glued focal length.]
Happy New Year!