This is not a how to do fine tuning, there are plenty of tutorials for your specific camera and lens. Generally speaking DSLR and camera manufactures have different ways to achieve better results when a lens is used with a certain camera body. Sigma went as far as offering a "USB dock" while Nikon included fine tuning settings in most of their camera bodies which is very nice and smart. We know all lenses manufactured have variations which may manifest on some camera bodies when using Autofocus tuning. The Camera thinks the image is in focus but it is not, and that problem needs to be addressed.
As stated this is not a how to perform lens tuning but why you should. Buying any lens has expense and you are entitled to "getting your money's worth". No better way than taking time to tune the lens to the camera body. Sometimes you get lens and have no doubts sharpness is spot on, while others leave you in question. If you experience mixed image quality or soft images overall consider fine tuning that lens to your camera body. While Nikon Cameras bodies remembers 20 Lens and Teleconvertor combinations others like Canon may have similar capabilities. Nikon Camera bodies know that a 500mm will have one setting while a Nikon 500mm and a TC 1.4 attached has a second setting. Nikon makes this all automatic once you save the settings, so each time you mount the lens the camera remembers the best auto focus settings to use based on your input.
I encourage you to break open the manual or reliable You Tube and explore setting up your custom lens & camera settings for maximum result - it does make a difference.
The Newer Nikon Bodies feature "automatic tuning" which may take all of five minutes. - Go for it..