You will never be able to include all the effects (nonlinearities, nonidealities) in your hand analysis that Spice can include in its simulation.
So the best thing isn't to try to replicate Spice results with hand analysis, but learn to know what details you need to include in a Spice model to get an accurate result, and how to tell when Spice is giving you an unrealistic result (usually because you didn't give it a good enough model).