How does an end notch in a ceiling beam affect deflection calculations?
A notch in the end of a beam does not affect the strength (or deflection) of a beam, unless it’s more than 1/4 th the height of the beam (or joist) at the ends out to the face of the bearing point. (See Code ICC R502.8.1) 

Code does not allow notches in middle 1/3 span and Code allows 1/6 th depth of beam in the last 1/3 rd span at each end of beam. 

In fact, in your case, you could probably cut the whole end of the beam off where it’s notched and it would not affect it structurally. (That size beam needs about 2” of solid bearing, depending on the grade and species.)