Hi Kevin,
What formula are you using, exactly? For a sharp notch (instead of a gradual reduction) for a 4x9 down to a 4x4 you pay a "penalty" by increasing the shear stress by a factor of d'/d bacause it's concentrated in one spot.
I suggest reconsidering your joist sizing though, and make them wider. Having joists that are deeper than the carrying sill is odd.
