A medical implant bone screw assembly (214) includes a head (212), a shank (220) adapted to be implanted in a bone (224), the head being located at an upper end (34) of the shank and having opposed first pair of upright arms (228) forming a channel (216) therebetween adapted to receive a rod (218), a fastener assembly (200) comprising of a fastener base (204) and a set screw (206), the set screw including an internal central drive structure (186) opening into a flat top surface thereof and having an internal lower tool seating surface (189) near a bottom (77) thereof and being threadably received in a threaded bore (254) in the fastener base and the fastener assembly being entirely received within and between substantially an entire elevation of the head opposed first pair of upright arms.