A system for controlling a multiple cylinder internal combustion engine is presented. The system operates a first portion of cylinders in a homogeneous charge compression ignition (HCCI) mode and a second portion of cylinders in a non-HCCI mode, and uses an engine controller that is coupled to the first and second portions of cylinders to electronically actuate valves to hold a combusted air and fuel charge in the second portion of cylinders, and exhaust the combusted air and fuel charge to adjust the residual air-to-fuel ratio of the engine.