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For a container terminal system, efficient berth and quay crane (QC) schedules have great impact on the improvement of both operation efficiency and customer satisfaction. In this paper we address both berth and quay crane scheduling problems in a simultaneous way, with uncertainty of container handling time. The berth is of discrete type and vessels arrive dynamically with different service priorities. Besides we assume QCs can move to other berths before finishing processing on currently assigned vessels, adding more flexibility to the terminal system. A mixed integer programming model is established, and a simulation based Genetic Algorithm (GA) search procedure is applied to generate robust berth and QC schedule proactively. Computational experiment shows the satisfied performance of our developed algorithm.