We have developed the AIR software, which is an Artificial Intelligence-based protein 3D structure Refinement method. AIR is constructed using a multi-objective particle swarm optimization(PSO) protocol. We use multiple energy functions as multi-objectives so as to correct the potential inaccuracy from a single function. Given several initial 3D models for one sequence, AIR takes each initial structure as the particle, with the process of structure refinement, the particles will also move around. The quality of current particles (structures) will be evaluated by three energy functions, and the non-dominated particles will be put into a set called Pareto set. After the iteration converges, the particles from the Pareto set will be screened and part of them will be outputted, which are the final refined structures. The AIR is published in Bioinformatics, 2019.