I recently submitted a heterotetrameric complex for refinement on the FG-MD server(job id S7259). The input file consists of 4 chains, 2 core chains which are from a crystal structure and two surrounding chains which are modelled. However the output downloaded file only shows the two core chains and the outer two chains are missing. Interestingly the visual output on the result link (http://zhanglab.ccmb.med.umich.edu/FG-MD/output/S7259) does show all the chains, they are just missing in the output file when downloaded.