removed `/scratch/xiaobo/28312/xdp-8058115.94/working/protonate/xdp-protomers-expanded.ism' removed `/scratch/xiaobo/28312/xdp-8058115.94/working/protonate/xdp-protonated-manual.ism' removed `/scratch/xiaobo/28312/xdp-8058115.94/working/protonate/xdp-protomers.ism' removed directory: `/scratch/xiaobo/28312/xdp-8058115.94/working/protonate' removed `/scratch/xiaobo/28312/xdp-8058115.94/working/input-smiles.ism'