removed `/scratch/xiaobo/200760/xde-8058097.83/working/protonate/xde-protonated-manual.ism' removed `/scratch/xiaobo/200760/xde-8058097.83/working/protonate/xde-protomers-expanded.ism' removed `/scratch/xiaobo/200760/xde-8058097.83/working/protonate/xde-protomers.ism' removed directory: `/scratch/xiaobo/200760/xde-8058097.83/working/protonate' removed `/scratch/xiaobo/200760/xde-8058097.83/working/input-smiles.ism'