removed `/scratch/xiaobo/308318/xdq-8058097.95/working/protonate/xdq-protomers.ism' removed `/scratch/xiaobo/308318/xdq-8058097.95/working/protonate/xdq-protonated-manual.ism' removed `/scratch/xiaobo/308318/xdq-8058097.95/working/protonate/xdq-protomers-expanded.ism' removed directory: `/scratch/xiaobo/308318/xdq-8058097.95/working/protonate' removed `/scratch/xiaobo/308318/xdq-8058097.95/working/input-smiles.ism'