removed `/scratch/xiaobo/6332/xch-8058097.60/working/protonate/xch-protomers.ism' removed `/scratch/xiaobo/6332/xch-8058097.60/working/protonate/xch-protonated-manual.ism' removed `/scratch/xiaobo/6332/xch-8058097.60/working/protonate/xch-protomers-expanded.ism' removed directory: `/scratch/xiaobo/6332/xch-8058097.60/working/protonate' removed `/scratch/xiaobo/6332/xch-8058097.60/working/input-smiles.ism'