removed `/scratch/xiaobo/20504/xao-8058097.15/working/protonate/xao-protonated-manual.ism' removed `/scratch/xiaobo/20504/xao-8058097.15/working/protonate/xao-protomers.ism' removed `/scratch/xiaobo/20504/xao-8058097.15/working/protonate/xao-protomers-expanded.ism' removed directory: `/scratch/xiaobo/20504/xao-8058097.15/working/protonate' removed `/scratch/xiaobo/20504/xao-8058097.15/working/input-smiles.ism'