removed `/scratch/xiaobo/143495/xay-8058097.25/working/protonate/xay-protomers-expanded.ism' removed `/scratch/xiaobo/143495/xay-8058097.25/working/protonate/xay-protonated-manual.ism' removed `/scratch/xiaobo/143495/xay-8058097.25/working/protonate/xay-protomers.ism' removed directory: `/scratch/xiaobo/143495/xay-8058097.25/working/protonate' removed `/scratch/xiaobo/143495/xay-8058097.25/working/input-smiles.ism'