removed `/scratch/xiaobo/24974/xau-8058097.21/working/protonate/xau-protomers-expanded.ism' removed `/scratch/xiaobo/24974/xau-8058097.21/working/protonate/xau-protomers.ism' removed `/scratch/xiaobo/24974/xau-8058097.21/working/protonate/xau-protonated-manual.ism' removed directory: `/scratch/xiaobo/24974/xau-8058097.21/working/protonate' removed `/scratch/xiaobo/24974/xau-8058097.21/working/input-smiles.ism'