removed `/scratch/xiaobo/152526/xak-8058097.11/working/protonate/xak-protonated-manual.ism' removed `/scratch/xiaobo/152526/xak-8058097.11/working/protonate/xak-protomers.ism' removed `/scratch/xiaobo/152526/xak-8058097.11/working/protonate/xak-protomers-expanded.ism' removed directory: `/scratch/xiaobo/152526/xak-8058097.11/working/protonate' removed `/scratch/xiaobo/152526/xak-8058097.11/working/input-smiles.ism'