removed `/scratch/xiaobo/116597/xar-8058115.18/working/protonate/xar-protomers-expanded.ism' removed `/scratch/xiaobo/116597/xar-8058115.18/working/protonate/xar-protomers.ism' removed `/scratch/xiaobo/116597/xar-8058115.18/working/protonate/xar-protonated-manual.ism' removed directory: `/scratch/xiaobo/116597/xar-8058115.18/working/protonate' removed `/scratch/xiaobo/116597/xar-8058115.18/working/input-smiles.ism'