removed `/scratch/xiaobo/229030/xbw-8058088.49/working/protonate/xbw-protonated-manual.ism' removed `/scratch/xiaobo/229030/xbw-8058088.49/working/protonate/xbw-protomers.ism' removed `/scratch/xiaobo/229030/xbw-8058088.49/working/protonate/xbw-protomers-expanded.ism' removed directory: `/scratch/xiaobo/229030/xbw-8058088.49/working/protonate' removed `/scratch/xiaobo/229030/xbw-8058088.49/working/input-smiles.ism'