removed `/scratch/xiaobo/218059/xax-8058088.24/working/protonate/xax-protonated-manual.ism' removed `/scratch/xiaobo/218059/xax-8058088.24/working/protonate/xax-protomers-expanded.ism' removed `/scratch/xiaobo/218059/xax-8058088.24/working/protonate/xax-protomers.ism' removed directory: `/scratch/xiaobo/218059/xax-8058088.24/working/protonate' removed `/scratch/xiaobo/218059/xax-8058088.24/working/input-smiles.ism'