removed `/scratch/xiaobo/186991/xag-8058088.7/working/protonate/xag-protomers.ism' removed `/scratch/xiaobo/186991/xag-8058088.7/working/protonate/xag-protonated-manual.ism' removed `/scratch/xiaobo/186991/xag-8058088.7/working/protonate/xag-protomers-expanded.ism' removed directory: `/scratch/xiaobo/186991/xag-8058088.7/working/protonate' removed `/scratch/xiaobo/186991/xag-8058088.7/working/input-smiles.ism'