removed `/scratch/xiaobo/9689/xac-8058097.3/working/protonate/xac-protomers-expanded.ism' removed `/scratch/xiaobo/9689/xac-8058097.3/working/protonate/xac-protomers.ism' removed `/scratch/xiaobo/9689/xac-8058097.3/working/protonate/xac-protonated-manual.ism' removed directory: `/scratch/xiaobo/9689/xac-8058097.3/working/protonate' removed `/scratch/xiaobo/9689/xac-8058097.3/working/input-smiles.ism'