removed `/scratch/xiaobo/28289/xby-8058097.51/working/protonate/xby-protomers-expanded.ism' removed `/scratch/xiaobo/28289/xby-8058097.51/working/protonate/xby-protonated-manual.ism' removed `/scratch/xiaobo/28289/xby-8058097.51/working/protonate/xby-protomers.ism' removed directory: `/scratch/xiaobo/28289/xby-8058097.51/working/protonate' removed `/scratch/xiaobo/28289/xby-8058097.51/working/input-smiles.ism'