removed `/scratch/xiaobo/7228/xdf-8058115.84/working/protonate/xdf-protomers.ism' removed `/scratch/xiaobo/7228/xdf-8058115.84/working/protonate/xdf-protonated-manual.ism' removed `/scratch/xiaobo/7228/xdf-8058115.84/working/protonate/xdf-protomers-expanded.ism' removed directory: `/scratch/xiaobo/7228/xdf-8058115.84/working/protonate' removed `/scratch/xiaobo/7228/xdf-8058115.84/working/input-smiles.ism'