removed `/scratch/xiaobo/30047/xbc-8058115.29/working/protonate/xbc-protomers-expanded.ism' removed `/scratch/xiaobo/30047/xbc-8058115.29/working/protonate/xbc-protomers.ism' removed `/scratch/xiaobo/30047/xbc-8058115.29/working/protonate/xbc-protonated-manual.ism' removed directory: `/scratch/xiaobo/30047/xbc-8058115.29/working/protonate' removed `/scratch/xiaobo/30047/xbc-8058115.29/working/input-smiles.ism'