removed `/scratch/xiaobo/440022/xbi-8058097.35/working/protonate/xbi-protomers-expanded.ism' removed `/scratch/xiaobo/440022/xbi-8058097.35/working/protonate/xbi-protonated-manual.ism' removed `/scratch/xiaobo/440022/xbi-8058097.35/working/protonate/xbi-protomers.ism' removed directory: `/scratch/xiaobo/440022/xbi-8058097.35/working/protonate' removed `/scratch/xiaobo/440022/xbi-8058097.35/working/input-smiles.ism'