removed `/scratch/xiaobo/13056/xcd-8058097.56/working/protonate/xcd-protomers-expanded.ism' removed `/scratch/xiaobo/13056/xcd-8058097.56/working/protonate/xcd-protomers.ism' removed `/scratch/xiaobo/13056/xcd-8058097.56/working/protonate/xcd-protonated-manual.ism' removed directory: `/scratch/xiaobo/13056/xcd-8058097.56/working/protonate' removed `/scratch/xiaobo/13056/xcd-8058097.56/working/input-smiles.ism'