removed `/scratch/xiaobo/31207/xab-8058115.2/working/protonate/xab-protomers.ism' removed `/scratch/xiaobo/31207/xab-8058115.2/working/protonate/xab-protonated-manual.ism' removed `/scratch/xiaobo/31207/xab-8058115.2/working/protonate/xab-protomers-expanded.ism' removed directory: `/scratch/xiaobo/31207/xab-8058115.2/working/protonate' removed `/scratch/xiaobo/31207/xab-8058115.2/working/input-smiles.ism'