removed `/scratch/xiaobo/206079/xco-8058115.67/working/protonate/xco-protomers.ism' removed `/scratch/xiaobo/206079/xco-8058115.67/working/protonate/xco-protonated-manual.ism' removed `/scratch/xiaobo/206079/xco-8058115.67/working/protonate/xco-protomers-expanded.ism' removed directory: `/scratch/xiaobo/206079/xco-8058115.67/working/protonate' removed `/scratch/xiaobo/206079/xco-8058115.67/working/input-smiles.ism'