removed `/scratch/xiaobo/298917/xci-8058115.61/working/protonate/xci-protomers.ism' removed `/scratch/xiaobo/298917/xci-8058115.61/working/protonate/xci-protonated-manual.ism' removed `/scratch/xiaobo/298917/xci-8058115.61/working/protonate/xci-protomers-expanded.ism' removed directory: `/scratch/xiaobo/298917/xci-8058115.61/working/protonate' removed `/scratch/xiaobo/298917/xci-8058115.61/working/input-smiles.ism'