removed `/scratch/xiaobo/316102/xbz-8058115.52/working/protonate/xbz-protonated-manual.ism' removed `/scratch/xiaobo/316102/xbz-8058115.52/working/protonate/xbz-protomers-expanded.ism' removed `/scratch/xiaobo/316102/xbz-8058115.52/working/protonate/xbz-protomers.ism' removed directory: `/scratch/xiaobo/316102/xbz-8058115.52/working/protonate' removed `/scratch/xiaobo/316102/xbz-8058115.52/working/input-smiles.ism'