removed `/scratch/xiaobo/19020/xbp-8058097.42/working/protonate/xbp-protomers-expanded.ism' removed `/scratch/xiaobo/19020/xbp-8058097.42/working/protonate/xbp-protomers.ism' removed `/scratch/xiaobo/19020/xbp-8058097.42/working/protonate/xbp-protonated-manual.ism' removed directory: `/scratch/xiaobo/19020/xbp-8058097.42/working/protonate' removed `/scratch/xiaobo/19020/xbp-8058097.42/working/input-smiles.ism'