removed `/scratch/xiaobo/157140/xas-8058115.19/working/protonate/xas-protonated-manual.ism' removed `/scratch/xiaobo/157140/xas-8058115.19/working/protonate/xas-protomers-expanded.ism' removed `/scratch/xiaobo/157140/xas-8058115.19/working/protonate/xas-protomers.ism' removed directory: `/scratch/xiaobo/157140/xas-8058115.19/working/protonate' removed `/scratch/xiaobo/157140/xas-8058115.19/working/input-smiles.ism'