removed `/scratch/xiaobo/45684/xaa-8058097.1/working/protonate/xaa-protonated-manual.ism' removed `/scratch/xiaobo/45684/xaa-8058097.1/working/protonate/xaa-protomers.ism' removed `/scratch/xiaobo/45684/xaa-8058097.1/working/protonate/xaa-protomers-expanded.ism' removed directory: `/scratch/xiaobo/45684/xaa-8058097.1/working/protonate' removed `/scratch/xiaobo/45684/xaa-8058097.1/working/input-smiles.ism'