removed `/scratch/xiaobo/329540/xbb-8058097.28/working/protonate/xbb-protomers-expanded.ism' removed `/scratch/xiaobo/329540/xbb-8058097.28/working/protonate/xbb-protomers.ism' removed `/scratch/xiaobo/329540/xbb-8058097.28/working/protonate/xbb-protonated-manual.ism' removed directory: `/scratch/xiaobo/329540/xbb-8058097.28/working/protonate' removed `/scratch/xiaobo/329540/xbb-8058097.28/working/input-smiles.ism'