removed `/scratch/xiaobo/271123/xce-8058088.57/working/protonate/xce-protonated-manual.ism' removed `/scratch/xiaobo/271123/xce-8058088.57/working/protonate/xce-protomers.ism' removed `/scratch/xiaobo/271123/xce-8058088.57/working/protonate/xce-protomers-expanded.ism' removed directory: `/scratch/xiaobo/271123/xce-8058088.57/working/protonate' removed `/scratch/xiaobo/271123/xce-8058088.57/working/input-smiles.ism'