Starting phenix.real_space_refine (version: dev) on Fri Apr 8 20:49:44 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qxm_4669/04_2022/6qxm_4669.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qxm_4669/04_2022/6qxm_4669.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qxm_4669/04_2022/6qxm_4669.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qxm_4669/04_2022/6qxm_4669.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qxm_4669/04_2022/6qxm_4669.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qxm_4669/04_2022/6qxm_4669.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ASP 23": "OD1" <-> "OD2" Residue "A ASP 107": "OD1" <-> "OD2" Residue "A PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 208": "OD1" <-> "OD2" Residue "A ASP 212": "OD1" <-> "OD2" Residue "A TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A GLU 236": "OE1" <-> "OE2" Residue "A ASP 241": "OD1" <-> "OD2" Residue "A TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 266": "NH1" <-> "NH2" Residue "A TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 318": "OD1" <-> "OD2" Residue "A GLU 325": "OE1" <-> "OE2" Residue "A ASP 326": "OD1" <-> "OD2" Residue "A GLU 333": "OE1" <-> "OE2" Residue "A ASP 337": "OD1" <-> "OD2" Residue "A ARG 351": "NH1" <-> "NH2" Residue "A GLU 380": "OE1" <-> "OE2" Residue "A GLU 382": "OE1" <-> "OE2" Residue "A ASP 383": "OD1" <-> "OD2" Residue "A GLU 395": "OE1" <-> "OE2" Residue "B ASP 23": "OD1" <-> "OD2" Residue "B ASP 107": "OD1" <-> "OD2" Residue "B PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 208": "OD1" <-> "OD2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "B TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 230": "OE1" <-> "OE2" Residue "B GLU 236": "OE1" <-> "OE2" Residue "B ASP 241": "OD1" <-> "OD2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 266": "NH1" <-> "NH2" Residue "B TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 318": "OD1" <-> "OD2" Residue "B GLU 325": "OE1" <-> "OE2" Residue "B ASP 326": "OD1" <-> "OD2" Residue "B GLU 333": "OE1" <-> "OE2" Residue "B ASP 337": "OD1" <-> "OD2" Residue "B ARG 351": "NH1" <-> "NH2" Residue "B GLU 380": "OE1" <-> "OE2" Residue "B GLU 382": "OE1" <-> "OE2" Residue "B ASP 383": "OD1" <-> "OD2" Residue "B GLU 395": "OE1" <-> "OE2" Residue "C ASP 23": "OD1" <-> "OD2" Residue "C ASP 107": "OD1" <-> "OD2" Residue "C PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 208": "OD1" <-> "OD2" Residue "C ASP 212": "OD1" <-> "OD2" Residue "C TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 230": "OE1" <-> "OE2" Residue "C GLU 236": "OE1" <-> "OE2" Residue "C ASP 241": "OD1" <-> "OD2" Residue "C TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 266": "NH1" <-> "NH2" Residue "C TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 318": "OD1" <-> "OD2" Residue "C GLU 325": "OE1" <-> "OE2" Residue "C ASP 326": "OD1" <-> "OD2" Residue "C GLU 333": "OE1" <-> "OE2" Residue "C ASP 337": "OD1" <-> "OD2" Residue "C ARG 351": "NH1" <-> "NH2" Residue "C GLU 380": "OE1" <-> "OE2" Residue "C GLU 382": "OE1" <-> "OE2" Residue "C ASP 383": "OD1" <-> "OD2" Residue "C GLU 395": "OE1" <-> "OE2" Residue "D ASP 23": "OD1" <-> "OD2" Residue "D ASP 107": "OD1" <-> "OD2" Residue "D PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 208": "OD1" <-> "OD2" Residue "D ASP 212": "OD1" <-> "OD2" Residue "D TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 230": "OE1" <-> "OE2" Residue "D GLU 236": "OE1" <-> "OE2" Residue "D ASP 241": "OD1" <-> "OD2" Residue "D TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 266": "NH1" <-> "NH2" Residue "D TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 318": "OD1" <-> "OD2" Residue "D GLU 325": "OE1" <-> "OE2" Residue "D ASP 326": "OD1" <-> "OD2" Residue "D GLU 333": "OE1" <-> "OE2" Residue "D ASP 337": "OD1" <-> "OD2" Residue "D ARG 351": "NH1" <-> "NH2" Residue "D GLU 380": "OE1" <-> "OE2" Residue "D GLU 382": "OE1" <-> "OE2" Residue "D ASP 383": "OD1" <-> "OD2" Residue "D GLU 395": "OE1" <-> "OE2" Residue "E ASP 23": "OD1" <-> "OD2" Residue "E ASP 107": "OD1" <-> "OD2" Residue "E PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 208": "OD1" <-> "OD2" Residue "E ASP 212": "OD1" <-> "OD2" Residue "E TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 230": "OE1" <-> "OE2" Residue "E GLU 236": "OE1" <-> "OE2" Residue "E ASP 241": "OD1" <-> "OD2" Residue "E TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 266": "NH1" <-> "NH2" Residue "E TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 318": "OD1" <-> "OD2" Residue "E GLU 325": "OE1" <-> "OE2" Residue "E ASP 326": "OD1" <-> "OD2" Residue "E GLU 333": "OE1" <-> "OE2" Residue "E ASP 337": "OD1" <-> "OD2" Residue "E ARG 351": "NH1" <-> "NH2" Residue "E GLU 380": "OE1" <-> "OE2" Residue "E GLU 382": "OE1" <-> "OE2" Residue "E ASP 383": "OD1" <-> "OD2" Residue "E GLU 395": "OE1" <-> "OE2" Residue "F ASP 23": "OD1" <-> "OD2" Residue "F ASP 107": "OD1" <-> "OD2" Residue "F PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 208": "OD1" <-> "OD2" Residue "F ASP 212": "OD1" <-> "OD2" Residue "F TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 230": "OE1" <-> "OE2" Residue "F GLU 236": "OE1" <-> "OE2" Residue "F ASP 241": "OD1" <-> "OD2" Residue "F TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 266": "NH1" <-> "NH2" Residue "F TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 318": "OD1" <-> "OD2" Residue "F GLU 325": "OE1" <-> "OE2" Residue "F ASP 326": "OD1" <-> "OD2" Residue "F GLU 333": "OE1" <-> "OE2" Residue "F ASP 337": "OD1" <-> "OD2" Residue "F ARG 351": "NH1" <-> "NH2" Residue "F GLU 380": "OE1" <-> "OE2" Residue "F GLU 382": "OE1" <-> "OE2" Residue "F ASP 383": "OD1" <-> "OD2" Residue "F GLU 395": "OE1" <-> "OE2" Residue "G ASP 23": "OD1" <-> "OD2" Residue "G ASP 107": "OD1" <-> "OD2" Residue "G PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 208": "OD1" <-> "OD2" Residue "G ASP 212": "OD1" <-> "OD2" Residue "G TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 230": "OE1" <-> "OE2" Residue "G GLU 236": "OE1" <-> "OE2" Residue "G ASP 241": "OD1" <-> "OD2" Residue "G TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 266": "NH1" <-> "NH2" Residue "G TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 318": "OD1" <-> "OD2" Residue "G GLU 325": "OE1" <-> "OE2" Residue "G ASP 326": "OD1" <-> "OD2" Residue "G GLU 333": "OE1" <-> "OE2" Residue "G ASP 337": "OD1" <-> "OD2" Residue "G ARG 351": "NH1" <-> "NH2" Residue "G GLU 380": "OE1" <-> "OE2" Residue "G GLU 382": "OE1" <-> "OE2" Residue "G ASP 383": "OD1" <-> "OD2" Residue "G GLU 395": "OE1" <-> "OE2" Residue "H ASP 23": "OD1" <-> "OD2" Residue "H ASP 107": "OD1" <-> "OD2" Residue "H PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 208": "OD1" <-> "OD2" Residue "H ASP 212": "OD1" <-> "OD2" Residue "H TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 230": "OE1" <-> "OE2" Residue "H GLU 236": "OE1" <-> "OE2" Residue "H ASP 241": "OD1" <-> "OD2" Residue "H TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 266": "NH1" <-> "NH2" Residue "H TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 318": "OD1" <-> "OD2" Residue "H GLU 325": "OE1" <-> "OE2" Residue "H ASP 326": "OD1" <-> "OD2" Residue "H GLU 333": "OE1" <-> "OE2" Residue "H ASP 337": "OD1" <-> "OD2" Residue "H ARG 351": "NH1" <-> "NH2" Residue "H GLU 380": "OE1" <-> "OE2" Residue "H GLU 382": "OE1" <-> "OE2" Residue "H ASP 383": "OD1" <-> "OD2" Residue "H GLU 395": "OE1" <-> "OE2" Residue "I ASP 23": "OD1" <-> "OD2" Residue "I ASP 107": "OD1" <-> "OD2" Residue "I PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 208": "OD1" <-> "OD2" Residue "I ASP 212": "OD1" <-> "OD2" Residue "I TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 230": "OE1" <-> "OE2" Residue "I GLU 236": "OE1" <-> "OE2" Residue "I ASP 241": "OD1" <-> "OD2" Residue "I TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 266": "NH1" <-> "NH2" Residue "I TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 318": "OD1" <-> "OD2" Residue "I GLU 325": "OE1" <-> "OE2" Residue "I ASP 326": "OD1" <-> "OD2" Residue "I GLU 333": "OE1" <-> "OE2" Residue "I ASP 337": "OD1" <-> "OD2" Residue "I ARG 351": "NH1" <-> "NH2" Residue "I GLU 380": "OE1" <-> "OE2" Residue "I GLU 382": "OE1" <-> "OE2" Residue "I ASP 383": "OD1" <-> "OD2" Residue "I GLU 395": "OE1" <-> "OE2" Residue "J ASP 23": "OD1" <-> "OD2" Residue "J ASP 107": "OD1" <-> "OD2" Residue "J PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 208": "OD1" <-> "OD2" Residue "J ASP 212": "OD1" <-> "OD2" Residue "J TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 230": "OE1" <-> "OE2" Residue "J GLU 236": "OE1" <-> "OE2" Residue "J ASP 241": "OD1" <-> "OD2" Residue "J TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 266": "NH1" <-> "NH2" Residue "J TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 318": "OD1" <-> "OD2" Residue "J GLU 325": "OE1" <-> "OE2" Residue "J ASP 326": "OD1" <-> "OD2" Residue "J GLU 333": "OE1" <-> "OE2" Residue "J ASP 337": "OD1" <-> "OD2" Residue "J ARG 351": "NH1" <-> "NH2" Residue "J GLU 380": "OE1" <-> "OE2" Residue "J GLU 382": "OE1" <-> "OE2" Residue "J ASP 383": "OD1" <-> "OD2" Residue "J GLU 395": "OE1" <-> "OE2" Residue "K ASP 23": "OD1" <-> "OD2" Residue "K ASP 107": "OD1" <-> "OD2" Residue "K PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 208": "OD1" <-> "OD2" Residue "K ASP 212": "OD1" <-> "OD2" Residue "K TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 230": "OE1" <-> "OE2" Residue "K GLU 236": "OE1" <-> "OE2" Residue "K ASP 241": "OD1" <-> "OD2" Residue "K TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 266": "NH1" <-> "NH2" Residue "K TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 318": "OD1" <-> "OD2" Residue "K GLU 325": "OE1" <-> "OE2" Residue "K ASP 326": "OD1" <-> "OD2" Residue "K GLU 333": "OE1" <-> "OE2" Residue "K ASP 337": "OD1" <-> "OD2" Residue "K ARG 351": "NH1" <-> "NH2" Residue "K GLU 380": "OE1" <-> "OE2" Residue "K GLU 382": "OE1" <-> "OE2" Residue "K ASP 383": "OD1" <-> "OD2" Residue "K GLU 395": "OE1" <-> "OE2" Residue "L ASP 23": "OD1" <-> "OD2" Residue "L ASP 107": "OD1" <-> "OD2" Residue "L PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 208": "OD1" <-> "OD2" Residue "L ASP 212": "OD1" <-> "OD2" Residue "L TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 230": "OE1" <-> "OE2" Residue "L GLU 236": "OE1" <-> "OE2" Residue "L ASP 241": "OD1" <-> "OD2" Residue "L TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 266": "NH1" <-> "NH2" Residue "L TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 318": "OD1" <-> "OD2" Residue "L GLU 325": "OE1" <-> "OE2" Residue "L ASP 326": "OD1" <-> "OD2" Residue "L GLU 333": "OE1" <-> "OE2" Residue "L ASP 337": "OD1" <-> "OD2" Residue "L ARG 351": "NH1" <-> "NH2" Residue "L GLU 380": "OE1" <-> "OE2" Residue "L GLU 382": "OE1" <-> "OE2" Residue "L ASP 383": "OD1" <-> "OD2" Residue "L GLU 395": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 37164 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3097 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 19, 'TRANS': 372} Chain breaks: 2 Chain: "B" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3097 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 19, 'TRANS': 372} Chain breaks: 2 Chain: "C" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3097 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 19, 'TRANS': 372} Chain breaks: 2 Chain: "D" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3097 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 19, 'TRANS': 372} Chain breaks: 2 Chain: "E" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3097 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 19, 'TRANS': 372} Chain breaks: 2 Chain: "F" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3097 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 19, 'TRANS': 372} Chain breaks: 2 Chain: "G" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3097 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 19, 'TRANS': 372} Chain breaks: 2 Chain: "H" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3097 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 19, 'TRANS': 372} Chain breaks: 2 Chain: "I" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3097 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 19, 'TRANS': 372} Chain breaks: 2 Chain: "J" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3097 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 19, 'TRANS': 372} Chain breaks: 2 Chain: "K" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3097 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 19, 'TRANS': 372} Chain breaks: 2 Chain: "L" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3097 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 19, 'TRANS': 372} Chain breaks: 2 Time building chain proxies: 19.57, per 1000 atoms: 0.53 Number of scatterers: 37164 At special positions: 0 Unit cell: (188.24, 188.24, 111.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 168 16.00 O 7200 8.00 N 6264 7.00 C 23532 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.32 Conformation dependent library (CDL) restraints added in 5.4 seconds 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8808 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 48 sheets defined 41.9% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.15 Creating SS restraints... Processing helix chain 'A' and resid 13 through 21 removed outlier: 3.648A pdb=" N TYR A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 36 removed outlier: 3.570A pdb=" N ARG A 30 " --> pdb=" O PRO A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 78 removed outlier: 3.740A pdb=" N ARG A 64 " --> pdb=" O ALA A 60 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN A 67 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU A 75 " --> pdb=" O SER A 71 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A 78 " --> pdb=" O MET A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 124 removed outlier: 3.522A pdb=" N VAL A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE A 117 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N MET A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU A 122 " --> pdb=" O MET A 118 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN A 124 " --> pdb=" O TYR A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 138 removed outlier: 4.226A pdb=" N THR A 129 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE A 131 " --> pdb=" O ARG A 127 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU A 132 " --> pdb=" O VAL A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 199 removed outlier: 3.777A pdb=" N VAL A 198 " --> pdb=" O ILE A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 295 removed outlier: 4.395A pdb=" N ALA A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS A 295 " --> pdb=" O MET A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 313 removed outlier: 3.793A pdb=" N LEU A 311 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS A 313 " --> pdb=" O ARG A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 356 removed outlier: 3.503A pdb=" N THR A 339 " --> pdb=" O GLN A 335 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 386 removed outlier: 4.070A pdb=" N TYR A 376 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY A 386 " --> pdb=" O GLU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 392 Processing helix chain 'A' and resid 396 through 407 removed outlier: 3.714A pdb=" N VAL A 401 " --> pdb=" O GLN A 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 21 Processing helix chain 'B' and resid 24 through 36 removed outlier: 3.570A pdb=" N ARG B 30 " --> pdb=" O PRO B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 78 removed outlier: 3.740A pdb=" N ARG B 64 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN B 67 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU B 75 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE B 78 " --> pdb=" O MET B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 124 removed outlier: 3.523A pdb=" N VAL B 113 " --> pdb=" O GLY B 109 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE B 117 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N MET B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU B 122 " --> pdb=" O MET B 118 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER B 123 " --> pdb=" O ASN B 119 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN B 124 " --> pdb=" O TYR B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 138 removed outlier: 4.226A pdb=" N THR B 129 " --> pdb=" O SER B 125 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU B 132 " --> pdb=" O VAL B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 199 removed outlier: 3.777A pdb=" N VAL B 198 " --> pdb=" O ILE B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 295 removed outlier: 4.395A pdb=" N ALA B 285 " --> pdb=" O ASN B 281 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS B 295 " --> pdb=" O MET B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 313 removed outlier: 3.793A pdb=" N LEU B 311 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS B 313 " --> pdb=" O ARG B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 356 removed outlier: 3.503A pdb=" N THR B 339 " --> pdb=" O GLN B 335 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA B 341 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 386 removed outlier: 4.069A pdb=" N TYR B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY B 386 " --> pdb=" O GLU B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 392 Processing helix chain 'B' and resid 396 through 407 removed outlier: 3.716A pdb=" N VAL B 401 " --> pdb=" O GLN B 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 21 Processing helix chain 'C' and resid 24 through 36 removed outlier: 3.569A pdb=" N ARG C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 78 removed outlier: 3.740A pdb=" N ARG C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN C 67 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU C 75 " --> pdb=" O SER C 71 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE C 78 " --> pdb=" O MET C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 124 removed outlier: 3.522A pdb=" N VAL C 113 " --> pdb=" O GLY C 109 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE C 117 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N MET C 118 " --> pdb=" O GLU C 114 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU C 122 " --> pdb=" O MET C 118 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER C 123 " --> pdb=" O ASN C 119 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN C 124 " --> pdb=" O TYR C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 138 removed outlier: 4.226A pdb=" N THR C 129 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE C 131 " --> pdb=" O ARG C 127 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU C 132 " --> pdb=" O VAL C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 199 removed outlier: 3.777A pdb=" N VAL C 198 " --> pdb=" O ILE C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 295 removed outlier: 4.396A pdb=" N ALA C 285 " --> pdb=" O ASN C 281 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS C 295 " --> pdb=" O MET C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 313 removed outlier: 3.793A pdb=" N LEU C 311 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS C 313 " --> pdb=" O ARG C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 356 removed outlier: 3.503A pdb=" N THR C 339 " --> pdb=" O GLN C 335 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA C 341 " --> pdb=" O ASP C 337 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 386 removed outlier: 4.070A pdb=" N TYR C 376 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY C 386 " --> pdb=" O GLU C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 392 Processing helix chain 'C' and resid 396 through 407 removed outlier: 3.715A pdb=" N VAL C 401 " --> pdb=" O GLN C 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 21 Processing helix chain 'D' and resid 24 through 36 removed outlier: 3.569A pdb=" N ARG D 30 " --> pdb=" O PRO D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 78 removed outlier: 3.740A pdb=" N ARG D 64 " --> pdb=" O ALA D 60 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN D 67 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU D 75 " --> pdb=" O SER D 71 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE D 78 " --> pdb=" O MET D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 124 removed outlier: 3.522A pdb=" N VAL D 113 " --> pdb=" O GLY D 109 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE D 117 " --> pdb=" O VAL D 113 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N MET D 118 " --> pdb=" O GLU D 114 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU D 122 " --> pdb=" O MET D 118 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER D 123 " --> pdb=" O ASN D 119 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN D 124 " --> pdb=" O TYR D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 138 removed outlier: 4.226A pdb=" N THR D 129 " --> pdb=" O SER D 125 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE D 131 " --> pdb=" O ARG D 127 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU D 132 " --> pdb=" O VAL D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 199 removed outlier: 3.777A pdb=" N VAL D 198 " --> pdb=" O ILE D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 295 removed outlier: 4.396A pdb=" N ALA D 285 " --> pdb=" O ASN D 281 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE D 292 " --> pdb=" O LYS D 288 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS D 295 " --> pdb=" O MET D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 313 removed outlier: 3.792A pdb=" N LEU D 311 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS D 313 " --> pdb=" O ARG D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 356 removed outlier: 3.503A pdb=" N THR D 339 " --> pdb=" O GLN D 335 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA D 341 " --> pdb=" O ASP D 337 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE D 354 " --> pdb=" O ALA D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 386 removed outlier: 4.070A pdb=" N TYR D 376 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY D 386 " --> pdb=" O GLU D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 392 Processing helix chain 'D' and resid 396 through 407 removed outlier: 3.715A pdb=" N VAL D 401 " --> pdb=" O GLN D 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 21 Processing helix chain 'E' and resid 24 through 36 removed outlier: 3.569A pdb=" N ARG E 30 " --> pdb=" O PRO E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 78 removed outlier: 3.740A pdb=" N ARG E 64 " --> pdb=" O ALA E 60 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN E 67 " --> pdb=" O ALA E 63 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU E 75 " --> pdb=" O SER E 71 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE E 78 " --> pdb=" O MET E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 124 removed outlier: 3.522A pdb=" N VAL E 113 " --> pdb=" O GLY E 109 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE E 117 " --> pdb=" O VAL E 113 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N MET E 118 " --> pdb=" O GLU E 114 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU E 122 " --> pdb=" O MET E 118 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER E 123 " --> pdb=" O ASN E 119 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN E 124 " --> pdb=" O TYR E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 138 removed outlier: 4.226A pdb=" N THR E 129 " --> pdb=" O SER E 125 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE E 131 " --> pdb=" O ARG E 127 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU E 132 " --> pdb=" O VAL E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 199 removed outlier: 3.777A pdb=" N VAL E 198 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 295 removed outlier: 4.395A pdb=" N ALA E 285 " --> pdb=" O ASN E 281 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS E 295 " --> pdb=" O MET E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 313 removed outlier: 3.793A pdb=" N LEU E 311 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS E 313 " --> pdb=" O ARG E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 356 removed outlier: 3.504A pdb=" N THR E 339 " --> pdb=" O GLN E 335 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL E 340 " --> pdb=" O ALA E 336 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA E 341 " --> pdb=" O ASP E 337 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE E 354 " --> pdb=" O ALA E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 386 removed outlier: 4.070A pdb=" N TYR E 376 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY E 386 " --> pdb=" O GLU E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 392 Processing helix chain 'E' and resid 396 through 407 removed outlier: 3.715A pdb=" N VAL E 401 " --> pdb=" O GLN E 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 21 Processing helix chain 'F' and resid 24 through 36 removed outlier: 3.569A pdb=" N ARG F 30 " --> pdb=" O PRO F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 78 removed outlier: 3.740A pdb=" N ARG F 64 " --> pdb=" O ALA F 60 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN F 67 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU F 75 " --> pdb=" O SER F 71 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE F 78 " --> pdb=" O MET F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 124 removed outlier: 3.522A pdb=" N VAL F 113 " --> pdb=" O GLY F 109 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE F 117 " --> pdb=" O VAL F 113 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N MET F 118 " --> pdb=" O GLU F 114 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU F 122 " --> pdb=" O MET F 118 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER F 123 " --> pdb=" O ASN F 119 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN F 124 " --> pdb=" O TYR F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 138 removed outlier: 4.226A pdb=" N THR F 129 " --> pdb=" O SER F 125 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE F 131 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU F 132 " --> pdb=" O VAL F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 199 removed outlier: 3.777A pdb=" N VAL F 198 " --> pdb=" O ILE F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 295 removed outlier: 4.395A pdb=" N ALA F 285 " --> pdb=" O ASN F 281 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS F 295 " --> pdb=" O MET F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 313 removed outlier: 3.793A pdb=" N LEU F 311 " --> pdb=" O GLN F 307 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS F 313 " --> pdb=" O ARG F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 356 removed outlier: 3.504A pdb=" N THR F 339 " --> pdb=" O GLN F 335 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL F 340 " --> pdb=" O ALA F 336 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA F 341 " --> pdb=" O ASP F 337 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE F 354 " --> pdb=" O ALA F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 386 removed outlier: 4.070A pdb=" N TYR F 376 " --> pdb=" O GLU F 372 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY F 386 " --> pdb=" O GLU F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 392 Processing helix chain 'F' and resid 396 through 407 removed outlier: 3.715A pdb=" N VAL F 401 " --> pdb=" O GLN F 397 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 21 Processing helix chain 'G' and resid 24 through 36 removed outlier: 3.570A pdb=" N ARG G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 78 removed outlier: 3.740A pdb=" N ARG G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU G 75 " --> pdb=" O SER G 71 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE G 78 " --> pdb=" O MET G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 124 removed outlier: 3.521A pdb=" N VAL G 113 " --> pdb=" O GLY G 109 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE G 117 " --> pdb=" O VAL G 113 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N MET G 118 " --> pdb=" O GLU G 114 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU G 122 " --> pdb=" O MET G 118 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER G 123 " --> pdb=" O ASN G 119 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN G 124 " --> pdb=" O TYR G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 138 removed outlier: 4.227A pdb=" N THR G 129 " --> pdb=" O SER G 125 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE G 131 " --> pdb=" O ARG G 127 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU G 132 " --> pdb=" O VAL G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 199 removed outlier: 3.777A pdb=" N VAL G 198 " --> pdb=" O ILE G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 272 through 295 removed outlier: 4.396A pdb=" N ALA G 285 " --> pdb=" O ASN G 281 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE G 292 " --> pdb=" O LYS G 288 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS G 295 " --> pdb=" O MET G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 313 removed outlier: 3.793A pdb=" N LEU G 311 " --> pdb=" O GLN G 307 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS G 313 " --> pdb=" O ARG G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 356 removed outlier: 3.503A pdb=" N THR G 339 " --> pdb=" O GLN G 335 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL G 340 " --> pdb=" O ALA G 336 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA G 341 " --> pdb=" O ASP G 337 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE G 354 " --> pdb=" O ALA G 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 372 through 386 removed outlier: 4.070A pdb=" N TYR G 376 " --> pdb=" O GLU G 372 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY G 386 " --> pdb=" O GLU G 382 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 392 Processing helix chain 'G' and resid 396 through 407 removed outlier: 3.716A pdb=" N VAL G 401 " --> pdb=" O GLN G 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 21 Processing helix chain 'H' and resid 24 through 36 removed outlier: 3.569A pdb=" N ARG H 30 " --> pdb=" O PRO H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 78 removed outlier: 3.740A pdb=" N ARG H 64 " --> pdb=" O ALA H 60 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN H 67 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU H 75 " --> pdb=" O SER H 71 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE H 78 " --> pdb=" O MET H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 124 removed outlier: 3.522A pdb=" N VAL H 113 " --> pdb=" O GLY H 109 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE H 117 " --> pdb=" O VAL H 113 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N MET H 118 " --> pdb=" O GLU H 114 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU H 122 " --> pdb=" O MET H 118 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER H 123 " --> pdb=" O ASN H 119 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN H 124 " --> pdb=" O TYR H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 138 removed outlier: 4.226A pdb=" N THR H 129 " --> pdb=" O SER H 125 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE H 131 " --> pdb=" O ARG H 127 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU H 132 " --> pdb=" O VAL H 128 " (cutoff:3.500A) Processing helix chain 'H' and resid 194 through 199 removed outlier: 3.777A pdb=" N VAL H 198 " --> pdb=" O ILE H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 272 through 295 removed outlier: 4.395A pdb=" N ALA H 285 " --> pdb=" O ASN H 281 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE H 292 " --> pdb=" O LYS H 288 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS H 295 " --> pdb=" O MET H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 307 through 313 removed outlier: 3.794A pdb=" N LEU H 311 " --> pdb=" O GLN H 307 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS H 313 " --> pdb=" O ARG H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 335 through 356 removed outlier: 3.503A pdb=" N THR H 339 " --> pdb=" O GLN H 335 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL H 340 " --> pdb=" O ALA H 336 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA H 341 " --> pdb=" O ASP H 337 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE H 354 " --> pdb=" O ALA H 350 " (cutoff:3.500A) Processing helix chain 'H' and resid 372 through 386 removed outlier: 4.070A pdb=" N TYR H 376 " --> pdb=" O GLU H 372 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY H 386 " --> pdb=" O GLU H 382 " (cutoff:3.500A) Processing helix chain 'H' and resid 387 through 392 Processing helix chain 'H' and resid 396 through 407 removed outlier: 3.715A pdb=" N VAL H 401 " --> pdb=" O GLN H 397 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 21 Processing helix chain 'I' and resid 24 through 36 removed outlier: 3.569A pdb=" N ARG I 30 " --> pdb=" O PRO I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 78 removed outlier: 3.740A pdb=" N ARG I 64 " --> pdb=" O ALA I 60 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN I 67 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU I 75 " --> pdb=" O SER I 71 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE I 78 " --> pdb=" O MET I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 124 removed outlier: 3.522A pdb=" N VAL I 113 " --> pdb=" O GLY I 109 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE I 117 " --> pdb=" O VAL I 113 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N MET I 118 " --> pdb=" O GLU I 114 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU I 122 " --> pdb=" O MET I 118 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER I 123 " --> pdb=" O ASN I 119 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN I 124 " --> pdb=" O TYR I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 138 removed outlier: 4.226A pdb=" N THR I 129 " --> pdb=" O SER I 125 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE I 131 " --> pdb=" O ARG I 127 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU I 132 " --> pdb=" O VAL I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 194 through 199 removed outlier: 3.777A pdb=" N VAL I 198 " --> pdb=" O ILE I 194 " (cutoff:3.500A) Processing helix chain 'I' and resid 272 through 295 removed outlier: 4.396A pdb=" N ALA I 285 " --> pdb=" O ASN I 281 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE I 292 " --> pdb=" O LYS I 288 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS I 295 " --> pdb=" O MET I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 307 through 313 removed outlier: 3.793A pdb=" N LEU I 311 " --> pdb=" O GLN I 307 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS I 313 " --> pdb=" O ARG I 309 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 356 removed outlier: 3.503A pdb=" N THR I 339 " --> pdb=" O GLN I 335 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL I 340 " --> pdb=" O ALA I 336 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA I 341 " --> pdb=" O ASP I 337 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE I 354 " --> pdb=" O ALA I 350 " (cutoff:3.500A) Processing helix chain 'I' and resid 372 through 386 removed outlier: 4.070A pdb=" N TYR I 376 " --> pdb=" O GLU I 372 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY I 386 " --> pdb=" O GLU I 382 " (cutoff:3.500A) Processing helix chain 'I' and resid 387 through 392 Processing helix chain 'I' and resid 396 through 407 removed outlier: 3.714A pdb=" N VAL I 401 " --> pdb=" O GLN I 397 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 21 Processing helix chain 'J' and resid 24 through 36 removed outlier: 3.568A pdb=" N ARG J 30 " --> pdb=" O PRO J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 78 removed outlier: 3.740A pdb=" N ARG J 64 " --> pdb=" O ALA J 60 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN J 67 " --> pdb=" O ALA J 63 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU J 75 " --> pdb=" O SER J 71 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE J 78 " --> pdb=" O MET J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 124 removed outlier: 3.522A pdb=" N VAL J 113 " --> pdb=" O GLY J 109 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE J 117 " --> pdb=" O VAL J 113 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N MET J 118 " --> pdb=" O GLU J 114 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER J 123 " --> pdb=" O ASN J 119 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN J 124 " --> pdb=" O TYR J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 138 removed outlier: 4.226A pdb=" N THR J 129 " --> pdb=" O SER J 125 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE J 131 " --> pdb=" O ARG J 127 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU J 132 " --> pdb=" O VAL J 128 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 199 removed outlier: 3.777A pdb=" N VAL J 198 " --> pdb=" O ILE J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 272 through 295 removed outlier: 4.396A pdb=" N ALA J 285 " --> pdb=" O ASN J 281 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE J 292 " --> pdb=" O LYS J 288 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS J 295 " --> pdb=" O MET J 291 " (cutoff:3.500A) Processing helix chain 'J' and resid 307 through 313 removed outlier: 3.793A pdb=" N LEU J 311 " --> pdb=" O GLN J 307 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS J 313 " --> pdb=" O ARG J 309 " (cutoff:3.500A) Processing helix chain 'J' and resid 335 through 356 removed outlier: 3.503A pdb=" N THR J 339 " --> pdb=" O GLN J 335 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL J 340 " --> pdb=" O ALA J 336 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA J 341 " --> pdb=" O ASP J 337 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE J 354 " --> pdb=" O ALA J 350 " (cutoff:3.500A) Processing helix chain 'J' and resid 372 through 386 removed outlier: 4.070A pdb=" N TYR J 376 " --> pdb=" O GLU J 372 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY J 386 " --> pdb=" O GLU J 382 " (cutoff:3.500A) Processing helix chain 'J' and resid 387 through 392 Processing helix chain 'J' and resid 396 through 407 removed outlier: 3.714A pdb=" N VAL J 401 " --> pdb=" O GLN J 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 21 Processing helix chain 'K' and resid 24 through 36 removed outlier: 3.570A pdb=" N ARG K 30 " --> pdb=" O PRO K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 78 removed outlier: 3.739A pdb=" N ARG K 64 " --> pdb=" O ALA K 60 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN K 67 " --> pdb=" O ALA K 63 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU K 75 " --> pdb=" O SER K 71 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE K 78 " --> pdb=" O MET K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 124 removed outlier: 3.522A pdb=" N VAL K 113 " --> pdb=" O GLY K 109 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE K 117 " --> pdb=" O VAL K 113 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N MET K 118 " --> pdb=" O GLU K 114 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU K 122 " --> pdb=" O MET K 118 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER K 123 " --> pdb=" O ASN K 119 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN K 124 " --> pdb=" O TYR K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 125 through 138 removed outlier: 4.226A pdb=" N THR K 129 " --> pdb=" O SER K 125 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE K 131 " --> pdb=" O ARG K 127 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU K 132 " --> pdb=" O VAL K 128 " (cutoff:3.500A) Processing helix chain 'K' and resid 194 through 199 removed outlier: 3.777A pdb=" N VAL K 198 " --> pdb=" O ILE K 194 " (cutoff:3.500A) Processing helix chain 'K' and resid 272 through 295 removed outlier: 4.395A pdb=" N ALA K 285 " --> pdb=" O ASN K 281 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE K 292 " --> pdb=" O LYS K 288 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS K 295 " --> pdb=" O MET K 291 " (cutoff:3.500A) Processing helix chain 'K' and resid 307 through 313 removed outlier: 3.793A pdb=" N LEU K 311 " --> pdb=" O GLN K 307 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS K 313 " --> pdb=" O ARG K 309 " (cutoff:3.500A) Processing helix chain 'K' and resid 335 through 356 removed outlier: 3.503A pdb=" N THR K 339 " --> pdb=" O GLN K 335 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL K 340 " --> pdb=" O ALA K 336 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA K 341 " --> pdb=" O ASP K 337 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE K 354 " --> pdb=" O ALA K 350 " (cutoff:3.500A) Processing helix chain 'K' and resid 372 through 386 removed outlier: 4.070A pdb=" N TYR K 376 " --> pdb=" O GLU K 372 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY K 386 " --> pdb=" O GLU K 382 " (cutoff:3.500A) Processing helix chain 'K' and resid 387 through 392 Processing helix chain 'K' and resid 396 through 407 removed outlier: 3.715A pdb=" N VAL K 401 " --> pdb=" O GLN K 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 21 Processing helix chain 'L' and resid 24 through 36 removed outlier: 3.569A pdb=" N ARG L 30 " --> pdb=" O PRO L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 60 through 78 removed outlier: 3.740A pdb=" N ARG L 64 " --> pdb=" O ALA L 60 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN L 67 " --> pdb=" O ALA L 63 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU L 75 " --> pdb=" O SER L 71 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE L 78 " --> pdb=" O MET L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 124 removed outlier: 3.523A pdb=" N VAL L 113 " --> pdb=" O GLY L 109 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE L 117 " --> pdb=" O VAL L 113 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N MET L 118 " --> pdb=" O GLU L 114 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU L 122 " --> pdb=" O MET L 118 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER L 123 " --> pdb=" O ASN L 119 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN L 124 " --> pdb=" O TYR L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 138 removed outlier: 4.226A pdb=" N THR L 129 " --> pdb=" O SER L 125 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE L 131 " --> pdb=" O ARG L 127 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU L 132 " --> pdb=" O VAL L 128 " (cutoff:3.500A) Processing helix chain 'L' and resid 194 through 199 removed outlier: 3.777A pdb=" N VAL L 198 " --> pdb=" O ILE L 194 " (cutoff:3.500A) Processing helix chain 'L' and resid 272 through 295 removed outlier: 4.396A pdb=" N ALA L 285 " --> pdb=" O ASN L 281 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE L 292 " --> pdb=" O LYS L 288 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS L 295 " --> pdb=" O MET L 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 307 through 313 removed outlier: 3.793A pdb=" N LEU L 311 " --> pdb=" O GLN L 307 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS L 313 " --> pdb=" O ARG L 309 " (cutoff:3.500A) Processing helix chain 'L' and resid 335 through 356 removed outlier: 3.503A pdb=" N THR L 339 " --> pdb=" O GLN L 335 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL L 340 " --> pdb=" O ALA L 336 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA L 341 " --> pdb=" O ASP L 337 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE L 354 " --> pdb=" O ALA L 350 " (cutoff:3.500A) Processing helix chain 'L' and resid 372 through 386 removed outlier: 4.070A pdb=" N TYR L 376 " --> pdb=" O GLU L 372 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY L 386 " --> pdb=" O GLU L 382 " (cutoff:3.500A) Processing helix chain 'L' and resid 387 through 392 Processing helix chain 'L' and resid 396 through 407 removed outlier: 3.715A pdb=" N VAL L 401 " --> pdb=" O GLN L 397 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 161 removed outlier: 3.630A pdb=" N ILE A 252 " --> pdb=" O LEU A 145 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN A 178 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU A 177 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 211 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN A 178 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU A 177 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 211 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 300 removed outlier: 5.524A pdb=" N GLY A 298 " --> pdb=" O VAL L 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 319 through 321 removed outlier: 3.610A pdb=" N VAL B 300 " --> pdb=" O VAL A 320 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 160 through 161 removed outlier: 3.630A pdb=" N ILE B 252 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN B 178 " --> pdb=" O GLN B 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU B 177 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE B 211 " --> pdb=" O ILE B 185 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN B 178 " --> pdb=" O GLN B 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU B 177 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE B 211 " --> pdb=" O ILE B 185 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 319 through 321 removed outlier: 3.634A pdb=" N VAL C 300 " --> pdb=" O VAL B 320 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 160 through 161 removed outlier: 3.631A pdb=" N ILE C 252 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN C 178 " --> pdb=" O GLN C 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU C 177 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE C 211 " --> pdb=" O ILE C 185 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN C 178 " --> pdb=" O GLN C 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU C 177 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE C 211 " --> pdb=" O ILE C 185 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 319 through 321 removed outlier: 3.670A pdb=" N VAL D 300 " --> pdb=" O VAL C 320 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 160 through 161 removed outlier: 3.630A pdb=" N ILE D 252 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN D 178 " --> pdb=" O GLN D 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU D 177 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE D 211 " --> pdb=" O ILE D 185 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN D 178 " --> pdb=" O GLN D 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU D 177 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE D 211 " --> pdb=" O ILE D 185 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 319 through 321 removed outlier: 3.642A pdb=" N VAL E 300 " --> pdb=" O VAL D 320 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 160 through 161 removed outlier: 3.630A pdb=" N ILE E 252 " --> pdb=" O LEU E 145 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN E 178 " --> pdb=" O GLN E 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU E 177 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE E 211 " --> pdb=" O ILE E 185 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN E 178 " --> pdb=" O GLN E 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU E 177 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE E 211 " --> pdb=" O ILE E 185 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 319 through 321 removed outlier: 3.584A pdb=" N VAL F 300 " --> pdb=" O VAL E 320 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 160 through 161 removed outlier: 3.630A pdb=" N ILE F 252 " --> pdb=" O LEU F 145 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN F 178 " --> pdb=" O GLN F 169 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU F 177 " --> pdb=" O LEU F 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE F 211 " --> pdb=" O ILE F 185 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN F 178 " --> pdb=" O GLN F 169 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU F 177 " --> pdb=" O LEU F 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE F 211 " --> pdb=" O ILE F 185 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 319 through 321 removed outlier: 3.723A pdb=" N VAL G 300 " --> pdb=" O VAL F 320 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 160 through 161 removed outlier: 3.629A pdb=" N ILE G 252 " --> pdb=" O LEU G 145 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN G 178 " --> pdb=" O GLN G 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU G 177 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE G 211 " --> pdb=" O ILE G 185 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN G 178 " --> pdb=" O GLN G 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU G 177 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE G 211 " --> pdb=" O ILE G 185 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 319 through 321 removed outlier: 3.611A pdb=" N VAL H 300 " --> pdb=" O VAL G 320 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 160 through 161 removed outlier: 3.631A pdb=" N ILE H 252 " --> pdb=" O LEU H 145 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN H 178 " --> pdb=" O GLN H 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU H 177 " --> pdb=" O LEU H 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE H 211 " --> pdb=" O ILE H 185 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN H 178 " --> pdb=" O GLN H 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU H 177 " --> pdb=" O LEU H 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE H 211 " --> pdb=" O ILE H 185 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 319 through 321 removed outlier: 3.600A pdb=" N VAL I 300 " --> pdb=" O VAL H 320 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 160 through 161 removed outlier: 3.630A pdb=" N ILE I 252 " --> pdb=" O LEU I 145 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 166 through 170 removed outlier: 3.903A pdb=" N GLN I 178 " --> pdb=" O GLN I 169 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU I 177 " --> pdb=" O LEU I 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE I 211 " --> pdb=" O ILE I 185 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 166 through 170 removed outlier: 3.903A pdb=" N GLN I 178 " --> pdb=" O GLN I 169 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU I 177 " --> pdb=" O LEU I 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE I 211 " --> pdb=" O ILE I 185 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 319 through 321 removed outlier: 3.725A pdb=" N VAL J 300 " --> pdb=" O VAL I 320 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 160 through 161 removed outlier: 3.629A pdb=" N ILE J 252 " --> pdb=" O LEU J 145 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN J 178 " --> pdb=" O GLN J 169 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU J 177 " --> pdb=" O LEU J 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE J 211 " --> pdb=" O ILE J 185 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN J 178 " --> pdb=" O GLN J 169 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU J 177 " --> pdb=" O LEU J 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE J 211 " --> pdb=" O ILE J 185 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 319 through 321 removed outlier: 3.613A pdb=" N VAL K 300 " --> pdb=" O VAL J 320 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 160 through 161 removed outlier: 3.630A pdb=" N ILE K 252 " --> pdb=" O LEU K 145 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 166 through 170 removed outlier: 3.901A pdb=" N GLN K 178 " --> pdb=" O GLN K 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU K 177 " --> pdb=" O LEU K 219 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE K 211 " --> pdb=" O ILE K 185 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 166 through 170 removed outlier: 3.901A pdb=" N GLN K 178 " --> pdb=" O GLN K 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU K 177 " --> pdb=" O LEU K 219 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE K 211 " --> pdb=" O ILE K 185 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 319 through 321 removed outlier: 3.583A pdb=" N VAL L 300 " --> pdb=" O VAL K 320 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 160 through 161 removed outlier: 3.629A pdb=" N ILE L 252 " --> pdb=" O LEU L 145 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 166 through 170 removed outlier: 3.901A pdb=" N GLN L 178 " --> pdb=" O GLN L 169 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU L 177 " --> pdb=" O LEU L 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE L 211 " --> pdb=" O ILE L 185 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 166 through 170 removed outlier: 3.901A pdb=" N GLN L 178 " --> pdb=" O GLN L 169 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU L 177 " --> pdb=" O LEU L 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE L 211 " --> pdb=" O ILE L 185 " (cutoff:3.500A) 1595 hydrogen bonds defined for protein. 4641 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.55 Time building geometry restraints manager: 15.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12229 1.34 - 1.46: 6591 1.46 - 1.58: 18632 1.58 - 1.69: 24 1.69 - 1.81: 312 Bond restraints: 37788 Sorted by residual: bond pdb=" C LEU E 417 " pdb=" N PRO E 418 " ideal model delta sigma weight residual 1.328 1.377 -0.049 1.25e-02 6.40e+03 1.52e+01 bond pdb=" C LEU I 417 " pdb=" N PRO I 418 " ideal model delta sigma weight residual 1.328 1.376 -0.048 1.25e-02 6.40e+03 1.50e+01 bond pdb=" C LEU F 417 " pdb=" N PRO F 418 " ideal model delta sigma weight residual 1.328 1.376 -0.048 1.25e-02 6.40e+03 1.49e+01 bond pdb=" C LEU C 417 " pdb=" N PRO C 418 " ideal model delta sigma weight residual 1.328 1.376 -0.048 1.25e-02 6.40e+03 1.47e+01 bond pdb=" C LEU J 417 " pdb=" N PRO J 418 " ideal model delta sigma weight residual 1.328 1.376 -0.048 1.25e-02 6.40e+03 1.47e+01 ... (remaining 37783 not shown) Histogram of bond angle deviations from ideal: 97.43 - 104.75: 780 104.75 - 112.07: 16879 112.07 - 119.38: 14044 119.38 - 126.70: 19127 126.70 - 134.02: 302 Bond angle restraints: 51132 Sorted by residual: angle pdb=" N ILE I 305 " pdb=" CA ILE I 305 " pdb=" C ILE I 305 " ideal model delta sigma weight residual 112.96 106.84 6.12 1.00e+00 1.00e+00 3.75e+01 angle pdb=" N ILE D 305 " pdb=" CA ILE D 305 " pdb=" C ILE D 305 " ideal model delta sigma weight residual 112.96 106.85 6.11 1.00e+00 1.00e+00 3.73e+01 angle pdb=" N ILE H 305 " pdb=" CA ILE H 305 " pdb=" C ILE H 305 " ideal model delta sigma weight residual 112.96 106.86 6.10 1.00e+00 1.00e+00 3.72e+01 angle pdb=" N ILE B 305 " pdb=" CA ILE B 305 " pdb=" C ILE B 305 " ideal model delta sigma weight residual 112.96 106.86 6.10 1.00e+00 1.00e+00 3.72e+01 angle pdb=" N ILE E 305 " pdb=" CA ILE E 305 " pdb=" C ILE E 305 " ideal model delta sigma weight residual 112.96 106.87 6.09 1.00e+00 1.00e+00 3.71e+01 ... (remaining 51127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 19316 17.23 - 34.46: 2657 34.46 - 51.69: 935 51.69 - 68.92: 240 68.92 - 86.15: 96 Dihedral angle restraints: 23244 sinusoidal: 9516 harmonic: 13728 Sorted by residual: dihedral pdb=" CA GLN H 59 " pdb=" C GLN H 59 " pdb=" N ALA H 60 " pdb=" CA ALA H 60 " ideal model delta harmonic sigma weight residual 180.00 -153.75 -26.25 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA GLN A 59 " pdb=" C GLN A 59 " pdb=" N ALA A 60 " pdb=" CA ALA A 60 " ideal model delta harmonic sigma weight residual -180.00 -153.77 -26.23 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA GLN F 59 " pdb=" C GLN F 59 " pdb=" N ALA F 60 " pdb=" CA ALA F 60 " ideal model delta harmonic sigma weight residual -180.00 -153.77 -26.23 0 5.00e+00 4.00e-02 2.75e+01 ... (remaining 23241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 4242 0.059 - 0.117: 1159 0.117 - 0.176: 325 0.176 - 0.234: 22 0.234 - 0.293: 12 Chirality restraints: 5760 Sorted by residual: chirality pdb=" CB VAL F 237 " pdb=" CA VAL F 237 " pdb=" CG1 VAL F 237 " pdb=" CG2 VAL F 237 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CB VAL B 237 " pdb=" CA VAL B 237 " pdb=" CG1 VAL B 237 " pdb=" CG2 VAL B 237 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CB VAL C 237 " pdb=" CA VAL C 237 " pdb=" CG1 VAL C 237 " pdb=" CG2 VAL C 237 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 5757 not shown) Planarity restraints: 6660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS I 419 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.64e+00 pdb=" C LYS I 419 " 0.048 2.00e-02 2.50e+03 pdb=" O LYS I 419 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU I 420 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 419 " 0.014 2.00e-02 2.50e+03 2.76e-02 7.61e+00 pdb=" C LYS C 419 " -0.048 2.00e-02 2.50e+03 pdb=" O LYS C 419 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU C 420 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 419 " 0.014 2.00e-02 2.50e+03 2.76e-02 7.59e+00 pdb=" C LYS D 419 " -0.048 2.00e-02 2.50e+03 pdb=" O LYS D 419 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU D 420 " 0.016 2.00e-02 2.50e+03 ... (remaining 6657 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 12389 2.85 - 3.36: 33862 3.36 - 3.87: 59613 3.87 - 4.39: 63121 4.39 - 4.90: 108188 Nonbonded interactions: 277173 Sorted by model distance: nonbonded pdb=" O GLU B 380 " pdb=" OG1 THR B 384 " model vdw 2.333 2.440 nonbonded pdb=" O GLU G 380 " pdb=" OG1 THR G 384 " model vdw 2.333 2.440 nonbonded pdb=" O GLU F 380 " pdb=" OG1 THR F 384 " model vdw 2.333 2.440 nonbonded pdb=" O GLU H 380 " pdb=" OG1 THR H 384 " model vdw 2.333 2.440 nonbonded pdb=" O GLU I 380 " pdb=" OG1 THR I 384 " model vdw 2.333 2.440 ... (remaining 277168 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 168 5.16 5 C 23532 2.51 5 N 6264 2.21 5 O 7200 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.10 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 6.320 Check model and map are aligned: 0.550 Convert atoms to be neutral: 0.340 Process input model: 87.430 Find NCS groups from input model: 2.590 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.062 37788 Z= 0.507 Angle : 1.251 13.257 51132 Z= 0.719 Chirality : 0.058 0.293 5760 Planarity : 0.008 0.068 6660 Dihedral : 18.913 86.145 14436 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer Outliers : 8.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.78 (0.09), residues: 4632 helix: -3.25 (0.07), residues: 1728 sheet: -1.94 (0.17), residues: 576 loop : -3.47 (0.11), residues: 2328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1365 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 348 poor density : 1017 time to evaluate : 4.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 348 outliers final: 138 residues processed: 1269 average time/residue: 0.5008 time to fit residues: 1020.6372 Evaluate side-chains 970 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 832 time to evaluate : 4.272 Switching outliers to nearest non-outliers outliers start: 138 outliers final: 0 residues processed: 138 average time/residue: 0.4137 time to fit residues: 105.4308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 395 optimal weight: 5.9990 chunk 354 optimal weight: 0.9980 chunk 196 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 239 optimal weight: 2.9990 chunk 189 optimal weight: 5.9990 chunk 366 optimal weight: 0.7980 chunk 141 optimal weight: 0.9990 chunk 223 optimal weight: 9.9990 chunk 273 optimal weight: 10.0000 chunk 424 optimal weight: 0.0030 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN A 201 GLN A 409 GLN B 124 ASN B 175 ASN B 201 GLN B 409 GLN C 175 ASN C 184 GLN C 201 GLN C 409 GLN D 201 GLN D 409 GLN E 124 ASN E 175 ASN E 201 GLN E 409 GLN F 124 ASN F 175 ASN F 201 GLN ** F 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 409 GLN G 124 ASN G 175 ASN G 201 GLN G 409 GLN H 124 ASN H 175 ASN H 201 GLN ** H 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 409 GLN I 124 ASN I 175 ASN I 201 GLN ** I 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 409 GLN J 124 ASN J 201 GLN J 409 GLN K 124 ASN K 175 ASN K 201 GLN ** K 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 409 GLN L 175 ASN L 184 GLN L 201 GLN ** L 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 409 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 37788 Z= 0.213 Angle : 0.698 8.454 51132 Z= 0.355 Chirality : 0.043 0.148 5760 Planarity : 0.005 0.055 6660 Dihedral : 5.707 25.739 5208 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.11), residues: 4632 helix: -1.42 (0.11), residues: 1836 sheet: -1.62 (0.18), residues: 576 loop : -3.18 (0.11), residues: 2220 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 940 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 933 time to evaluate : 4.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 933 average time/residue: 0.4670 time to fit residues: 713.0414 Evaluate side-chains 828 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 827 time to evaluate : 4.231 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3110 time to fit residues: 6.6985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 236 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 chunk 353 optimal weight: 0.9990 chunk 289 optimal weight: 0.0050 chunk 117 optimal weight: 10.0000 chunk 425 optimal weight: 0.8980 chunk 459 optimal weight: 3.9990 chunk 379 optimal weight: 6.9990 chunk 422 optimal weight: 6.9990 chunk 145 optimal weight: 10.0000 chunk 341 optimal weight: 3.9990 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN A 394 GLN A 412 GLN B 124 ASN B 335 GLN B 412 GLN C 124 ASN C 281 ASN C 412 GLN D 175 ASN D 412 GLN E 124 ASN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 ASN F 175 ASN F 281 ASN F 412 GLN G 81 GLN G 394 GLN G 412 GLN H 124 ASN H 412 GLN I 281 ASN I 412 GLN J 81 GLN J 394 GLN J 412 GLN K 124 ASN K 412 GLN L 124 ASN L 412 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 37788 Z= 0.210 Angle : 0.631 8.063 51132 Z= 0.319 Chirality : 0.042 0.148 5760 Planarity : 0.005 0.053 6660 Dihedral : 5.176 23.536 5208 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.12), residues: 4632 helix: -0.50 (0.12), residues: 1788 sheet: -1.25 (0.18), residues: 636 loop : -2.86 (0.12), residues: 2208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 929 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 919 time to evaluate : 4.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 922 average time/residue: 0.4621 time to fit residues: 701.3453 Evaluate side-chains 829 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 826 time to evaluate : 4.507 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3114 time to fit residues: 8.1969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 420 optimal weight: 3.9990 chunk 320 optimal weight: 3.9990 chunk 220 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 203 optimal weight: 2.9990 chunk 285 optimal weight: 0.6980 chunk 427 optimal weight: 9.9990 chunk 452 optimal weight: 0.7980 chunk 223 optimal weight: 0.0270 chunk 404 optimal weight: 0.0470 chunk 121 optimal weight: 1.9990 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN A 394 GLN B 124 ASN ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN E 124 ASN E 394 GLN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 ASN H 124 ASN H 394 GLN I 124 ASN J 124 ASN ** J 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 124 ASN ** L 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 281 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6553 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 37788 Z= 0.167 Angle : 0.601 8.014 51132 Z= 0.303 Chirality : 0.041 0.164 5760 Planarity : 0.005 0.053 6660 Dihedral : 4.960 21.901 5208 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.12), residues: 4632 helix: -0.05 (0.13), residues: 1812 sheet: -1.11 (0.19), residues: 564 loop : -2.81 (0.12), residues: 2256 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 890 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 884 time to evaluate : 4.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 885 average time/residue: 0.4687 time to fit residues: 685.3993 Evaluate side-chains 800 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 799 time to evaluate : 4.141 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3202 time to fit residues: 6.7689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 376 optimal weight: 7.9990 chunk 256 optimal weight: 0.5980 chunk 6 optimal weight: 7.9990 chunk 336 optimal weight: 0.6980 chunk 186 optimal weight: 4.9990 chunk 386 optimal weight: 0.4980 chunk 312 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 230 optimal weight: 4.9990 chunk 406 optimal weight: 9.9990 chunk 114 optimal weight: 0.7980 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 394 GLN B 124 ASN B 283 GLN B 335 GLN B 394 GLN C 307 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 ASN E 136 GLN E 283 GLN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 ASN G 32 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 394 GLN H 124 ASN H 394 GLN I 124 ASN J 32 GLN J 394 GLN K 124 ASN L 307 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 37788 Z= 0.217 Angle : 0.622 8.547 51132 Z= 0.310 Chirality : 0.042 0.170 5760 Planarity : 0.005 0.056 6660 Dihedral : 4.904 20.635 5208 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.12), residues: 4632 helix: 0.32 (0.13), residues: 1764 sheet: -0.94 (0.20), residues: 564 loop : -2.61 (0.12), residues: 2304 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 910 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 902 time to evaluate : 4.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 904 average time/residue: 0.4741 time to fit residues: 703.9413 Evaluate side-chains 807 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 805 time to evaluate : 4.510 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3954 time to fit residues: 7.6874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 152 optimal weight: 2.9990 chunk 407 optimal weight: 9.9990 chunk 89 optimal weight: 0.9990 chunk 265 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 452 optimal weight: 0.7980 chunk 375 optimal weight: 0.8980 chunk 209 optimal weight: 5.9990 chunk 37 optimal weight: 0.1980 chunk 149 optimal weight: 20.0000 chunk 237 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 124 ASN B 136 GLN B 178 GLN C 175 ASN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 ASN D 307 GLN E 124 ASN E 136 GLN E 409 GLN E 412 GLN F 124 ASN F 307 GLN ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 ASN H 178 GLN J 307 GLN J 394 GLN K 124 ASN K 136 GLN K 178 GLN ** K 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6558 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 37788 Z= 0.175 Angle : 0.585 7.476 51132 Z= 0.293 Chirality : 0.041 0.175 5760 Planarity : 0.004 0.062 6660 Dihedral : 4.803 22.334 5208 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.12), residues: 4632 helix: 0.53 (0.13), residues: 1764 sheet: -0.81 (0.20), residues: 564 loop : -2.52 (0.12), residues: 2304 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 895 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 890 time to evaluate : 4.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 890 average time/residue: 0.4718 time to fit residues: 694.4209 Evaluate side-chains 793 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 793 time to evaluate : 4.247 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.0795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 436 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 257 optimal weight: 0.9990 chunk 330 optimal weight: 9.9990 chunk 256 optimal weight: 0.9990 chunk 381 optimal weight: 0.8980 chunk 252 optimal weight: 10.0000 chunk 451 optimal weight: 7.9990 chunk 282 optimal weight: 0.6980 chunk 275 optimal weight: 0.6980 chunk 208 optimal weight: 9.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN A 307 GLN B 124 ASN B 178 GLN C 124 ASN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 ASN F 124 ASN G 136 GLN H 124 ASN H 136 GLN H 178 GLN I 124 ASN J 136 GLN J 307 GLN J 394 GLN K 124 ASN K 178 GLN ** K 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 124 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6554 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 37788 Z= 0.179 Angle : 0.592 7.977 51132 Z= 0.296 Chirality : 0.041 0.187 5760 Planarity : 0.004 0.073 6660 Dihedral : 4.734 21.317 5208 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.12), residues: 4632 helix: 0.78 (0.13), residues: 1740 sheet: -0.44 (0.21), residues: 492 loop : -2.41 (0.12), residues: 2400 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 890 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 882 time to evaluate : 4.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 0 residues processed: 882 average time/residue: 0.4713 time to fit residues: 690.7816 Evaluate side-chains 802 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 802 time to evaluate : 4.417 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.2200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 279 optimal weight: 4.9990 chunk 180 optimal weight: 0.6980 chunk 269 optimal weight: 0.9980 chunk 135 optimal weight: 9.9990 chunk 88 optimal weight: 7.9990 chunk 87 optimal weight: 0.8980 chunk 286 optimal weight: 0.8980 chunk 307 optimal weight: 9.9990 chunk 223 optimal weight: 0.9980 chunk 42 optimal weight: 0.0020 chunk 354 optimal weight: 4.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN A 394 GLN B 124 ASN B 175 ASN B 178 GLN C 124 ASN ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 GLN D 178 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 ASN G 124 ASN G 136 GLN H 124 ASN H 178 GLN I 124 ASN J 124 ASN J 394 GLN K 124 ASN K 178 GLN K 407 GLN L 124 ASN ** L 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.093 37788 Z= 0.178 Angle : 0.587 7.244 51132 Z= 0.293 Chirality : 0.041 0.196 5760 Planarity : 0.005 0.067 6660 Dihedral : 4.661 22.016 5208 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.12), residues: 4632 helix: 0.91 (0.13), residues: 1740 sheet: -0.36 (0.21), residues: 492 loop : -2.34 (0.12), residues: 2400 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 870 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 861 time to evaluate : 4.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 862 average time/residue: 0.4559 time to fit residues: 652.9832 Evaluate side-chains 789 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 788 time to evaluate : 4.238 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3103 time to fit residues: 6.7734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 410 optimal weight: 2.9990 chunk 432 optimal weight: 0.8980 chunk 394 optimal weight: 1.9990 chunk 420 optimal weight: 0.9990 chunk 253 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 330 optimal weight: 10.0000 chunk 128 optimal weight: 0.3980 chunk 379 optimal weight: 2.9990 chunk 397 optimal weight: 0.9980 chunk 418 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN B 32 GLN B 124 ASN B 178 GLN C 124 ASN C 178 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 ASN D 136 GLN D 178 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 ASN E 136 GLN F 32 GLN G 32 GLN G 136 GLN H 124 ASN H 178 GLN I 136 GLN J 124 ASN K 124 ASN K 136 GLN K 178 GLN K 407 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6558 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.106 37788 Z= 0.198 Angle : 0.590 7.913 51132 Z= 0.295 Chirality : 0.042 0.200 5760 Planarity : 0.004 0.058 6660 Dihedral : 4.641 20.403 5208 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.12), residues: 4632 helix: 0.68 (0.13), residues: 1824 sheet: -0.24 (0.20), residues: 492 loop : -2.40 (0.12), residues: 2316 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 861 time to evaluate : 4.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 0 residues processed: 862 average time/residue: 0.4712 time to fit residues: 671.4443 Evaluate side-chains 786 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 786 time to evaluate : 4.485 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.2721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 276 optimal weight: 0.0770 chunk 444 optimal weight: 0.9990 chunk 271 optimal weight: 0.0980 chunk 210 optimal weight: 30.0000 chunk 308 optimal weight: 6.9990 chunk 466 optimal weight: 3.9990 chunk 429 optimal weight: 10.0000 chunk 371 optimal weight: 6.9990 chunk 38 optimal weight: 0.4980 chunk 286 optimal weight: 4.9990 chunk 227 optimal weight: 4.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 124 ASN B 178 GLN C 124 ASN C 136 GLN C 178 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 ASN D 178 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 ASN G 124 ASN G 178 GLN H 124 ASN H 178 GLN I 136 GLN I 307 GLN K 124 ASN K 136 GLN K 178 GLN ** K 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 136 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6568 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.113 37788 Z= 0.202 Angle : 0.602 8.723 51132 Z= 0.301 Chirality : 0.042 0.204 5760 Planarity : 0.004 0.062 6660 Dihedral : 4.632 21.083 5208 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.12), residues: 4632 helix: 0.61 (0.13), residues: 1848 sheet: -0.17 (0.21), residues: 492 loop : -2.35 (0.12), residues: 2292 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 855 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 849 time to evaluate : 4.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 849 average time/residue: 0.4616 time to fit residues: 655.1101 Evaluate side-chains 788 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 787 time to evaluate : 4.132 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3218 time to fit residues: 6.5260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 294 optimal weight: 5.9990 chunk 395 optimal weight: 0.0770 chunk 113 optimal weight: 4.9990 chunk 342 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 371 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 381 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 68 optimal weight: 0.0020 overall best weight: 0.3946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN B 124 ASN B 178 GLN C 178 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 GLN D 283 GLN E 124 ASN G 32 GLN G 178 GLN H 124 ASN H 136 GLN H 178 GLN I 124 ASN I 136 GLN J 32 GLN J 216 HIS K 124 ASN K 178 GLN ** K 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.181722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.150568 restraints weight = 51670.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.154733 restraints weight = 32830.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.157601 restraints weight = 23098.014| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4180 r_free = 0.4180 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4168 r_free = 0.4168 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 58 | |-----------------------------------------------------------------------------| r_final: 0.4168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6468 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.134 37788 Z= 0.183 Angle : 0.587 10.553 51132 Z= 0.292 Chirality : 0.041 0.205 5760 Planarity : 0.004 0.070 6660 Dihedral : 4.506 20.344 5208 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.12), residues: 4632 helix: 0.80 (0.13), residues: 1848 sheet: -0.06 (0.21), residues: 492 loop : -2.29 (0.12), residues: 2292 =============================================================================== Job complete usr+sys time: 10605.46 seconds wall clock time: 190 minutes 42.92 seconds (11442.92 seconds total)