Starting phenix.real_space_refine on Mon Feb 19 02:01:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m15_30037/02_2024/6m15_30037_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m15_30037/02_2024/6m15_30037.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m15_30037/02_2024/6m15_30037.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m15_30037/02_2024/6m15_30037.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m15_30037/02_2024/6m15_30037_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m15_30037/02_2024/6m15_30037_neut.pdb" } resolution = 2.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.000 sd= 0.008 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 129 5.16 5 C 14889 2.51 5 N 3840 2.21 5 O 4613 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 205": "NH1" <-> "NH2" Residue "B TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 468": "NH1" <-> "NH2" Residue "B PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 543": "NH1" <-> "NH2" Residue "B ARG 607": "NH1" <-> "NH2" Residue "B ARG 620": "NH1" <-> "NH2" Residue "B ARG 671": "NH1" <-> "NH2" Residue "B ARG 964": "NH1" <-> "NH2" Residue "B ARG 982": "NH1" <-> "NH2" Residue "B ARG 991": "NH1" <-> "NH2" Residue "A PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 205": "NH1" <-> "NH2" Residue "A TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 468": "NH1" <-> "NH2" Residue "A PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 543": "NH1" <-> "NH2" Residue "A ARG 607": "NH1" <-> "NH2" Residue "A ARG 620": "NH1" <-> "NH2" Residue "A ARG 671": "NH1" <-> "NH2" Residue "A ARG 964": "NH1" <-> "NH2" Residue "A ARG 982": "NH1" <-> "NH2" Residue "A ARG 991": "NH1" <-> "NH2" Residue "C PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 205": "NH1" <-> "NH2" Residue "C TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 468": "NH1" <-> "NH2" Residue "C PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 543": "NH1" <-> "NH2" Residue "C ARG 607": "NH1" <-> "NH2" Residue "C ARG 620": "NH1" <-> "NH2" Residue "C ARG 671": "NH1" <-> "NH2" Residue "C ARG 964": "NH1" <-> "NH2" Residue "C ARG 982": "NH1" <-> "NH2" Residue "C ARG 991": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23471 Number of models: 1 Model: "" Number of chains: 30 Chain: "B" Number of atoms: 7467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 965, 7467 Classifications: {'peptide': 965} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 925} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 53 Chain: "A" Number of atoms: 7467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 965, 7467 Classifications: {'peptide': 965} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 925} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 53 Chain: "C" Number of atoms: 7467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 965, 7467 Classifications: {'peptide': 965} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 925} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 53 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Time building chain proxies: 12.29, per 1000 atoms: 0.52 Number of scatterers: 23471 At special positions: 0 Unit cell: (132.625, 126.259, 162.333, 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 129 16.00 O 4613 8.00 N 3840 7.00 C 14889 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS B 17 " - pdb=" SG CYS B 56 " distance=2.03 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 234 " - pdb=" SG CYS B 244 " distance=2.02 Simple disulfide: pdb=" SG CYS B 277 " - pdb=" SG CYS B 300 " distance=2.03 Simple disulfide: pdb=" SG CYS B 285 " - pdb=" SG CYS B 290 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 369 " distance=2.03 Simple disulfide: pdb=" SG CYS B 341 " - pdb=" SG CYS B 397 " distance=2.04 Simple disulfide: pdb=" SG CYS B 409 " - pdb=" SG CYS B 458 " distance=2.05 Simple disulfide: pdb=" SG CYS B 482 " - pdb=" SG CYS B 509 " distance=2.02 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 533 " distance=2.03 Simple disulfide: pdb=" SG CYS B 590 " - pdb=" SG CYS B 612 " distance=2.03 Simple disulfide: pdb=" SG CYS B 595 " - pdb=" SG CYS B 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 696 " - pdb=" SG CYS B 706 " distance=2.04 Simple disulfide: pdb=" SG CYS B 884 " - pdb=" SG CYS B 895 " distance=2.03 Simple disulfide: pdb=" SG CYS B 934 " - pdb=" SG CYS B 943 " distance=2.03 Simple disulfide: pdb=" SG CYS A 17 " - pdb=" SG CYS A 56 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 244 " distance=2.02 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS A 300 " distance=2.03 Simple disulfide: pdb=" SG CYS A 285 " - pdb=" SG CYS A 290 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 369 " distance=2.03 Simple disulfide: pdb=" SG CYS A 341 " - pdb=" SG CYS A 397 " distance=2.04 Simple disulfide: pdb=" SG CYS A 409 " - pdb=" SG CYS A 458 " distance=2.05 Simple disulfide: pdb=" SG CYS A 482 " - pdb=" SG CYS A 509 " distance=2.02 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 533 " distance=2.03 Simple disulfide: pdb=" SG CYS A 590 " - pdb=" SG CYS A 612 " distance=2.03 Simple disulfide: pdb=" SG CYS A 595 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS A 696 " - pdb=" SG CYS A 706 " distance=2.04 Simple disulfide: pdb=" SG CYS A 884 " - pdb=" SG CYS A 895 " distance=2.03 Simple disulfide: pdb=" SG CYS A 934 " - pdb=" SG CYS A 943 " distance=2.03 Simple disulfide: pdb=" SG CYS C 17 " - pdb=" SG CYS C 56 " distance=2.03 Simple disulfide: pdb=" SG CYS C 124 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 234 " - pdb=" SG CYS C 244 " distance=2.02 Simple disulfide: pdb=" SG CYS C 277 " - pdb=" SG CYS C 300 " distance=2.03 Simple disulfide: pdb=" SG CYS C 285 " - pdb=" SG CYS C 290 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 369 " distance=2.03 Simple disulfide: pdb=" SG CYS C 341 " - pdb=" SG CYS C 397 " distance=2.04 Simple disulfide: pdb=" SG CYS C 409 " - pdb=" SG CYS C 458 " distance=2.05 Simple disulfide: pdb=" SG CYS C 482 " - pdb=" SG CYS C 509 " distance=2.02 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 533 " distance=2.03 Simple disulfide: pdb=" SG CYS C 590 " - pdb=" SG CYS C 612 " distance=2.03 Simple disulfide: pdb=" SG CYS C 595 " - pdb=" SG CYS C 601 " distance=2.03 Simple disulfide: pdb=" SG CYS C 696 " - pdb=" SG CYS C 706 " distance=2.04 Simple disulfide: pdb=" SG CYS C 884 " - pdb=" SG CYS C 895 " distance=2.03 Simple disulfide: pdb=" SG CYS C 934 " - pdb=" SG CYS C 943 " distance=2.03 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " NAG-ASN " NAG A1203 " - " ASN A 985 " " NAG A1204 " - " ASN A 37 " " NAG A1207 " - " ASN A 118 " " NAG A1210 " - " ASN A 273 " " NAG A1213 " - " ASN A 356 " " NAG A1214 " - " ASN A 427 " " NAG A1218 " - " ASN A 523 " " NAG A1221 " - " ASN A 922 " " NAG B1203 " - " ASN B 985 " " NAG B1204 " - " ASN B 37 " " NAG B1207 " - " ASN B 118 " " NAG B1210 " - " ASN B 273 " " NAG B1213 " - " ASN B 356 " " NAG B1214 " - " ASN B 427 " " NAG B1218 " - " ASN B 523 " " NAG B1221 " - " ASN B 922 " " NAG C1203 " - " ASN C 985 " " NAG C1204 " - " ASN C 37 " " NAG C1207 " - " ASN C 118 " " NAG C1210 " - " ASN C 273 " " NAG C1213 " - " ASN C 356 " " NAG C1214 " - " ASN C 427 " " NAG C1218 " - " ASN C 523 " " NAG C1221 " - " ASN C 922 " " NAG D 1 " - " ASN B 955 " " NAG E 1 " - " ASN B 102 " " NAG F 1 " - " ASN B 152 " " NAG G 1 " - " ASN B 303 " " NAG H 1 " - " ASN B 501 " " NAG I 1 " - " ASN B 652 " " NAG J 1 " - " ASN B 971 " " NAG K 1 " - " ASN A 955 " " NAG L 1 " - " ASN A 102 " " NAG M 1 " - " ASN A 152 " " NAG N 1 " - " ASN A 303 " " NAG O 1 " - " ASN A 501 " " NAG P 1 " - " ASN A 652 " " NAG Q 1 " - " ASN A 971 " " NAG R 1 " - " ASN C 955 " " NAG S 1 " - " ASN C 102 " " NAG T 1 " - " ASN C 152 " " NAG U 1 " - " ASN C 303 " " NAG V 1 " - " ASN C 501 " " NAG W 1 " - " ASN C 652 " " NAG X 1 " - " ASN C 971 " Time building additional restraints: 9.68 Conformation dependent library (CDL) restraints added in 4.6 seconds 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5352 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 36 sheets defined 25.0% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.05 Creating SS restraints... Processing helix chain 'B' and resid 21 through 29 removed outlier: 3.776A pdb=" N ASN B 26 " --> pdb=" O ARG B 23 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY B 27 " --> pdb=" O LEU B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 52 No H-bonds generated for 'chain 'B' and resid 50 through 52' Processing helix chain 'B' and resid 237 through 247 removed outlier: 3.542A pdb=" N LEU B 242 " --> pdb=" O PHE B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 308 removed outlier: 3.550A pdb=" N THR B 308 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 316 removed outlier: 3.955A pdb=" N TYR B 315 " --> pdb=" O LEU B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 319 No H-bonds generated for 'chain 'B' and resid 317 through 319' Processing helix chain 'B' and resid 483 through 488 Processing helix chain 'B' and resid 497 through 501 removed outlier: 3.580A pdb=" N ASN B 501 " --> pdb=" O PRO B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 595 Processing helix chain 'B' and resid 598 through 603 Processing helix chain 'B' and resid 604 through 608 removed outlier: 3.502A pdb=" N ARG B 607 " --> pdb=" O LEU B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 638 removed outlier: 3.583A pdb=" N ARG B 620 " --> pdb=" O GLU B 616 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY B 632 " --> pdb=" O SER B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 681 Processing helix chain 'B' and resid 688 through 700 Processing helix chain 'B' and resid 721 through 725 Processing helix chain 'B' and resid 749 through 761 Processing helix chain 'B' and resid 768 through 785 Processing helix chain 'B' and resid 786 through 789 Processing helix chain 'B' and resid 794 through 817 removed outlier: 3.623A pdb=" N VAL B 803 " --> pdb=" O ALA B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 828 through 836 Processing helix chain 'B' and resid 837 through 885 removed outlier: 4.364A pdb=" N ASN B 872 " --> pdb=" O ALA B 868 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG B 875 " --> pdb=" O ARG B 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 29 removed outlier: 3.776A pdb=" N ASN A 26 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY A 27 " --> pdb=" O LEU A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 52 No H-bonds generated for 'chain 'A' and resid 50 through 52' Processing helix chain 'A' and resid 237 through 247 removed outlier: 3.543A pdb=" N LEU A 242 " --> pdb=" O PHE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 308 removed outlier: 3.550A pdb=" N THR A 308 " --> pdb=" O THR A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 316 removed outlier: 3.955A pdb=" N TYR A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 497 through 501 removed outlier: 3.581A pdb=" N ASN A 501 " --> pdb=" O PRO A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 595 Processing helix chain 'A' and resid 598 through 603 Processing helix chain 'A' and resid 604 through 608 removed outlier: 3.501A pdb=" N ARG A 607 " --> pdb=" O LEU A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 638 removed outlier: 3.583A pdb=" N ARG A 620 " --> pdb=" O GLU A 616 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY A 632 " --> pdb=" O SER A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 681 Processing helix chain 'A' and resid 688 through 700 Processing helix chain 'A' and resid 721 through 725 Processing helix chain 'A' and resid 749 through 761 Processing helix chain 'A' and resid 768 through 785 Processing helix chain 'A' and resid 786 through 789 Processing helix chain 'A' and resid 794 through 817 removed outlier: 3.623A pdb=" N VAL A 803 " --> pdb=" O ALA A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 836 Processing helix chain 'A' and resid 837 through 885 removed outlier: 4.364A pdb=" N ASN A 872 " --> pdb=" O ALA A 868 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG A 875 " --> pdb=" O ARG A 871 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 29 removed outlier: 3.776A pdb=" N ASN C 26 " --> pdb=" O ARG C 23 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY C 27 " --> pdb=" O LEU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 52 No H-bonds generated for 'chain 'C' and resid 50 through 52' Processing helix chain 'C' and resid 237 through 247 removed outlier: 3.543A pdb=" N LEU C 242 " --> pdb=" O PHE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 308 removed outlier: 3.550A pdb=" N THR C 308 " --> pdb=" O THR C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 316 removed outlier: 3.955A pdb=" N TYR C 315 " --> pdb=" O LEU C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 319 No H-bonds generated for 'chain 'C' and resid 317 through 319' Processing helix chain 'C' and resid 483 through 488 Processing helix chain 'C' and resid 497 through 501 removed outlier: 3.580A pdb=" N ASN C 501 " --> pdb=" O PRO C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 595 Processing helix chain 'C' and resid 598 through 603 Processing helix chain 'C' and resid 604 through 608 removed outlier: 3.501A pdb=" N ARG C 607 " --> pdb=" O LEU C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 638 removed outlier: 3.583A pdb=" N ARG C 620 " --> pdb=" O GLU C 616 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY C 632 " --> pdb=" O SER C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 681 Processing helix chain 'C' and resid 688 through 700 Processing helix chain 'C' and resid 721 through 725 Processing helix chain 'C' and resid 749 through 761 Processing helix chain 'C' and resid 768 through 785 Processing helix chain 'C' and resid 786 through 789 Processing helix chain 'C' and resid 794 through 817 removed outlier: 3.623A pdb=" N VAL C 803 " --> pdb=" O ALA C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 828 through 836 Processing helix chain 'C' and resid 837 through 885 removed outlier: 4.364A pdb=" N ASN C 872 " --> pdb=" O ALA C 868 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG C 875 " --> pdb=" O ARG C 871 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 34 through 35 removed outlier: 6.829A pdb=" N GLY B 34 " --> pdb=" O TYR C 438 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU C 437 " --> pdb=" O LYS C 444 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LYS C 444 " --> pdb=" O VAL C 455 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 39 through 44 removed outlier: 7.437A pdb=" N SER B 217 " --> pdb=" O TYR B 233 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N TYR B 233 " --> pdb=" O SER B 217 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU B 219 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TYR B 231 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU B 221 " --> pdb=" O THR B 229 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 54 through 55 removed outlier: 4.022A pdb=" N TYR B 163 " --> pdb=" O THR B 76 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 64 through 68 removed outlier: 6.497A pdb=" N VAL B 119 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER B 154 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL B 121 " --> pdb=" O ASN B 152 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN B 152 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU B 123 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU B 148 " --> pdb=" O ARG B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 254 through 260 removed outlier: 5.612A pdb=" N VAL B 255 " --> pdb=" O PHE B 467 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N PHE B 467 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N SER B 257 " --> pdb=" O VAL B 465 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL B 465 " --> pdb=" O SER B 257 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N SER B 472 " --> pdb=" O ARG B 468 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 265 through 268 removed outlier: 5.738A pdb=" N LYS B 444 " --> pdb=" O VAL B 455 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU B 437 " --> pdb=" O LYS B 444 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 275 through 276 removed outlier: 6.823A pdb=" N SER B 275 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N CYS B 300 " --> pdb=" O CYS B 397 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 294 through 297 removed outlier: 6.688A pdb=" N ILE B 381 " --> pdb=" O ASN B 375 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU B 368 " --> pdb=" O ASN B 332 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 514 through 521 removed outlier: 4.479A pdb=" N ARG B 544 " --> pdb=" O ALA B 516 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ASN B 518 " --> pdb=" O ARG B 544 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N PHE B 532 " --> pdb=" O LEU B 528 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 562 through 580 removed outlier: 6.539A pdb=" N ASN B 923 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N HIS B 570 " --> pdb=" O PRO B 921 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU B 572 " --> pdb=" O LEU B 919 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU B 919 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU B 574 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR B 917 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLU B 576 " --> pdb=" O PHE B 915 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE B 915 " --> pdb=" O GLU B 576 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE B 578 " --> pdb=" O MET B 913 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N MET B 913 " --> pdb=" O PHE B 578 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLN B 580 " --> pdb=" O GLY B 911 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLY B 911 " --> pdb=" O GLN B 580 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU B 919 " --> pdb=" O HIS B 900 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N HIS B 900 " --> pdb=" O LEU B 919 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 562 through 580 removed outlier: 6.539A pdb=" N ASN B 923 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N HIS B 570 " --> pdb=" O PRO B 921 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU B 572 " --> pdb=" O LEU B 919 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU B 919 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU B 574 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR B 917 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLU B 576 " --> pdb=" O PHE B 915 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE B 915 " --> pdb=" O GLU B 576 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE B 578 " --> pdb=" O MET B 913 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N MET B 913 " --> pdb=" O PHE B 578 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLN B 580 " --> pdb=" O GLY B 911 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLY B 911 " --> pdb=" O GLN B 580 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR B 930 " --> pdb=" O LEU B 951 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU B 951 " --> pdb=" O THR B 930 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 585 through 588 Processing sheet with id=AB4, first strand: chain 'B' and resid 977 through 980 removed outlier: 3.725A pdb=" N CYS B 943 " --> pdb=" O VAL B 980 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 39 through 44 removed outlier: 7.437A pdb=" N SER A 217 " --> pdb=" O TYR A 233 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N TYR A 233 " --> pdb=" O SER A 217 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU A 219 " --> pdb=" O TYR A 231 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TYR A 231 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU A 221 " --> pdb=" O THR A 229 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 54 through 55 removed outlier: 4.023A pdb=" N TYR A 163 " --> pdb=" O THR A 76 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 64 through 68 removed outlier: 6.498A pdb=" N VAL A 119 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER A 154 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL A 121 " --> pdb=" O ASN A 152 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASN A 152 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU A 123 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU A 148 " --> pdb=" O ARG A 125 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 254 through 260 removed outlier: 5.612A pdb=" N VAL A 255 " --> pdb=" O PHE A 467 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N PHE A 467 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N SER A 257 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL A 465 " --> pdb=" O SER A 257 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER A 472 " --> pdb=" O ARG A 468 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 265 through 268 removed outlier: 5.738A pdb=" N LYS A 444 " --> pdb=" O VAL A 455 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU A 437 " --> pdb=" O LYS A 444 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 275 through 276 removed outlier: 6.823A pdb=" N SER A 275 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N CYS A 300 " --> pdb=" O CYS A 397 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 294 through 297 removed outlier: 6.688A pdb=" N ILE A 381 " --> pdb=" O ASN A 375 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU A 368 " --> pdb=" O ASN A 332 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 514 through 521 removed outlier: 4.480A pdb=" N ARG A 544 " --> pdb=" O ALA A 516 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ASN A 518 " --> pdb=" O ARG A 544 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N PHE A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 562 through 580 removed outlier: 6.539A pdb=" N ASN A 923 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N HIS A 570 " --> pdb=" O PRO A 921 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU A 572 " --> pdb=" O LEU A 919 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU A 919 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU A 574 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR A 917 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLU A 576 " --> pdb=" O PHE A 915 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE A 915 " --> pdb=" O GLU A 576 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE A 578 " --> pdb=" O MET A 913 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N MET A 913 " --> pdb=" O PHE A 578 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLN A 580 " --> pdb=" O GLY A 911 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLY A 911 " --> pdb=" O GLN A 580 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU A 919 " --> pdb=" O HIS A 900 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N HIS A 900 " --> pdb=" O LEU A 919 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 562 through 580 removed outlier: 6.539A pdb=" N ASN A 923 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N HIS A 570 " --> pdb=" O PRO A 921 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU A 572 " --> pdb=" O LEU A 919 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU A 919 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU A 574 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR A 917 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLU A 576 " --> pdb=" O PHE A 915 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE A 915 " --> pdb=" O GLU A 576 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE A 578 " --> pdb=" O MET A 913 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N MET A 913 " --> pdb=" O PHE A 578 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLN A 580 " --> pdb=" O GLY A 911 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLY A 911 " --> pdb=" O GLN A 580 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR A 930 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU A 951 " --> pdb=" O THR A 930 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 585 through 588 Processing sheet with id=AC7, first strand: chain 'A' and resid 977 through 980 removed outlier: 3.726A pdb=" N CYS A 943 " --> pdb=" O VAL A 980 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 39 through 44 removed outlier: 7.437A pdb=" N SER C 217 " --> pdb=" O TYR C 233 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N TYR C 233 " --> pdb=" O SER C 217 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU C 219 " --> pdb=" O TYR C 231 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TYR C 231 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU C 221 " --> pdb=" O THR C 229 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 54 through 55 removed outlier: 4.022A pdb=" N TYR C 163 " --> pdb=" O THR C 76 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 64 through 68 removed outlier: 6.498A pdb=" N VAL C 119 " --> pdb=" O SER C 154 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER C 154 " --> pdb=" O VAL C 119 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL C 121 " --> pdb=" O ASN C 152 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN C 152 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU C 123 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU C 148 " --> pdb=" O ARG C 125 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 254 through 260 removed outlier: 5.612A pdb=" N VAL C 255 " --> pdb=" O PHE C 467 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N PHE C 467 " --> pdb=" O VAL C 255 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N SER C 257 " --> pdb=" O VAL C 465 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL C 465 " --> pdb=" O SER C 257 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER C 472 " --> pdb=" O ARG C 468 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 275 through 276 removed outlier: 6.822A pdb=" N SER C 275 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N CYS C 300 " --> pdb=" O CYS C 397 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 294 through 297 removed outlier: 6.688A pdb=" N ILE C 381 " --> pdb=" O ASN C 375 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU C 368 " --> pdb=" O ASN C 332 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 514 through 521 removed outlier: 4.480A pdb=" N ARG C 544 " --> pdb=" O ALA C 516 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ASN C 518 " --> pdb=" O ARG C 544 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N PHE C 532 " --> pdb=" O LEU C 528 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 562 through 580 removed outlier: 6.539A pdb=" N ASN C 923 " --> pdb=" O LEU C 568 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N HIS C 570 " --> pdb=" O PRO C 921 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU C 572 " --> pdb=" O LEU C 919 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU C 919 " --> pdb=" O LEU C 572 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU C 574 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR C 917 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLU C 576 " --> pdb=" O PHE C 915 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N PHE C 915 " --> pdb=" O GLU C 576 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE C 578 " --> pdb=" O MET C 913 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N MET C 913 " --> pdb=" O PHE C 578 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLN C 580 " --> pdb=" O GLY C 911 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLY C 911 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU C 919 " --> pdb=" O HIS C 900 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N HIS C 900 " --> pdb=" O LEU C 919 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 562 through 580 removed outlier: 6.539A pdb=" N ASN C 923 " --> pdb=" O LEU C 568 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N HIS C 570 " --> pdb=" O PRO C 921 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU C 572 " --> pdb=" O LEU C 919 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU C 919 " --> pdb=" O LEU C 572 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU C 574 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR C 917 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLU C 576 " --> pdb=" O PHE C 915 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N PHE C 915 " --> pdb=" O GLU C 576 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE C 578 " --> pdb=" O MET C 913 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N MET C 913 " --> pdb=" O PHE C 578 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLN C 580 " --> pdb=" O GLY C 911 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLY C 911 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR C 930 " --> pdb=" O LEU C 951 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU C 951 " --> pdb=" O THR C 930 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 585 through 588 Processing sheet with id=AD9, first strand: chain 'C' and resid 977 through 980 removed outlier: 3.725A pdb=" N CYS C 943 " --> pdb=" O VAL C 980 " (cutoff:3.500A) 940 hydrogen bonds defined for protein. 2499 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: 10.37 Time building geometry restraints manager: 10.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6974 1.34 - 1.47: 6652 1.47 - 1.59: 10143 1.59 - 1.72: 0 1.72 - 1.85: 168 Bond restraints: 23937 Sorted by residual: bond pdb=" C1 NAG A1217 " pdb=" O5 NAG A1217 " ideal model delta sigma weight residual 1.406 1.496 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C1 NAG B1217 " pdb=" O5 NAG B1217 " ideal model delta sigma weight residual 1.406 1.496 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C1 NAG C1217 " pdb=" O5 NAG C1217 " ideal model delta sigma weight residual 1.406 1.496 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C1 BMA Q 3 " pdb=" C2 BMA Q 3 " ideal model delta sigma weight residual 1.519 1.587 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C1 BMA X 3 " pdb=" C2 BMA X 3 " ideal model delta sigma weight residual 1.519 1.587 -0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 23932 not shown) Histogram of bond angle deviations from ideal: 97.71 - 105.09: 372 105.09 - 112.46: 12191 112.46 - 119.83: 8385 119.83 - 127.20: 11384 127.20 - 134.57: 278 Bond angle restraints: 32610 Sorted by residual: angle pdb=" CA TYR B 91 " pdb=" CB TYR B 91 " pdb=" CG TYR B 91 " ideal model delta sigma weight residual 113.90 124.10 -10.20 1.80e+00 3.09e-01 3.21e+01 angle pdb=" CA TYR C 91 " pdb=" CB TYR C 91 " pdb=" CG TYR C 91 " ideal model delta sigma weight residual 113.90 124.10 -10.20 1.80e+00 3.09e-01 3.21e+01 angle pdb=" CA TYR A 91 " pdb=" CB TYR A 91 " pdb=" CG TYR A 91 " ideal model delta sigma weight residual 113.90 124.09 -10.19 1.80e+00 3.09e-01 3.21e+01 angle pdb=" C ASP C 339 " pdb=" N ASP C 340 " pdb=" CA ASP C 340 " ideal model delta sigma weight residual 121.54 130.52 -8.98 1.91e+00 2.74e-01 2.21e+01 angle pdb=" C ASP B 339 " pdb=" N ASP B 340 " pdb=" CA ASP B 340 " ideal model delta sigma weight residual 121.54 130.49 -8.95 1.91e+00 2.74e-01 2.20e+01 ... (remaining 32605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.14: 14454 22.14 - 44.29: 330 44.29 - 66.43: 129 66.43 - 88.57: 42 88.57 - 110.72: 48 Dihedral angle restraints: 15003 sinusoidal: 6633 harmonic: 8370 Sorted by residual: dihedral pdb=" CB CYS C 409 " pdb=" SG CYS C 409 " pdb=" SG CYS C 458 " pdb=" CB CYS C 458 " ideal model delta sinusoidal sigma weight residual 93.00 4.26 88.74 1 1.00e+01 1.00e-02 9.39e+01 dihedral pdb=" CB CYS B 409 " pdb=" SG CYS B 409 " pdb=" SG CYS B 458 " pdb=" CB CYS B 458 " ideal model delta sinusoidal sigma weight residual 93.00 4.28 88.72 1 1.00e+01 1.00e-02 9.39e+01 dihedral pdb=" CB CYS A 409 " pdb=" SG CYS A 409 " pdb=" SG CYS A 458 " pdb=" CB CYS A 458 " ideal model delta sinusoidal sigma weight residual 93.00 4.29 88.71 1 1.00e+01 1.00e-02 9.38e+01 ... (remaining 15000 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 3699 0.129 - 0.258: 177 0.258 - 0.388: 12 0.388 - 0.517: 0 0.517 - 0.646: 6 Chirality restraints: 3894 Sorted by residual: chirality pdb=" C1 NAG A1204 " pdb=" ND2 ASN A 37 " pdb=" C2 NAG A1204 " pdb=" O5 NAG A1204 " both_signs ideal model delta sigma weight residual False -2.40 -1.75 -0.65 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" C1 NAG B1204 " pdb=" ND2 ASN B 37 " pdb=" C2 NAG B1204 " pdb=" O5 NAG B1204 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" C1 NAG C1204 " pdb=" ND2 ASN C 37 " pdb=" C2 NAG C1204 " pdb=" O5 NAG C1204 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.04e+01 ... (remaining 3891 not shown) Planarity restraints: 4128 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 389 " -0.025 2.00e-02 2.50e+03 2.74e-02 1.31e+01 pdb=" CG PHE A 389 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE A 389 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 PHE A 389 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 389 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE A 389 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 389 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 389 " 0.024 2.00e-02 2.50e+03 2.73e-02 1.31e+01 pdb=" CG PHE B 389 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE B 389 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 PHE B 389 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE B 389 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE B 389 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE B 389 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 389 " -0.024 2.00e-02 2.50e+03 2.72e-02 1.30e+01 pdb=" CG PHE C 389 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE C 389 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 PHE C 389 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE C 389 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE C 389 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE C 389 " -0.008 2.00e-02 2.50e+03 ... (remaining 4125 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 619 2.69 - 3.24: 20897 3.24 - 3.80: 36560 3.80 - 4.35: 49327 4.35 - 4.90: 80692 Nonbonded interactions: 188095 Sorted by model distance: nonbonded pdb=" O ARG B 607 " pdb=" CG GLU C 820 " model vdw 2.141 3.440 nonbonded pdb=" CG GLU A 820 " pdb=" O ARG C 607 " model vdw 2.142 3.440 nonbonded pdb=" CG GLU B 820 " pdb=" O ARG A 607 " model vdw 2.148 3.440 nonbonded pdb=" OG1 THR B 31 " pdb=" O ARG B 33 " model vdw 2.335 2.440 nonbonded pdb=" OG1 THR C 31 " pdb=" O ARG C 33 " model vdw 2.336 2.440 ... (remaining 188090 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' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' } ncs_group { reference = chain 'J' selection = chain 'Q' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.130 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: 0.010 Extract box with map and model: 4.920 Check model and map are aligned: 0.370 Set scattering table: 0.220 Process input model: 63.600 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 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:12.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 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 : 0.009 0.134 23937 Z= 0.590 Angle : 1.050 10.552 32610 Z= 0.578 Chirality : 0.070 0.646 3894 Planarity : 0.007 0.066 4083 Dihedral : 13.409 110.717 9516 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.12 % Allowed : 1.24 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -2.43 (0.14), residues: 2877 helix: -2.92 (0.13), residues: 645 sheet: -1.04 (0.18), residues: 747 loop : -1.19 (0.14), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP A 127 HIS 0.021 0.004 HIS C 500 PHE 0.060 0.006 PHE B 389 TYR 0.060 0.005 TYR B 233 ARG 0.025 0.002 ARG C 447 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 357 time to evaluate : 2.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 ARG cc_start: 0.8138 (mtt180) cc_final: 0.7913 (mtm-85) REVERT: B 545 MET cc_start: 0.8491 (mtp) cc_final: 0.8246 (mtp) REVERT: A 853 MET cc_start: 0.8993 (mtp) cc_final: 0.8760 (mtm) REVERT: C 122 ARG cc_start: 0.8115 (mtt180) cc_final: 0.7827 (mtt-85) REVERT: C 754 MET cc_start: 0.8929 (mmt) cc_final: 0.8728 (mmt) outliers start: 3 outliers final: 0 residues processed: 360 average time/residue: 1.4490 time to fit residues: 590.7011 Evaluate side-chains 242 residues out of total 2490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 2.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 4.9990 chunk 218 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 225 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 chunk 261 optimal weight: 0.7980 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 GLN B 210 ASN ** B 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 526 ASN B 655 GLN B 710 HIS B 810 GLN B 878 GLN B 907 ASN B 976 ASN A 99 HIS A 159 GLN A 210 ASN ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 500 HIS A 526 ASN A 710 HIS A 765 GLN A 810 GLN A 857 GLN A 907 ASN C 99 HIS C 159 GLN C 210 ASN ** C 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 378 GLN C 500 HIS C 526 ASN C 710 HIS C 766 ASN C 810 GLN C 907 ASN C 976 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 23937 Z= 0.216 Angle : 0.673 12.251 32610 Z= 0.340 Chirality : 0.050 0.421 3894 Planarity : 0.005 0.051 4083 Dihedral : 11.709 68.506 4644 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.40 % Allowed : 5.36 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.68 (0.15), residues: 2877 helix: 0.26 (0.19), residues: 654 sheet: -0.47 (0.19), residues: 738 loop : -0.69 (0.15), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 127 HIS 0.010 0.002 HIS C 500 PHE 0.022 0.002 PHE C 430 TYR 0.026 0.002 TYR A 91 ARG 0.006 0.001 ARG C 447 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 254 time to evaluate : 2.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 206 MET cc_start: 0.6905 (ttt) cc_final: 0.6589 (ttt) REVERT: B 282 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7394 (mp0) REVERT: B 405 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7664 (ttm170) REVERT: B 459 PHE cc_start: 0.7917 (OUTLIER) cc_final: 0.6922 (m-80) REVERT: B 545 MET cc_start: 0.8474 (mtp) cc_final: 0.8150 (mtp) REVERT: B 620 ARG cc_start: 0.8022 (ttm110) cc_final: 0.7810 (ttm110) REVERT: A 214 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7355 (pp20) REVERT: A 405 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7412 (ttm170) REVERT: A 459 PHE cc_start: 0.7800 (OUTLIER) cc_final: 0.6772 (m-80) REVERT: A 702 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.8017 (tt0) REVERT: C 206 MET cc_start: 0.6827 (ttt) cc_final: 0.6615 (ttt) REVERT: C 214 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7243 (pm20) REVERT: C 330 GLU cc_start: 0.7633 (tp30) cc_final: 0.7315 (mm-30) REVERT: C 454 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8049 (tt0) REVERT: C 459 PHE cc_start: 0.7855 (OUTLIER) cc_final: 0.6955 (m-80) REVERT: C 485 LEU cc_start: 0.7970 (mm) cc_final: 0.7765 (mt) REVERT: C 545 MET cc_start: 0.8642 (mtp) cc_final: 0.8398 (mtp) REVERT: C 754 MET cc_start: 0.8944 (mmt) cc_final: 0.8573 (mmt) REVERT: C 837 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7702 (p0) outliers start: 34 outliers final: 9 residues processed: 276 average time/residue: 1.4737 time to fit residues: 464.7667 Evaluate side-chains 253 residues out of total 2490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 233 time to evaluate : 2.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 702 GLN Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain A residue 766 ASN Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 454 GLU Chi-restraints excluded: chain C residue 459 PHE Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 837 ASP Chi-restraints excluded: chain C residue 838 LYS Chi-restraints excluded: chain C residue 973 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 217 optimal weight: 0.9990 chunk 178 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 262 optimal weight: 9.9990 chunk 283 optimal weight: 3.9990 chunk 233 optimal weight: 8.9990 chunk 259 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 210 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 HIS B 326 ASN ** B 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 GLN B 766 ASN B 805 ASN A 326 ASN A 483 ASN A 765 GLN A 805 ASN A 892 ASN C 99 HIS C 326 ASN C 766 ASN C 805 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 23937 Z= 0.291 Angle : 0.715 13.136 32610 Z= 0.360 Chirality : 0.054 0.715 3894 Planarity : 0.005 0.048 4083 Dihedral : 10.781 64.726 4644 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.94 % Allowed : 6.26 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.16 (0.15), residues: 2877 helix: 1.32 (0.20), residues: 636 sheet: -0.26 (0.19), residues: 720 loop : -0.60 (0.16), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 127 HIS 0.008 0.002 HIS C 900 PHE 0.023 0.002 PHE C 430 TYR 0.034 0.002 TYR B 91 ARG 0.007 0.001 ARG C 447 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 241 time to evaluate : 2.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7528 (mtm180) REVERT: B 206 MET cc_start: 0.7052 (ttt) cc_final: 0.6744 (ttt) REVERT: B 405 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7700 (ttm170) REVERT: B 459 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.7492 (m-80) REVERT: B 583 MET cc_start: 0.8131 (mtm) cc_final: 0.7821 (ttp) REVERT: B 853 MET cc_start: 0.8905 (mtm) cc_final: 0.8692 (mtm) REVERT: A 279 GLN cc_start: 0.8498 (mm110) cc_final: 0.8254 (mm-40) REVERT: A 405 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7483 (ttm170) REVERT: A 459 PHE cc_start: 0.8103 (OUTLIER) cc_final: 0.7279 (m-80) REVERT: A 702 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7990 (tt0) REVERT: C 99 HIS cc_start: 0.7974 (m-70) cc_final: 0.7676 (m90) REVERT: C 206 MET cc_start: 0.6883 (ttt) cc_final: 0.6666 (ttt) REVERT: C 330 GLU cc_start: 0.7659 (tp30) cc_final: 0.7321 (mm-30) REVERT: C 459 PHE cc_start: 0.8082 (OUTLIER) cc_final: 0.7477 (m-80) REVERT: C 545 MET cc_start: 0.8646 (mtp) cc_final: 0.8402 (mtp) REVERT: C 754 MET cc_start: 0.8967 (mmt) cc_final: 0.8628 (mmt) outliers start: 47 outliers final: 15 residues processed: 275 average time/residue: 1.4305 time to fit residues: 448.8839 Evaluate side-chains 259 residues out of total 2490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 237 time to evaluate : 2.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 702 GLN Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain A residue 766 ASN Chi-restraints excluded: chain C residue 454 GLU Chi-restraints excluded: chain C residue 459 PHE Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 731 ILE Chi-restraints excluded: chain C residue 838 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 3.9990 chunk 196 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 175 optimal weight: 0.1980 chunk 262 optimal weight: 9.9990 chunk 278 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 249 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 GLN A 560 ASN A 765 GLN C 766 ASN C 897 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 23937 Z= 0.204 Angle : 0.633 13.247 32610 Z= 0.315 Chirality : 0.049 0.513 3894 Planarity : 0.004 0.042 4083 Dihedral : 9.495 59.723 4644 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.48 % Allowed : 7.21 % Favored : 91.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.22 (0.16), residues: 2877 helix: 1.64 (0.21), residues: 654 sheet: 0.09 (0.19), residues: 711 loop : -0.45 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 126 HIS 0.006 0.001 HIS B 500 PHE 0.017 0.001 PHE B 430 TYR 0.024 0.002 TYR B 91 ARG 0.003 0.000 ARG C 447 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 252 time to evaluate : 2.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7440 (mtm180) REVERT: B 206 MET cc_start: 0.6923 (ttt) cc_final: 0.6576 (ttt) REVERT: B 405 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7724 (ttm170) REVERT: B 459 PHE cc_start: 0.8017 (OUTLIER) cc_final: 0.7306 (m-80) REVERT: B 583 MET cc_start: 0.8078 (mtm) cc_final: 0.7771 (ttp) REVERT: A 214 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7314 (pp20) REVERT: A 279 GLN cc_start: 0.8468 (mm110) cc_final: 0.8263 (mm-40) REVERT: A 405 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7471 (ttm170) REVERT: A 459 PHE cc_start: 0.7991 (OUTLIER) cc_final: 0.7198 (m-80) REVERT: A 702 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7968 (tt0) REVERT: A 721 ASP cc_start: 0.7781 (t0) cc_final: 0.7533 (t0) REVERT: C 99 HIS cc_start: 0.7986 (m-70) cc_final: 0.7736 (m90) REVERT: C 206 MET cc_start: 0.6905 (ttt) cc_final: 0.6617 (ttt) REVERT: C 330 GLU cc_start: 0.7614 (tp30) cc_final: 0.7299 (mm-30) REVERT: C 454 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8089 (tt0) REVERT: C 545 MET cc_start: 0.8643 (mtp) cc_final: 0.8320 (mtp) outliers start: 36 outliers final: 11 residues processed: 276 average time/residue: 1.5235 time to fit residues: 478.3702 Evaluate side-chains 256 residues out of total 2490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 237 time to evaluate : 2.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 702 GLN Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain C residue 454 GLU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 731 ILE Chi-restraints excluded: chain C residue 838 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 4.9990 chunk 158 optimal weight: 0.0980 chunk 4 optimal weight: 9.9990 chunk 207 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 237 optimal weight: 4.9990 chunk 192 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 142 optimal weight: 9.9990 chunk 249 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 HIS ** B 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 GLN B 766 ASN B 892 ASN B 897 GLN A 765 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.120 23937 Z= 0.380 Angle : 0.777 18.108 32610 Z= 0.394 Chirality : 0.055 0.582 3894 Planarity : 0.005 0.047 4083 Dihedral : 9.626 59.514 4644 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.98 % Allowed : 7.70 % Favored : 90.32 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.56 % 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: 0.05 (0.16), residues: 2877 helix: 1.59 (0.20), residues: 636 sheet: -0.19 (0.19), residues: 720 loop : -0.47 (0.16), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 169 HIS 0.007 0.002 HIS C 900 PHE 0.025 0.002 PHE C 430 TYR 0.036 0.003 TYR A 91 ARG 0.007 0.001 ARG A 671 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 242 time to evaluate : 2.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 122 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7555 (mtm180) REVERT: B 206 MET cc_start: 0.7059 (ttt) cc_final: 0.6746 (ttt) REVERT: B 405 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7728 (ttm170) REVERT: B 459 PHE cc_start: 0.8250 (OUTLIER) cc_final: 0.7634 (m-80) REVERT: B 583 MET cc_start: 0.8149 (mtm) cc_final: 0.7757 (ttp) REVERT: A 214 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7369 (pp20) REVERT: A 279 GLN cc_start: 0.8508 (mm110) cc_final: 0.8285 (mm-40) REVERT: A 405 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7668 (ttm170) REVERT: A 459 PHE cc_start: 0.8281 (OUTLIER) cc_final: 0.7636 (m-80) REVERT: A 702 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.8011 (tt0) REVERT: C 122 ARG cc_start: 0.8148 (mtt180) cc_final: 0.7932 (mtt-85) REVERT: C 206 MET cc_start: 0.6906 (ttt) cc_final: 0.6671 (ttt) REVERT: C 330 GLU cc_start: 0.7678 (tp30) cc_final: 0.7351 (mm-30) REVERT: C 459 PHE cc_start: 0.8069 (OUTLIER) cc_final: 0.7708 (m-80) REVERT: C 545 MET cc_start: 0.8592 (mtp) cc_final: 0.8265 (mtp) REVERT: C 837 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.7617 (p0) outliers start: 48 outliers final: 17 residues processed: 276 average time/residue: 1.4176 time to fit residues: 446.5165 Evaluate side-chains 264 residues out of total 2490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 238 time to evaluate : 2.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 458 CYS Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 702 GLN Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 596 ASP Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain C residue 454 GLU Chi-restraints excluded: chain C residue 459 PHE Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 731 ILE Chi-restraints excluded: chain C residue 837 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 5.9990 chunk 250 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 163 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 278 optimal weight: 0.6980 chunk 231 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 146 optimal weight: 6.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 655 GLN A 560 ASN A 765 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 23937 Z= 0.208 Angle : 0.656 14.025 32610 Z= 0.327 Chirality : 0.049 0.435 3894 Planarity : 0.003 0.041 4083 Dihedral : 8.933 59.553 4644 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.61 % Allowed : 8.12 % Favored : 90.28 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.56 % 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: 0.37 (0.16), residues: 2877 helix: 1.86 (0.21), residues: 651 sheet: 0.09 (0.19), residues: 726 loop : -0.34 (0.17), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 126 HIS 0.005 0.001 HIS B 500 PHE 0.016 0.001 PHE B 430 TYR 0.022 0.001 TYR B 91 ARG 0.002 0.000 ARG C 447 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 245 time to evaluate : 2.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 122 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7460 (mtm180) REVERT: B 206 MET cc_start: 0.6943 (ttt) cc_final: 0.6590 (ttt) REVERT: B 405 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7732 (ttm170) REVERT: B 459 PHE cc_start: 0.8012 (OUTLIER) cc_final: 0.7266 (m-80) REVERT: B 583 MET cc_start: 0.8103 (mtm) cc_final: 0.7823 (ttp) REVERT: B 853 MET cc_start: 0.8958 (mtm) cc_final: 0.8748 (mtm) REVERT: A 214 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7308 (pp20) REVERT: A 405 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7423 (ttm170) REVERT: A 459 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.7245 (m-80) REVERT: A 702 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7968 (tt0) REVERT: A 721 ASP cc_start: 0.7849 (t0) cc_final: 0.7614 (t0) REVERT: C 206 MET cc_start: 0.6934 (ttt) cc_final: 0.6649 (ttt) REVERT: C 454 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8116 (tt0) REVERT: C 545 MET cc_start: 0.8538 (mtp) cc_final: 0.8198 (mtp) outliers start: 39 outliers final: 13 residues processed: 270 average time/residue: 1.4367 time to fit residues: 442.3234 Evaluate side-chains 257 residues out of total 2490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 236 time to evaluate : 2.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 702 GLN Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 539 ASN Chi-restraints excluded: chain A residue 596 ASP Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain C residue 454 GLU Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 731 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 158 optimal weight: 0.0370 chunk 203 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 234 optimal weight: 0.7980 chunk 155 optimal weight: 0.8980 chunk 277 optimal weight: 8.9990 chunk 173 optimal weight: 0.9990 chunk 169 optimal weight: 0.6980 chunk 128 optimal weight: 7.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 655 GLN B 766 ASN A 560 ASN A 765 GLN A 897 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 23937 Z= 0.176 Angle : 0.622 13.947 32610 Z= 0.307 Chirality : 0.047 0.423 3894 Planarity : 0.003 0.037 4083 Dihedral : 8.412 58.450 4644 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.15 % Allowed : 8.86 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.53 (0.16), residues: 2877 helix: 2.06 (0.21), residues: 651 sheet: 0.20 (0.19), residues: 726 loop : -0.28 (0.17), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 108 HIS 0.004 0.001 HIS B 500 PHE 0.013 0.001 PHE B 430 TYR 0.017 0.001 TYR A 91 ARG 0.002 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 252 time to evaluate : 2.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7524 (mtm180) REVERT: B 206 MET cc_start: 0.6857 (ttt) cc_final: 0.6488 (ttt) REVERT: B 405 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7727 (ttm170) REVERT: B 459 PHE cc_start: 0.7916 (OUTLIER) cc_final: 0.7038 (m-80) REVERT: B 583 MET cc_start: 0.7982 (mtm) cc_final: 0.7731 (ttp) REVERT: A 214 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7271 (pp20) REVERT: A 405 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7486 (ttm170) REVERT: A 459 PHE cc_start: 0.7921 (OUTLIER) cc_final: 0.7132 (m-80) REVERT: A 721 ASP cc_start: 0.7774 (t0) cc_final: 0.7518 (t0) REVERT: A 837 ASP cc_start: 0.7763 (p0) cc_final: 0.7520 (p0) REVERT: C 122 ARG cc_start: 0.8103 (mtt180) cc_final: 0.7802 (mtt-85) REVERT: C 206 MET cc_start: 0.6872 (ttt) cc_final: 0.6606 (ttt) REVERT: C 214 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7229 (pp20) REVERT: C 454 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7974 (tt0) REVERT: C 545 MET cc_start: 0.8514 (mtp) cc_final: 0.8116 (mtp) outliers start: 28 outliers final: 13 residues processed: 269 average time/residue: 1.4370 time to fit residues: 441.4929 Evaluate side-chains 266 residues out of total 2490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 245 time to evaluate : 2.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 458 CYS Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 539 ASN Chi-restraints excluded: chain A residue 596 ASP Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 454 GLU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 731 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 chunk 165 optimal weight: 9.9990 chunk 83 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 176 optimal weight: 6.9990 chunk 189 optimal weight: 4.9990 chunk 137 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 218 optimal weight: 1.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 655 GLN A 560 ASN A 765 GLN C 99 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.123 23937 Z= 0.279 Angle : 0.697 15.900 32610 Z= 0.352 Chirality : 0.050 0.401 3894 Planarity : 0.004 0.039 4083 Dihedral : 8.500 59.523 4644 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.52 % Allowed : 8.74 % Favored : 89.74 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 2.56 % 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: 0.43 (0.16), residues: 2877 helix: 1.81 (0.21), residues: 654 sheet: 0.11 (0.18), residues: 726 loop : -0.24 (0.17), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 108 HIS 0.005 0.001 HIS B 500 PHE 0.019 0.002 PHE C 430 TYR 0.029 0.002 TYR A 91 ARG 0.004 0.001 ARG A 835 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 245 time to evaluate : 2.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7518 (mtm180) REVERT: B 206 MET cc_start: 0.6941 (ttt) cc_final: 0.6602 (ttt) REVERT: B 214 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7282 (pp20) REVERT: B 405 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7722 (ttm170) REVERT: B 459 PHE cc_start: 0.8074 (OUTLIER) cc_final: 0.7426 (m-80) REVERT: B 583 MET cc_start: 0.8101 (mtm) cc_final: 0.7817 (ttp) REVERT: A 214 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7354 (pp20) REVERT: A 405 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7631 (ttm170) REVERT: A 459 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7477 (m-80) REVERT: A 721 ASP cc_start: 0.7888 (t0) cc_final: 0.7652 (t0) REVERT: C 99 HIS cc_start: 0.8011 (m-70) cc_final: 0.7740 (m90) REVERT: C 206 MET cc_start: 0.6909 (ttt) cc_final: 0.6649 (ttt) REVERT: C 214 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7258 (pp20) REVERT: C 545 MET cc_start: 0.8501 (mtp) cc_final: 0.8206 (mtp) REVERT: C 616 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.6785 (mp0) REVERT: C 754 MET cc_start: 0.8854 (mmt) cc_final: 0.8611 (mmt) REVERT: C 837 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7635 (p0) outliers start: 37 outliers final: 19 residues processed: 270 average time/residue: 1.4271 time to fit residues: 442.3695 Evaluate side-chains 268 residues out of total 2490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 239 time to evaluate : 2.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 458 CYS Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 702 GLN Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 766 ASN Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 539 ASN Chi-restraints excluded: chain A residue 596 ASP Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 454 GLU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 616 GLU Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 731 ILE Chi-restraints excluded: chain C residue 837 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 4.9990 chunk 265 optimal weight: 0.0970 chunk 242 optimal weight: 7.9990 chunk 258 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 112 optimal weight: 0.1980 chunk 203 optimal weight: 0.0870 chunk 79 optimal weight: 7.9990 chunk 233 optimal weight: 8.9990 chunk 244 optimal weight: 2.9990 chunk 257 optimal weight: 4.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 655 GLN A 765 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 23937 Z= 0.184 Angle : 0.616 14.089 32610 Z= 0.307 Chirality : 0.047 0.357 3894 Planarity : 0.003 0.038 4083 Dihedral : 8.118 59.845 4644 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.24 % Allowed : 9.31 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.59 (0.16), residues: 2877 helix: 2.08 (0.21), residues: 651 sheet: 0.22 (0.19), residues: 726 loop : -0.23 (0.17), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 108 HIS 0.004 0.001 HIS B 500 PHE 0.014 0.001 PHE B 430 TYR 0.017 0.001 TYR A 91 ARG 0.002 0.000 ARG A 544 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 240 time to evaluate : 2.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7512 (mtm180) REVERT: B 206 MET cc_start: 0.6885 (ttt) cc_final: 0.6524 (ttt) REVERT: B 459 PHE cc_start: 0.7931 (OUTLIER) cc_final: 0.7137 (m-80) REVERT: B 583 MET cc_start: 0.8024 (mtm) cc_final: 0.7773 (ttp) REVERT: A 214 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7276 (pp20) REVERT: A 405 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7432 (ttm170) REVERT: A 459 PHE cc_start: 0.7900 (OUTLIER) cc_final: 0.7167 (m-80) REVERT: A 702 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7947 (tt0) REVERT: A 721 ASP cc_start: 0.7756 (t0) cc_final: 0.7489 (t0) REVERT: A 837 ASP cc_start: 0.7844 (p0) cc_final: 0.7585 (p0) REVERT: C 99 HIS cc_start: 0.7988 (m-70) cc_final: 0.7701 (m90) REVERT: C 206 MET cc_start: 0.6835 (ttt) cc_final: 0.6562 (ttt) REVERT: C 214 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7261 (pp20) REVERT: C 454 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7933 (tt0) REVERT: C 545 MET cc_start: 0.8477 (mtp) cc_final: 0.8176 (mtp) REVERT: C 754 MET cc_start: 0.8845 (mmt) cc_final: 0.8543 (mmp) outliers start: 30 outliers final: 13 residues processed: 259 average time/residue: 1.4369 time to fit residues: 424.7966 Evaluate side-chains 256 residues out of total 2490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 235 time to evaluate : 2.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 458 CYS Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 539 ASN Chi-restraints excluded: chain A residue 596 ASP Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 454 GLU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain C residue 641 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 0.0370 chunk 273 optimal weight: 0.7980 chunk 166 optimal weight: 9.9990 chunk 129 optimal weight: 6.9990 chunk 190 optimal weight: 7.9990 chunk 286 optimal weight: 1.9990 chunk 264 optimal weight: 8.9990 chunk 228 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 176 optimal weight: 0.9980 chunk 140 optimal weight: 6.9990 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 512 ASN B 655 GLN A 765 GLN A 766 ASN C 512 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 23937 Z= 0.210 Angle : 0.635 14.128 32610 Z= 0.318 Chirality : 0.047 0.404 3894 Planarity : 0.003 0.038 4083 Dihedral : 8.211 59.783 4644 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.19 % Allowed : 9.31 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.60 (0.16), residues: 2877 helix: 2.10 (0.21), residues: 651 sheet: 0.21 (0.19), residues: 726 loop : -0.21 (0.17), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 108 HIS 0.004 0.001 HIS B 500 PHE 0.016 0.001 PHE B 430 TYR 0.022 0.001 TYR A 91 ARG 0.002 0.000 ARG C 447 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 236 time to evaluate : 2.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7554 (mtm180) REVERT: B 206 MET cc_start: 0.6917 (ttt) cc_final: 0.6569 (ttt) REVERT: B 459 PHE cc_start: 0.7929 (OUTLIER) cc_final: 0.7172 (m-80) REVERT: B 583 MET cc_start: 0.8051 (mtm) cc_final: 0.7803 (ttp) REVERT: A 214 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7288 (pp20) REVERT: A 405 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7441 (ttm170) REVERT: A 459 PHE cc_start: 0.7982 (OUTLIER) cc_final: 0.7290 (m-80) REVERT: A 616 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7183 (mp0) REVERT: A 702 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7949 (tt0) REVERT: A 721 ASP cc_start: 0.7818 (t0) cc_final: 0.7560 (t0) REVERT: A 837 ASP cc_start: 0.7864 (p0) cc_final: 0.7604 (p0) REVERT: C 99 HIS cc_start: 0.7992 (m-70) cc_final: 0.7726 (m90) REVERT: C 206 MET cc_start: 0.6789 (ttt) cc_final: 0.6583 (ttt) REVERT: C 214 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7237 (pp20) REVERT: C 454 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7907 (tt0) REVERT: C 545 MET cc_start: 0.8463 (mtp) cc_final: 0.8180 (mtp) REVERT: C 754 MET cc_start: 0.8847 (mmt) cc_final: 0.8575 (mmt) outliers start: 29 outliers final: 16 residues processed: 256 average time/residue: 1.4228 time to fit residues: 416.6828 Evaluate side-chains 259 residues out of total 2490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 234 time to evaluate : 2.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 458 CYS Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 539 ASN Chi-restraints excluded: chain A residue 596 ASP Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain A residue 766 ASN Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 454 GLU Chi-restraints excluded: chain C residue 512 ASN Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain C residue 641 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 0.9980 chunk 243 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 210 optimal weight: 0.7980 chunk 33 optimal weight: 0.3980 chunk 63 optimal weight: 0.0970 chunk 228 optimal weight: 8.9990 chunk 95 optimal weight: 6.9990 chunk 234 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 GLN A 765 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.131930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.101822 restraints weight = 23151.105| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.75 r_work: 0.2947 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.136 23937 Z= 0.254 Angle : 0.800 59.200 32610 Z= 0.439 Chirality : 0.055 1.152 3894 Planarity : 0.003 0.038 4083 Dihedral : 8.442 76.489 4644 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.19 % Allowed : 9.39 % Favored : 89.41 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.60 (0.16), residues: 2877 helix: 2.09 (0.21), residues: 651 sheet: 0.21 (0.19), residues: 726 loop : -0.21 (0.17), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 108 HIS 0.004 0.001 HIS B 500 PHE 0.016 0.001 PHE B 430 TYR 0.022 0.001 TYR A 91 ARG 0.002 0.000 ARG C 447 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7934.42 seconds wall clock time: 142 minutes 32.82 seconds (8552.82 seconds total)