Starting phenix.real_space_refine on Wed Feb 21 01:23:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ohn_16882/02_2024/8ohn_16882.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ohn_16882/02_2024/8ohn_16882.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ohn_16882/02_2024/8ohn_16882.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ohn_16882/02_2024/8ohn_16882.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ohn_16882/02_2024/8ohn_16882.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ohn_16882/02_2024/8ohn_16882.pdb" } resolution = 3.4 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= 0.002 sd= 0.020 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 174 5.16 5 C 18633 2.51 5 N 4689 2.21 5 O 5832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29328 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 9373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1195, 9373 Classifications: {'peptide': 1195} Link IDs: {'PCIS': 3, 'PTRANS': 43, 'TRANS': 1148} Chain breaks: 1 Chain: "B" Number of atoms: 9373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1195, 9373 Classifications: {'peptide': 1195} Link IDs: {'PCIS': 3, 'PTRANS': 43, 'TRANS': 1148} Chain breaks: 1 Chain: "C" Number of atoms: 9373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1195, 9373 Classifications: {'peptide': 1195} Link IDs: {'PCIS': 3, 'PTRANS': 43, 'TRANS': 1148} Chain breaks: 1 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: 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: "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: 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: "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: 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: "Q" 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: "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: 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: "Y" 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: "Z" 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: "a" 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: "b" 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: "c" 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: "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: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 16.30, per 1000 atoms: 0.56 Number of scatterers: 29328 At special positions: 0 Unit cell: (150.511, 159.365, 164.898, 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 174 16.00 O 5832 8.00 N 4689 7.00 C 18633 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=72, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 183 " distance=2.04 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 242 " distance=2.04 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 352 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 605 " distance=2.03 Simple disulfide: pdb=" SG CYS A 466 " - pdb=" SG CYS A 546 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 567 " distance=2.03 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 516 " distance=2.03 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 518 " distance=2.03 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 533 " distance=2.03 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 569 " distance=2.04 Simple disulfide: pdb=" SG CYS A 582 " - pdb=" SG CYS A 588 " distance=2.04 Simple disulfide: pdb=" SG CYS A 621 " - pdb=" SG CYS A 674 " distance=2.03 Simple disulfide: pdb=" SG CYS A 699 " - pdb=" SG CYS A 720 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 744 " distance=2.03 Simple disulfide: pdb=" SG CYS A 818 " - pdb=" SG CYS A 840 " distance=2.03 Simple disulfide: pdb=" SG CYS A 823 " - pdb=" SG CYS A 829 " distance=2.03 Simple disulfide: pdb=" SG CYS A 894 " - pdb=" SG CYS A 899 " distance=2.03 Simple disulfide: pdb=" SG CYS A 929 " - pdb=" SG CYS A 940 " distance=2.03 Simple disulfide: pdb=" SG CYS A1117 " - pdb=" SG CYS A1128 " distance=2.03 Simple disulfide: pdb=" SG CYS A1167 " - pdb=" SG CYS A1212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 183 " distance=2.04 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 292 " distance=2.02 Simple disulfide: pdb=" SG CYS B 327 " - pdb=" SG CYS B 352 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 423 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 466 " - pdb=" SG CYS B 546 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 495 " distance=2.03 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG CYS B 567 " distance=2.03 Simple disulfide: pdb=" SG CYS B 485 " - pdb=" SG CYS B 516 " distance=2.03 Simple disulfide: pdb=" SG CYS B 504 " - pdb=" SG CYS B 518 " distance=2.03 Simple disulfide: pdb=" SG CYS B 520 " - pdb=" SG CYS B 533 " distance=2.03 Simple disulfide: pdb=" SG CYS B 556 " - pdb=" SG CYS B 569 " distance=2.04 Simple disulfide: pdb=" SG CYS B 582 " - pdb=" SG CYS B 588 " distance=2.04 Simple disulfide: pdb=" SG CYS B 621 " - pdb=" SG CYS B 674 " distance=2.03 Simple disulfide: pdb=" SG CYS B 699 " - pdb=" SG CYS B 720 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 744 " distance=2.03 Simple disulfide: pdb=" SG CYS B 818 " - pdb=" SG CYS B 840 " distance=2.03 Simple disulfide: pdb=" SG CYS B 823 " - pdb=" SG CYS B 829 " distance=2.03 Simple disulfide: pdb=" SG CYS B 894 " - pdb=" SG CYS B 899 " distance=2.03 Simple disulfide: pdb=" SG CYS B 929 " - pdb=" SG CYS B 940 " distance=2.03 Simple disulfide: pdb=" SG CYS B1117 " - pdb=" SG CYS B1128 " distance=2.03 Simple disulfide: pdb=" SG CYS B1167 " - pdb=" SG CYS B1212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 183 " distance=2.04 Simple disulfide: pdb=" SG CYS C 163 " - pdb=" SG CYS C 242 " distance=2.04 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 292 " distance=2.03 Simple disulfide: pdb=" SG CYS C 327 " - pdb=" SG CYS C 352 " distance=2.03 Simple disulfide: pdb=" SG CYS C 370 " - pdb=" SG CYS C 423 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 466 " - pdb=" SG CYS C 546 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 495 " distance=2.03 Simple disulfide: pdb=" SG CYS C 476 " - pdb=" SG CYS C 567 " distance=2.03 Simple disulfide: pdb=" SG CYS C 485 " - pdb=" SG CYS C 516 " distance=2.03 Simple disulfide: pdb=" SG CYS C 504 " - pdb=" SG CYS C 518 " distance=2.03 Simple disulfide: pdb=" SG CYS C 520 " - pdb=" SG CYS C 533 " distance=2.03 Simple disulfide: pdb=" SG CYS C 556 " - pdb=" SG CYS C 569 " distance=2.04 Simple disulfide: pdb=" SG CYS C 582 " - pdb=" SG CYS C 588 " distance=2.04 Simple disulfide: pdb=" SG CYS C 621 " - pdb=" SG CYS C 674 " distance=2.03 Simple disulfide: pdb=" SG CYS C 699 " - pdb=" SG CYS C 720 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 744 " distance=2.03 Simple disulfide: pdb=" SG CYS C 818 " - pdb=" SG CYS C 840 " distance=2.03 Simple disulfide: pdb=" SG CYS C 823 " - pdb=" SG CYS C 829 " distance=2.03 Simple disulfide: pdb=" SG CYS C 894 " - pdb=" SG CYS C 899 " distance=2.03 Simple disulfide: pdb=" SG CYS C 929 " - pdb=" SG CYS C 940 " distance=2.03 Simple disulfide: pdb=" SG CYS C1117 " - pdb=" SG CYS C1128 " distance=2.03 Simple disulfide: pdb=" SG CYS C1167 " - pdb=" SG CYS C1212 " 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 G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " 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 P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " 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 Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A1401 " - " ASN A 19 " " NAG A1402 " - " ASN A 171 " " NAG A1403 " - " ASN A 192 " " NAG A1404 " - " ASN A 454 " " NAG A1405 " - " ASN A 470 " " NAG A1406 " - " ASN A 775 " " NAG A1407 " - " ASN A 780 " " NAG A1408 " - " ASN A 797 " " NAG A1409 " - " ASN A 928 " " NAG A1410 " - " ASN A 433 " " NAG B1401 " - " ASN B 19 " " NAG B1402 " - " ASN B 171 " " NAG B1403 " - " ASN B 192 " " NAG B1404 " - " ASN B 454 " " NAG B1405 " - " ASN B 470 " " NAG B1406 " - " ASN B 775 " " NAG B1407 " - " ASN B 780 " " NAG B1408 " - " ASN B 797 " " NAG B1409 " - " ASN B 928 " " NAG B1410 " - " ASN B 433 " " NAG C1401 " - " ASN C 19 " " NAG C1402 " - " ASN C 171 " " NAG C1403 " - " ASN C 192 " " NAG C1404 " - " ASN C 454 " " NAG C1405 " - " ASN C 470 " " NAG C1406 " - " ASN C 775 " " NAG C1407 " - " ASN C 780 " " NAG C1408 " - " ASN C 797 " " NAG C1409 " - " ASN C 928 " " NAG C1410 " - " ASN C 433 " " NAG D 1 " - " ASN A 188 " " NAG E 1 " - " ASN A 705 " " NAG F 1 " - " ASN A 355 " " NAG G 1 " - " ASN A 132 " " NAG H 1 " - " ASN A 686 " " NAG I 1 " - " ASN A 726 " " NAG J 1 " - " ASN A1215 " " NAG K 1 " - " ASN A 58 " " NAG L 1 " - " ASN A 666 " " NAG M 1 " - " ASN B 188 " " NAG N 1 " - " ASN B 705 " " NAG O 1 " - " ASN B 355 " " NAG P 1 " - " ASN B 132 " " NAG Q 1 " - " ASN B 686 " " NAG R 1 " - " ASN B 726 " " NAG S 1 " - " ASN B1215 " " NAG T 1 " - " ASN B 58 " " NAG U 1 " - " ASN B 666 " " NAG V 1 " - " ASN C 188 " " NAG W 1 " - " ASN C 705 " " NAG X 1 " - " ASN C 355 " " NAG Y 1 " - " ASN C 132 " " NAG Z 1 " - " ASN C 686 " " NAG a 1 " - " ASN C 726 " " NAG b 1 " - " ASN C1215 " " NAG c 1 " - " ASN C 58 " " NAG d 1 " - " ASN C 666 " Time building additional restraints: 12.43 Conformation dependent library (CDL) restraints added in 5.4 seconds 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6762 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 60 sheets defined 24.2% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.88 Creating SS restraints... Processing helix chain 'A' and resid 88 through 91 removed outlier: 4.175A pdb=" N GLN A 91 " --> pdb=" O LEU A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 88 through 91' Processing helix chain 'A' and resid 285 through 295 Processing helix chain 'A' and resid 328 through 334 Processing helix chain 'A' and resid 355 through 363 removed outlier: 3.571A pdb=" N VAL A 363 " --> pdb=" O LEU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 402 removed outlier: 3.545A pdb=" N LEU A 401 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN A 402 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 413 Processing helix chain 'A' and resid 442 through 448 removed outlier: 3.765A pdb=" N TYR A 448 " --> pdb=" O TRP A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 485 removed outlier: 3.713A pdb=" N SER A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 706 Processing helix chain 'A' and resid 785 through 789 removed outlier: 4.114A pdb=" N GLY A 788 " --> pdb=" O SER A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 822 Processing helix chain 'A' and resid 826 through 833 Processing helix chain 'A' and resid 836 through 865 removed outlier: 3.526A pdb=" N CYS A 840 " --> pdb=" O TYR A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 915 removed outlier: 4.033A pdb=" N LEU A 910 " --> pdb=" O PHE A 906 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU A 911 " --> pdb=" O PHE A 907 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A 915 " --> pdb=" O LEU A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 928 Processing helix chain 'A' and resid 937 through 945 removed outlier: 4.236A pdb=" N VAL A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 972 Processing helix chain 'A' and resid 982 through 994 removed outlier: 3.804A pdb=" N LEU A 994 " --> pdb=" O ARG A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1003 removed outlier: 3.671A pdb=" N ASN A1002 " --> pdb=" O MET A 998 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS A1003 " --> pdb=" O ASP A 999 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 998 through 1003' Processing helix chain 'A' and resid 1004 through 1022 Processing helix chain 'A' and resid 1023 through 1025 No H-bonds generated for 'chain 'A' and resid 1023 through 1025' Processing helix chain 'A' and resid 1027 through 1050 Processing helix chain 'A' and resid 1051 through 1053 No H-bonds generated for 'chain 'A' and resid 1051 through 1053' Processing helix chain 'A' and resid 1061 through 1069 removed outlier: 3.570A pdb=" N ILE A1065 " --> pdb=" O SER A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1118 removed outlier: 3.920A pdb=" N GLN A1077 " --> pdb=" O GLU A1073 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A1118 " --> pdb=" O VAL A1114 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 91 removed outlier: 4.285A pdb=" N GLN B 91 " --> pdb=" O LEU B 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 88 through 91' Processing helix chain 'B' and resid 285 through 295 Processing helix chain 'B' and resid 328 through 334 Processing helix chain 'B' and resid 355 through 363 removed outlier: 3.590A pdb=" N VAL B 363 " --> pdb=" O LEU B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 402 removed outlier: 3.552A pdb=" N LEU B 401 " --> pdb=" O ARG B 398 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN B 402 " --> pdb=" O SER B 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 398 through 402' Processing helix chain 'B' and resid 407 through 413 Processing helix chain 'B' and resid 442 through 448 removed outlier: 3.771A pdb=" N TYR B 448 " --> pdb=" O TRP B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 485 removed outlier: 3.680A pdb=" N SER B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 706 Processing helix chain 'B' and resid 817 through 822 Processing helix chain 'B' and resid 826 through 833 Processing helix chain 'B' and resid 836 through 865 removed outlier: 3.555A pdb=" N CYS B 840 " --> pdb=" O TYR B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 905 through 915 removed outlier: 4.003A pdb=" N LEU B 910 " --> pdb=" O PHE B 906 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU B 911 " --> pdb=" O PHE B 907 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL B 915 " --> pdb=" O LEU B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 918 through 928 Processing helix chain 'B' and resid 937 through 945 removed outlier: 4.193A pdb=" N VAL B 941 " --> pdb=" O ASP B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 972 Processing helix chain 'B' and resid 982 through 994 removed outlier: 3.819A pdb=" N LEU B 994 " --> pdb=" O ARG B 990 " (cutoff:3.500A) Processing helix chain 'B' and resid 998 through 1003 removed outlier: 3.654A pdb=" N ASN B1002 " --> pdb=" O MET B 998 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS B1003 " --> pdb=" O ASP B 999 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 998 through 1003' Processing helix chain 'B' and resid 1004 through 1022 Processing helix chain 'B' and resid 1023 through 1025 No H-bonds generated for 'chain 'B' and resid 1023 through 1025' Processing helix chain 'B' and resid 1028 through 1050 Processing helix chain 'B' and resid 1051 through 1053 No H-bonds generated for 'chain 'B' and resid 1051 through 1053' Processing helix chain 'B' and resid 1061 through 1069 removed outlier: 3.544A pdb=" N ILE B1065 " --> pdb=" O SER B1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 1073 through 1118 removed outlier: 3.915A pdb=" N GLN B1077 " --> pdb=" O GLU B1073 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 91 removed outlier: 4.222A pdb=" N GLN C 91 " --> pdb=" O LEU C 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 88 through 91' Processing helix chain 'C' and resid 285 through 295 Processing helix chain 'C' and resid 328 through 334 Processing helix chain 'C' and resid 355 through 363 removed outlier: 3.592A pdb=" N VAL C 363 " --> pdb=" O LEU C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 378 removed outlier: 3.646A pdb=" N LYS C 377 " --> pdb=" O ASP C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 402 removed outlier: 3.571A pdb=" N LEU C 401 " --> pdb=" O ARG C 398 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN C 402 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 413 Processing helix chain 'C' and resid 442 through 448 removed outlier: 3.774A pdb=" N TYR C 448 " --> pdb=" O TRP C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 485 removed outlier: 3.703A pdb=" N SER C 484 " --> pdb=" O SER C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 698 through 706 Processing helix chain 'C' and resid 785 through 789 removed outlier: 4.122A pdb=" N GLY C 788 " --> pdb=" O SER C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 822 Processing helix chain 'C' and resid 826 through 833 Processing helix chain 'C' and resid 836 through 865 removed outlier: 3.539A pdb=" N CYS C 840 " --> pdb=" O TYR C 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 905 through 915 removed outlier: 4.041A pdb=" N LEU C 910 " --> pdb=" O PHE C 906 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU C 911 " --> pdb=" O PHE C 907 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL C 915 " --> pdb=" O LEU C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 918 through 928 Processing helix chain 'C' and resid 937 through 945 removed outlier: 4.196A pdb=" N VAL C 941 " --> pdb=" O ASP C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 955 through 972 Processing helix chain 'C' and resid 975 through 979 removed outlier: 3.515A pdb=" N ALA C 978 " --> pdb=" O TRP C 975 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA C 979 " --> pdb=" O SER C 976 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 975 through 979' Processing helix chain 'C' and resid 982 through 993 Processing helix chain 'C' and resid 998 through 1003 removed outlier: 3.704A pdb=" N ASN C1002 " --> pdb=" O MET C 998 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS C1003 " --> pdb=" O ASP C 999 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 998 through 1003' Processing helix chain 'C' and resid 1004 through 1022 Processing helix chain 'C' and resid 1023 through 1025 No H-bonds generated for 'chain 'C' and resid 1023 through 1025' Processing helix chain 'C' and resid 1027 through 1050 Processing helix chain 'C' and resid 1051 through 1053 No H-bonds generated for 'chain 'C' and resid 1051 through 1053' Processing helix chain 'C' and resid 1061 through 1069 removed outlier: 3.560A pdb=" N ILE C1065 " --> pdb=" O SER C1061 " (cutoff:3.500A) Processing helix chain 'C' and resid 1073 through 1118 removed outlier: 3.884A pdb=" N GLN C1077 " --> pdb=" O GLU C1073 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL C1118 " --> pdb=" O VAL C1114 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 55 removed outlier: 6.090A pdb=" N VAL A 55 " --> pdb=" O TYR C 651 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY C 659 " --> pdb=" O LEU C 650 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ILE C 658 " --> pdb=" O ILE C 671 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY C 631 " --> pdb=" O TYR C 624 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA C 315 " --> pdb=" O CYS C 621 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 60 through 68 removed outlier: 3.657A pdb=" N GLY A 65 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N GLY A 101 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N TYR A 213 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N PHE A 222 " --> pdb=" O TYR A 213 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 60 through 68 removed outlier: 3.657A pdb=" N GLY A 65 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN A 278 " --> pdb=" O LYS A 269 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 80 through 81 Processing sheet with id=AA6, first strand: chain 'A' and resid 109 through 112 removed outlier: 3.754A pdb=" N THR A 109 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 185 through 190 removed outlier: 4.106A pdb=" N PHE A 185 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS A 187 " --> pdb=" O ILE A 148 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 302 through 306 removed outlier: 3.676A pdb=" N VAL A 679 " --> pdb=" O LEU A 306 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 315 through 319 removed outlier: 4.340A pdb=" N ALA A 315 " --> pdb=" O CYS A 621 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG A 319 " --> pdb=" O ASP A 625 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY A 631 " --> pdb=" O TYR A 624 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ILE A 658 " --> pdb=" O ILE A 671 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY A 659 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 337 through 339 Processing sheet with id=AB2, first strand: chain 'A' and resid 345 through 349 removed outlier: 3.670A pdb=" N LEU A 388 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N PHE A 383 " --> pdb=" O ILE A 599 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE A 599 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER A 385 " --> pdb=" O ASN A 597 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASN A 597 " --> pdb=" O SER A 385 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N SER A 428 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N THR A 365 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 345 through 349 removed outlier: 3.670A pdb=" N LEU A 388 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 459 through 463 Processing sheet with id=AB5, first strand: chain 'A' and resid 466 through 468 removed outlier: 4.282A pdb=" N CYS A 466 " --> pdb=" O SER A 538 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS A 536 " --> pdb=" O SER A 468 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 505 through 507 Processing sheet with id=AB7, first strand: chain 'A' and resid 725 through 732 removed outlier: 9.011A pdb=" N PHE A 768 " --> pdb=" O THR A 728 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N TYR A 730 " --> pdb=" O PHE A 768 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N PHE A 743 " --> pdb=" O MET A 739 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 777 through 779 Processing sheet with id=AB9, first strand: chain 'A' and resid 790 through 807 removed outlier: 6.941A pdb=" N GLU A 791 " --> pdb=" O LEU A1161 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU A1161 " --> pdb=" O GLU A 791 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LYS A 793 " --> pdb=" O THR A1159 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N THR A1159 " --> pdb=" O LYS A 793 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE A1157 " --> pdb=" O PRO A 795 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ASN A 797 " --> pdb=" O ILE A1155 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY A1144 " --> pdb=" O ALA A1141 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A1135 " --> pdb=" O PHE A1150 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N TYR A1152 " --> pdb=" O HIS A1133 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N HIS A1133 " --> pdb=" O TYR A1152 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 790 through 807 removed outlier: 6.941A pdb=" N GLU A 791 " --> pdb=" O LEU A1161 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU A1161 " --> pdb=" O GLU A 791 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LYS A 793 " --> pdb=" O THR A1159 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N THR A1159 " --> pdb=" O LYS A 793 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE A1157 " --> pdb=" O PRO A 795 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ASN A 797 " --> pdb=" O ILE A1155 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU A1161 " --> pdb=" O LYS A1183 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS A1183 " --> pdb=" O LEU A1161 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 813 through 815 removed outlier: 4.388A pdb=" N LYS A 813 " --> pdb=" O LEU A 950 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 871 through 872 removed outlier: 6.465A pdb=" N LEU A 871 " --> pdb=" O VAL C 779 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'A' and resid 1206 through 1209 removed outlier: 3.635A pdb=" N ILE A1174 " --> pdb=" O LEU A1166 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A1166 " --> pdb=" O ILE A1174 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AC6, first strand: chain 'B' and resid 60 through 68 removed outlier: 3.643A pdb=" N GLY B 65 " --> pdb=" O ARG B 264 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLY B 101 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR B 203 " --> pdb=" O TYR B 210 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N TYR B 213 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N PHE B 222 " --> pdb=" O TYR B 213 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 60 through 68 removed outlier: 3.643A pdb=" N GLY B 65 " --> pdb=" O ARG B 264 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU B 267 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA B 279 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LYS B 269 " --> pdb=" O THR B 277 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AC9, first strand: chain 'B' and resid 109 through 112 removed outlier: 3.821A pdb=" N THR B 109 " --> pdb=" O GLU B 120 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 185 through 190 removed outlier: 4.140A pdb=" N PHE B 185 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 302 through 306 removed outlier: 3.683A pdb=" N VAL B 679 " --> pdb=" O LEU B 306 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 315 through 319 removed outlier: 4.279A pdb=" N ALA B 315 " --> pdb=" O CYS B 621 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP B 623 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG B 319 " --> pdb=" O ASP B 625 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY B 631 " --> pdb=" O TYR B 624 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ILE B 658 " --> pdb=" O ILE B 671 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY B 659 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 337 through 339 removed outlier: 7.044A pdb=" N VAL B 338 " --> pdb=" O ASN B 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 345 through 349 removed outlier: 3.525A pdb=" N LYS B 390 " --> pdb=" O GLU B 345 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 388 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N PHE B 383 " --> pdb=" O ILE B 599 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ILE B 599 " --> pdb=" O PHE B 383 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER B 385 " --> pdb=" O ASN B 597 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN B 597 " --> pdb=" O SER B 385 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N SER B 428 " --> pdb=" O THR B 365 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N THR B 365 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 345 through 349 removed outlier: 3.525A pdb=" N LYS B 390 " --> pdb=" O GLU B 345 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 388 " --> pdb=" O LYS B 347 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 459 through 463 Processing sheet with id=AD8, first strand: chain 'B' and resid 466 through 468 removed outlier: 4.237A pdb=" N CYS B 466 " --> pdb=" O SER B 538 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS B 536 " --> pdb=" O SER B 468 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 505 through 507 Processing sheet with id=AE1, first strand: chain 'B' and resid 725 through 732 removed outlier: 9.276A pdb=" N PHE B 768 " --> pdb=" O THR B 728 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TYR B 730 " --> pdb=" O PHE B 768 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N PHE B 743 " --> pdb=" O MET B 739 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 777 through 779 Processing sheet with id=AE3, first strand: chain 'B' and resid 790 through 807 removed outlier: 6.975A pdb=" N GLU B 791 " --> pdb=" O LEU B1161 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU B1161 " --> pdb=" O GLU B 791 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LYS B 793 " --> pdb=" O THR B1159 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR B1159 " --> pdb=" O LYS B 793 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N PHE B1157 " --> pdb=" O PRO B 795 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASN B 797 " --> pdb=" O ILE B1155 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY B1144 " --> pdb=" O ALA B1141 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU B1135 " --> pdb=" O PHE B1150 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N TYR B1152 " --> pdb=" O HIS B1133 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N HIS B1133 " --> pdb=" O TYR B1152 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 790 through 807 removed outlier: 6.975A pdb=" N GLU B 791 " --> pdb=" O LEU B1161 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU B1161 " --> pdb=" O GLU B 791 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LYS B 793 " --> pdb=" O THR B1159 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR B1159 " --> pdb=" O LYS B 793 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N PHE B1157 " --> pdb=" O PRO B 795 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASN B 797 " --> pdb=" O ILE B1155 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU B1161 " --> pdb=" O LYS B1183 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS B1183 " --> pdb=" O LEU B1161 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 813 through 815 removed outlier: 4.392A pdb=" N LYS B 813 " --> pdb=" O LEU B 950 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 1206 through 1209 removed outlier: 3.607A pdb=" N GLY B1173 " --> pdb=" O MET B1209 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE B1174 " --> pdb=" O LEU B1166 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B1166 " --> pdb=" O ILE B1174 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AE8, first strand: chain 'C' and resid 60 through 68 removed outlier: 3.609A pdb=" N GLY C 65 " --> pdb=" O ARG C 264 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N GLY C 101 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR C 203 " --> pdb=" O TYR C 210 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N TYR C 213 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N PHE C 222 " --> pdb=" O TYR C 213 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 60 through 68 removed outlier: 3.609A pdb=" N GLY C 65 " --> pdb=" O ARG C 264 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU C 267 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA C 279 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LYS C 269 " --> pdb=" O THR C 277 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 80 through 81 Processing sheet with id=AF2, first strand: chain 'C' and resid 109 through 112 removed outlier: 3.752A pdb=" N THR C 109 " --> pdb=" O GLU C 120 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 185 through 190 removed outlier: 4.182A pdb=" N PHE C 185 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 302 through 306 removed outlier: 3.741A pdb=" N VAL C 679 " --> pdb=" O LEU C 306 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 337 through 339 Processing sheet with id=AF6, first strand: chain 'C' and resid 345 through 349 removed outlier: 3.506A pdb=" N GLU C 345 " --> pdb=" O LYS C 390 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 388 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N PHE C 383 " --> pdb=" O ILE C 599 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE C 599 " --> pdb=" O PHE C 383 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER C 385 " --> pdb=" O ASN C 597 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN C 597 " --> pdb=" O SER C 385 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N SER C 428 " --> pdb=" O THR C 365 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N THR C 365 " --> pdb=" O SER C 428 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 345 through 349 removed outlier: 3.506A pdb=" N GLU C 345 " --> pdb=" O LYS C 390 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 388 " --> pdb=" O LYS C 347 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 459 through 463 Processing sheet with id=AF9, first strand: chain 'C' and resid 466 through 468 removed outlier: 4.288A pdb=" N CYS C 466 " --> pdb=" O SER C 538 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS C 536 " --> pdb=" O SER C 468 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 505 through 507 Processing sheet with id=AG2, first strand: chain 'C' and resid 725 through 732 removed outlier: 9.025A pdb=" N PHE C 768 " --> pdb=" O THR C 728 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N TYR C 730 " --> pdb=" O PHE C 768 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N PHE C 743 " --> pdb=" O MET C 739 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 790 through 807 removed outlier: 6.937A pdb=" N GLU C 791 " --> pdb=" O LEU C1161 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N LEU C1161 " --> pdb=" O GLU C 791 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LYS C 793 " --> pdb=" O THR C1159 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR C1159 " --> pdb=" O LYS C 793 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N PHE C1157 " --> pdb=" O PRO C 795 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ASN C 797 " --> pdb=" O ILE C1155 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY C1144 " --> pdb=" O ALA C1141 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C1137 " --> pdb=" O MET C1148 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU C1135 " --> pdb=" O PHE C1150 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N TYR C1152 " --> pdb=" O HIS C1133 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N HIS C1133 " --> pdb=" O TYR C1152 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 790 through 807 removed outlier: 6.937A pdb=" N GLU C 791 " --> pdb=" O LEU C1161 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N LEU C1161 " --> pdb=" O GLU C 791 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LYS C 793 " --> pdb=" O THR C1159 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR C1159 " --> pdb=" O LYS C 793 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N PHE C1157 " --> pdb=" O PRO C 795 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ASN C 797 " --> pdb=" O ILE C1155 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU C1161 " --> pdb=" O LYS C1183 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LYS C1183 " --> pdb=" O LEU C1161 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 813 through 815 removed outlier: 4.325A pdb=" N LYS C 813 " --> pdb=" O LEU C 950 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 1206 through 1209 removed outlier: 3.796A pdb=" N GLY C1173 " --> pdb=" O MET C1209 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU C1166 " --> pdb=" O ILE C1174 " (cutoff:3.500A) 1083 hydrogen bonds defined for protein. 3102 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.39 Time building geometry restraints manager: 13.41 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: 8859 1.34 - 1.46: 7651 1.46 - 1.58: 13302 1.58 - 1.71: 2 1.71 - 1.83: 204 Bond restraints: 30018 Sorted by residual: bond pdb=" CB PRO B1220 " pdb=" CG PRO B1220 " ideal model delta sigma weight residual 1.492 1.633 -0.141 5.00e-02 4.00e+02 7.96e+00 bond pdb=" CB PRO A1220 " pdb=" CG PRO A1220 " ideal model delta sigma weight residual 1.492 1.606 -0.114 5.00e-02 4.00e+02 5.21e+00 bond pdb=" C1 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.12e+00 bond pdb=" C1 NAG Z 1 " pdb=" O5 NAG Z 1 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.07e+00 bond pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.05e+00 ... (remaining 30013 not shown) Histogram of bond angle deviations from ideal: 98.01 - 105.20: 441 105.20 - 112.40: 15500 112.40 - 119.59: 9396 119.59 - 126.78: 15203 126.78 - 133.98: 311 Bond angle restraints: 40851 Sorted by residual: angle pdb=" CA PRO B1220 " pdb=" N PRO B1220 " pdb=" CD PRO B1220 " ideal model delta sigma weight residual 112.00 102.33 9.67 1.40e+00 5.10e-01 4.77e+01 angle pdb=" CA PRO C1220 " pdb=" N PRO C1220 " pdb=" CD PRO C1220 " ideal model delta sigma weight residual 112.00 104.82 7.18 1.40e+00 5.10e-01 2.63e+01 angle pdb=" CA PRO A1220 " pdb=" N PRO A1220 " pdb=" CD PRO A1220 " ideal model delta sigma weight residual 112.00 105.38 6.62 1.40e+00 5.10e-01 2.24e+01 angle pdb=" CA LEU B 510 " pdb=" CB LEU B 510 " pdb=" CG LEU B 510 " ideal model delta sigma weight residual 116.30 130.39 -14.09 3.50e+00 8.16e-02 1.62e+01 angle pdb=" CA LEU A 510 " pdb=" CB LEU A 510 " pdb=" CG LEU A 510 " ideal model delta sigma weight residual 116.30 130.06 -13.76 3.50e+00 8.16e-02 1.55e+01 ... (remaining 40846 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.88: 17522 21.88 - 43.76: 1205 43.76 - 65.64: 167 65.64 - 87.53: 38 87.53 - 109.41: 19 Dihedral angle restraints: 18951 sinusoidal: 8418 harmonic: 10533 Sorted by residual: dihedral pdb=" CB CYS A 476 " pdb=" SG CYS A 476 " pdb=" SG CYS A 567 " pdb=" CB CYS A 567 " ideal model delta sinusoidal sigma weight residual -86.00 -169.84 83.84 1 1.00e+01 1.00e-02 8.57e+01 dihedral pdb=" CB CYS C 476 " pdb=" SG CYS C 476 " pdb=" SG CYS C 567 " pdb=" CB CYS C 567 " ideal model delta sinusoidal sigma weight residual -86.00 -168.96 82.96 1 1.00e+01 1.00e-02 8.42e+01 dihedral pdb=" CB CYS B 476 " pdb=" SG CYS B 476 " pdb=" SG CYS B 567 " pdb=" CB CYS B 567 " ideal model delta sinusoidal sigma weight residual -86.00 -168.38 82.38 1 1.00e+01 1.00e-02 8.33e+01 ... (remaining 18948 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 3907 0.059 - 0.118: 845 0.118 - 0.177: 72 0.177 - 0.236: 14 0.236 - 0.295: 4 Chirality restraints: 4842 Sorted by residual: chirality pdb=" CB THR C 31 " pdb=" CA THR C 31 " pdb=" OG1 THR C 31 " pdb=" CG2 THR C 31 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" C5 BMA P 3 " pdb=" C4 BMA P 3 " pdb=" C6 BMA P 3 " pdb=" O5 BMA P 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.89e+00 ... (remaining 4839 not shown) Planarity restraints: 5181 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C1219 " 0.096 5.00e-02 4.00e+02 1.41e-01 3.17e+01 pdb=" N PRO C1220 " -0.243 5.00e-02 4.00e+02 pdb=" CA PRO C1220 " 0.075 5.00e-02 4.00e+02 pdb=" CD PRO C1220 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B1219 " 0.057 5.00e-02 4.00e+02 8.03e-02 1.03e+01 pdb=" N PRO B1220 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO B1220 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B1220 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A1219 " -0.054 5.00e-02 4.00e+02 7.80e-02 9.74e+00 pdb=" N PRO A1220 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO A1220 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A1220 " -0.043 5.00e-02 4.00e+02 ... (remaining 5178 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2405 2.75 - 3.28: 27524 3.28 - 3.82: 48079 3.82 - 4.36: 54555 4.36 - 4.90: 96541 Nonbonded interactions: 229104 Sorted by model distance: nonbonded pdb=" O PRO C 68 " pdb=" OH TYR C 266 " model vdw 2.208 2.440 nonbonded pdb=" O PRO A 68 " pdb=" OH TYR A 266 " model vdw 2.240 2.440 nonbonded pdb=" O PRO B 68 " pdb=" OH TYR B 266 " model vdw 2.259 2.440 nonbonded pdb=" OG SER B 506 " pdb=" OD1 ASP B 514 " model vdw 2.275 2.440 nonbonded pdb=" OD1 ASN A 337 " pdb=" OG1 THR A 435 " model vdw 2.278 2.440 ... (remaining 229099 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 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'G' selection = chain 'P' selection = chain 'Y' } 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: 1.660 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: 0.030 Extract box with map and model: 7.040 Check model and map are aligned: 0.430 Set scattering table: 0.290 Process input model: 79.710 Find NCS groups from input model: 1.770 Set up NCS constraints: 0.420 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: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 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 : 0.004 0.141 30018 Z= 0.281 Angle : 0.700 14.086 40851 Z= 0.334 Chirality : 0.048 0.295 4842 Planarity : 0.006 0.141 5124 Dihedral : 14.339 109.407 11973 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.13), residues: 3573 helix: 0.76 (0.18), residues: 723 sheet: -0.68 (0.18), residues: 828 loop : -1.59 (0.13), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 444 HIS 0.005 0.001 HIS B 201 PHE 0.026 0.001 PHE A 176 TYR 0.038 0.001 TYR C 266 ARG 0.002 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 696 time to evaluate : 3.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ILE cc_start: 0.8880 (pt) cc_final: 0.8486 (mm) REVERT: A 133 ASN cc_start: 0.8449 (p0) cc_final: 0.8209 (p0) REVERT: A 142 HIS cc_start: 0.7828 (m90) cc_final: 0.6663 (m90) REVERT: A 174 TRP cc_start: 0.8455 (p-90) cc_final: 0.7738 (p-90) REVERT: A 175 HIS cc_start: 0.8443 (p-80) cc_final: 0.7850 (p-80) REVERT: A 186 LYS cc_start: 0.8085 (ttmt) cc_final: 0.7826 (ttmm) REVERT: A 206 ARG cc_start: 0.8309 (mtm110) cc_final: 0.7971 (ptp-110) REVERT: A 262 SER cc_start: 0.7690 (t) cc_final: 0.7268 (p) REVERT: A 316 THR cc_start: 0.8891 (m) cc_final: 0.8391 (p) REVERT: A 326 ASP cc_start: 0.7211 (t70) cc_final: 0.6422 (t0) REVERT: A 328 ASP cc_start: 0.7587 (m-30) cc_final: 0.7175 (m-30) REVERT: A 397 ARG cc_start: 0.8446 (mmt180) cc_final: 0.8206 (mmm-85) REVERT: A 417 ASP cc_start: 0.7999 (t70) cc_final: 0.7784 (t0) REVERT: A 437 ASN cc_start: 0.8829 (t0) cc_final: 0.8358 (p0) REVERT: A 553 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7640 (mp0) REVERT: A 574 PHE cc_start: 0.8415 (m-80) cc_final: 0.7816 (m-80) REVERT: A 711 GLN cc_start: 0.7366 (pm20) cc_final: 0.6999 (mp10) REVERT: A 717 TYR cc_start: 0.8608 (t80) cc_final: 0.8381 (t80) REVERT: A 725 ASP cc_start: 0.7792 (p0) cc_final: 0.7489 (p0) REVERT: A 779 VAL cc_start: 0.8602 (t) cc_final: 0.7837 (m) REVERT: A 792 ILE cc_start: 0.8997 (tt) cc_final: 0.8538 (pt) REVERT: A 832 LEU cc_start: 0.8932 (mt) cc_final: 0.7897 (mm) REVERT: A 842 ASN cc_start: 0.8624 (m-40) cc_final: 0.8346 (m-40) REVERT: A 844 ASN cc_start: 0.8666 (m-40) cc_final: 0.7506 (m-40) REVERT: A 848 ASP cc_start: 0.8004 (m-30) cc_final: 0.7482 (m-30) REVERT: A 855 ASP cc_start: 0.7831 (m-30) cc_final: 0.7570 (m-30) REVERT: A 874 ASN cc_start: 0.8409 (m-40) cc_final: 0.7740 (p0) REVERT: A 887 ASN cc_start: 0.8967 (m-40) cc_final: 0.8551 (m-40) REVERT: A 889 LYS cc_start: 0.8783 (ttpt) cc_final: 0.8472 (ttmm) REVERT: A 909 ASP cc_start: 0.8275 (m-30) cc_final: 0.7382 (m-30) REVERT: A 910 LEU cc_start: 0.9257 (mp) cc_final: 0.8701 (mt) REVERT: A 938 LEU cc_start: 0.8547 (mm) cc_final: 0.8334 (mt) REVERT: A 999 ASP cc_start: 0.8080 (t0) cc_final: 0.7621 (t0) REVERT: A 1005 GLN cc_start: 0.8484 (tm-30) cc_final: 0.8080 (tm-30) REVERT: A 1010 THR cc_start: 0.9025 (m) cc_final: 0.8707 (p) REVERT: A 1054 LYS cc_start: 0.8876 (mttt) cc_final: 0.8560 (mmmm) REVERT: A 1079 ASP cc_start: 0.8305 (m-30) cc_final: 0.7696 (m-30) REVERT: A 1083 ASN cc_start: 0.8560 (m-40) cc_final: 0.8337 (m110) REVERT: A 1095 GLN cc_start: 0.7912 (tm-30) cc_final: 0.7579 (tm-30) REVERT: A 1209 MET cc_start: 0.7919 (mtt) cc_final: 0.7579 (mtt) REVERT: B 69 LYS cc_start: 0.8861 (tmtt) cc_final: 0.8601 (ttpp) REVERT: B 88 LEU cc_start: 0.9116 (mp) cc_final: 0.8888 (tp) REVERT: B 187 LYS cc_start: 0.8657 (tttt) cc_final: 0.7768 (ttmm) REVERT: B 197 TRP cc_start: 0.8455 (m100) cc_final: 0.7618 (m100) REVERT: B 316 THR cc_start: 0.8762 (m) cc_final: 0.8126 (p) REVERT: B 326 ASP cc_start: 0.6896 (t70) cc_final: 0.6031 (t0) REVERT: B 328 ASP cc_start: 0.7448 (m-30) cc_final: 0.6545 (m-30) REVERT: B 331 LYS cc_start: 0.8420 (mttt) cc_final: 0.8104 (mtpp) REVERT: B 397 ARG cc_start: 0.8419 (mmt180) cc_final: 0.7995 (mmm-85) REVERT: B 411 SER cc_start: 0.9234 (t) cc_final: 0.8855 (p) REVERT: B 448 TYR cc_start: 0.8409 (m-80) cc_final: 0.8013 (m-10) REVERT: B 450 PHE cc_start: 0.8419 (t80) cc_final: 0.7989 (t80) REVERT: B 462 TYR cc_start: 0.8109 (p90) cc_final: 0.7844 (p90) REVERT: B 578 SER cc_start: 0.7502 (p) cc_final: 0.6072 (p) REVERT: B 704 ASN cc_start: 0.7915 (p0) cc_final: 0.7580 (p0) REVERT: B 711 GLN cc_start: 0.7309 (pm20) cc_final: 0.7012 (mp10) REVERT: B 792 ILE cc_start: 0.9010 (tt) cc_final: 0.8657 (pt) REVERT: B 842 ASN cc_start: 0.8553 (m-40) cc_final: 0.8197 (m-40) REVERT: B 848 ASP cc_start: 0.8154 (m-30) cc_final: 0.7713 (m-30) REVERT: B 855 ASP cc_start: 0.7741 (m-30) cc_final: 0.7539 (m-30) REVERT: B 874 ASN cc_start: 0.8262 (m-40) cc_final: 0.7692 (p0) REVERT: B 908 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7604 (mt-10) REVERT: B 910 LEU cc_start: 0.9275 (mp) cc_final: 0.8661 (mt) REVERT: B 914 LYS cc_start: 0.8972 (mmtt) cc_final: 0.8754 (mmmt) REVERT: B 916 LYS cc_start: 0.8209 (pttt) cc_final: 0.7879 (ptmm) REVERT: B 999 ASP cc_start: 0.8108 (t0) cc_final: 0.7763 (t0) REVERT: B 1003 LYS cc_start: 0.8928 (mtpt) cc_final: 0.8503 (mtpp) REVERT: B 1004 ASN cc_start: 0.8036 (m-40) cc_final: 0.6342 (t0) REVERT: B 1010 THR cc_start: 0.8932 (m) cc_final: 0.8674 (p) REVERT: B 1045 ASN cc_start: 0.8749 (t0) cc_final: 0.8427 (t0) REVERT: B 1054 LYS cc_start: 0.8664 (mttt) cc_final: 0.8340 (mmmm) REVERT: B 1075 GLN cc_start: 0.7878 (mm-40) cc_final: 0.7244 (mm-40) REVERT: B 1079 ASP cc_start: 0.8165 (m-30) cc_final: 0.7747 (m-30) REVERT: B 1095 GLN cc_start: 0.7941 (tm-30) cc_final: 0.6490 (tm-30) REVERT: B 1099 ASP cc_start: 0.8219 (m-30) cc_final: 0.7138 (m-30) REVERT: B 1177 LYS cc_start: 0.8308 (ttmm) cc_final: 0.7949 (mmmm) REVERT: B 1210 ASN cc_start: 0.8957 (t0) cc_final: 0.8752 (m-40) REVERT: C 22 ASN cc_start: 0.8398 (p0) cc_final: 0.8181 (p0) REVERT: C 53 ASP cc_start: 0.7702 (m-30) cc_final: 0.7314 (m-30) REVERT: C 69 LYS cc_start: 0.8876 (tmtt) cc_final: 0.8611 (tttp) REVERT: C 92 LYS cc_start: 0.9109 (mttt) cc_final: 0.8661 (mtpp) REVERT: C 142 HIS cc_start: 0.7473 (m90) cc_final: 0.6937 (m-70) REVERT: C 206 ARG cc_start: 0.8099 (mtm110) cc_final: 0.7829 (ptp-170) REVERT: C 208 THR cc_start: 0.8136 (p) cc_final: 0.7888 (p) REVERT: C 262 SER cc_start: 0.7214 (t) cc_final: 0.6791 (p) REVERT: C 288 SER cc_start: 0.8663 (m) cc_final: 0.8215 (p) REVERT: C 289 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7640 (mm-30) REVERT: C 293 LYS cc_start: 0.8811 (ttpt) cc_final: 0.8491 (ptpp) REVERT: C 316 THR cc_start: 0.8845 (m) cc_final: 0.8229 (p) REVERT: C 331 LYS cc_start: 0.8451 (mttt) cc_final: 0.8145 (mtpp) REVERT: C 397 ARG cc_start: 0.8483 (mmt180) cc_final: 0.8184 (mmm-85) REVERT: C 437 ASN cc_start: 0.8499 (t0) cc_final: 0.8041 (p0) REVERT: C 439 TYR cc_start: 0.8164 (t80) cc_final: 0.7875 (t80) REVERT: C 448 TYR cc_start: 0.8718 (m-80) cc_final: 0.8380 (m-80) REVERT: C 460 VAL cc_start: 0.8550 (t) cc_final: 0.8343 (p) REVERT: C 481 PHE cc_start: 0.6684 (t80) cc_final: 0.6381 (t80) REVERT: C 500 ASN cc_start: 0.7551 (m-40) cc_final: 0.7319 (m-40) REVERT: C 574 PHE cc_start: 0.8432 (m-80) cc_final: 0.8086 (m-80) REVERT: C 580 ASP cc_start: 0.7889 (t0) cc_final: 0.7616 (t70) REVERT: C 713 TYR cc_start: 0.8026 (p90) cc_final: 0.7782 (p90) REVERT: C 779 VAL cc_start: 0.8517 (t) cc_final: 0.7667 (m) REVERT: C 792 ILE cc_start: 0.8957 (tt) cc_final: 0.8511 (tp) REVERT: C 832 LEU cc_start: 0.9135 (mt) cc_final: 0.8321 (mm) REVERT: C 842 ASN cc_start: 0.8599 (m-40) cc_final: 0.8356 (m-40) REVERT: C 848 ASP cc_start: 0.8080 (m-30) cc_final: 0.7644 (m-30) REVERT: C 849 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7441 (mm-30) REVERT: C 874 ASN cc_start: 0.8374 (m-40) cc_final: 0.7785 (p0) REVERT: C 881 PHE cc_start: 0.7419 (p90) cc_final: 0.7186 (p90) REVERT: C 887 ASN cc_start: 0.8690 (m-40) cc_final: 0.8425 (m-40) REVERT: C 889 LYS cc_start: 0.8979 (ttpt) cc_final: 0.8678 (ttpp) REVERT: C 909 ASP cc_start: 0.8218 (m-30) cc_final: 0.7426 (m-30) REVERT: C 910 LEU cc_start: 0.9204 (mp) cc_final: 0.8836 (mt) REVERT: C 998 MET cc_start: 0.8861 (tpp) cc_final: 0.8127 (mmm) REVERT: C 999 ASP cc_start: 0.8059 (t70) cc_final: 0.7543 (t0) REVERT: C 1010 THR cc_start: 0.8834 (m) cc_final: 0.8473 (p) REVERT: C 1045 ASN cc_start: 0.8882 (t0) cc_final: 0.8624 (t0) REVERT: C 1054 LYS cc_start: 0.8860 (mttt) cc_final: 0.8642 (mtpp) REVERT: C 1095 GLN cc_start: 0.7995 (tm-30) cc_final: 0.6869 (tm-30) REVERT: C 1099 ASP cc_start: 0.8187 (m-30) cc_final: 0.6604 (m-30) REVERT: C 1126 ASN cc_start: 0.8536 (m-40) cc_final: 0.8188 (t0) outliers start: 0 outliers final: 0 residues processed: 696 average time/residue: 0.4425 time to fit residues: 474.0734 Evaluate side-chains 498 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 498 time to evaluate : 2.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 301 optimal weight: 3.9990 chunk 270 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 182 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 279 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 170 optimal weight: 0.5980 chunk 208 optimal weight: 2.9990 chunk 324 optimal weight: 0.8980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN A 300 ASN A 413 ASN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 ASN ** A 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 685 GLN A 867 GLN B 364 HIS B 413 ASN ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 GLN B 858 GLN B 867 GLN B 945 ASN ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 HIS C 334 ASN C 364 HIS C 413 ASN ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 30018 Z= 0.312 Angle : 0.621 11.463 40851 Z= 0.321 Chirality : 0.045 0.231 4842 Planarity : 0.005 0.081 5124 Dihedral : 7.941 61.652 5688 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.52 % Allowed : 8.83 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -0.76 (0.14), residues: 3573 helix: 1.71 (0.19), residues: 747 sheet: -0.30 (0.18), residues: 756 loop : -1.49 (0.13), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 257 HIS 0.004 0.001 HIS B 175 PHE 0.023 0.002 PHE A 907 TYR 0.030 0.002 TYR A 713 ARG 0.007 0.001 ARG C 678 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 533 time to evaluate : 3.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 TYR cc_start: 0.8158 (m-80) cc_final: 0.7954 (m-80) REVERT: A 133 ASN cc_start: 0.8431 (p0) cc_final: 0.8165 (p0) REVERT: A 140 GLN cc_start: 0.7206 (tm-30) cc_final: 0.6353 (tm-30) REVERT: A 142 HIS cc_start: 0.7852 (m90) cc_final: 0.7210 (m90) REVERT: A 175 HIS cc_start: 0.8461 (p-80) cc_final: 0.8177 (p-80) REVERT: A 196 ASP cc_start: 0.7562 (OUTLIER) cc_final: 0.7323 (p0) REVERT: A 262 SER cc_start: 0.8047 (t) cc_final: 0.7692 (p) REVERT: A 289 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7801 (mm-30) REVERT: A 305 ASP cc_start: 0.7860 (m-30) cc_final: 0.6817 (p0) REVERT: A 326 ASP cc_start: 0.7110 (t70) cc_final: 0.6572 (t0) REVERT: A 331 LYS cc_start: 0.8746 (mtpt) cc_final: 0.8465 (mtpp) REVERT: A 376 SER cc_start: 0.9080 (m) cc_final: 0.8623 (p) REVERT: A 384 LYS cc_start: 0.8430 (pttp) cc_final: 0.8087 (pttt) REVERT: A 397 ARG cc_start: 0.8523 (mmt180) cc_final: 0.8316 (mmm-85) REVERT: A 437 ASN cc_start: 0.8831 (t0) cc_final: 0.8425 (t0) REVERT: A 446 ARG cc_start: 0.8579 (ttm-80) cc_final: 0.7658 (mtm-85) REVERT: A 553 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8051 (mm-30) REVERT: A 580 ASP cc_start: 0.8174 (t0) cc_final: 0.7856 (t0) REVERT: A 678 ARG cc_start: 0.7150 (mtm180) cc_final: 0.6808 (ttp-170) REVERT: A 704 ASN cc_start: 0.7740 (p0) cc_final: 0.7456 (p0) REVERT: A 711 GLN cc_start: 0.7648 (pm20) cc_final: 0.7282 (mp10) REVERT: A 842 ASN cc_start: 0.8711 (m-40) cc_final: 0.8395 (m-40) REVERT: A 844 ASN cc_start: 0.8840 (m-40) cc_final: 0.7774 (m-40) REVERT: A 848 ASP cc_start: 0.8065 (m-30) cc_final: 0.7627 (m-30) REVERT: A 849 GLU cc_start: 0.7820 (pp20) cc_final: 0.7589 (pp20) REVERT: A 858 GLN cc_start: 0.8202 (mm110) cc_final: 0.7953 (mm110) REVERT: A 867 GLN cc_start: 0.7649 (mm110) cc_final: 0.7338 (mm-40) REVERT: A 874 ASN cc_start: 0.8522 (m-40) cc_final: 0.8005 (p0) REVERT: A 889 LYS cc_start: 0.9052 (ttpt) cc_final: 0.8673 (ttpp) REVERT: A 909 ASP cc_start: 0.8235 (m-30) cc_final: 0.7501 (m-30) REVERT: A 938 LEU cc_start: 0.8764 (mm) cc_final: 0.8521 (mt) REVERT: A 956 GLU cc_start: 0.7230 (pm20) cc_final: 0.6957 (pm20) REVERT: A 999 ASP cc_start: 0.8211 (t0) cc_final: 0.7749 (t0) REVERT: A 1054 LYS cc_start: 0.8837 (mttt) cc_final: 0.8523 (mtpp) REVERT: A 1083 ASN cc_start: 0.8661 (m-40) cc_final: 0.8390 (m110) REVERT: A 1095 GLN cc_start: 0.8047 (tm-30) cc_final: 0.7640 (tm-30) REVERT: A 1177 LYS cc_start: 0.8229 (tppt) cc_final: 0.7706 (mptt) REVERT: A 1189 MET cc_start: 0.8070 (mtt) cc_final: 0.7700 (mtt) REVERT: A 1209 MET cc_start: 0.7855 (mtt) cc_final: 0.7569 (mtt) REVERT: B 69 LYS cc_start: 0.8983 (tmtt) cc_final: 0.8770 (tmmt) REVERT: B 88 LEU cc_start: 0.9158 (mp) cc_final: 0.8810 (tp) REVERT: B 107 LYS cc_start: 0.8610 (tttt) cc_final: 0.8322 (ttpp) REVERT: B 111 LEU cc_start: 0.8707 (mm) cc_final: 0.8240 (mt) REVERT: B 131 ILE cc_start: 0.8798 (mp) cc_final: 0.8542 (tp) REVERT: B 142 HIS cc_start: 0.8085 (m-70) cc_final: 0.7010 (m-70) REVERT: B 175 HIS cc_start: 0.8601 (p-80) cc_final: 0.8168 (p-80) REVERT: B 197 TRP cc_start: 0.8504 (m100) cc_final: 0.8009 (m100) REVERT: B 206 ARG cc_start: 0.8526 (ptp90) cc_final: 0.8257 (ptp90) REVERT: B 236 TYR cc_start: 0.7900 (t80) cc_final: 0.7636 (t80) REVERT: B 271 ASP cc_start: 0.7366 (p0) cc_final: 0.7132 (p0) REVERT: B 273 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7519 (mtp-110) REVERT: B 326 ASP cc_start: 0.6853 (t70) cc_final: 0.6051 (t0) REVERT: B 328 ASP cc_start: 0.7725 (m-30) cc_final: 0.7111 (m-30) REVERT: B 331 LYS cc_start: 0.8906 (mttt) cc_final: 0.8325 (mtpp) REVERT: B 397 ARG cc_start: 0.8504 (mmt180) cc_final: 0.7982 (mmm-85) REVERT: B 400 ASP cc_start: 0.7874 (m-30) cc_final: 0.7386 (m-30) REVERT: B 411 SER cc_start: 0.9231 (t) cc_final: 0.8777 (p) REVERT: B 417 ASP cc_start: 0.7863 (t70) cc_final: 0.7630 (t70) REVERT: B 446 ARG cc_start: 0.8814 (ttm110) cc_final: 0.8406 (ttm110) REVERT: B 448 TYR cc_start: 0.8459 (m-80) cc_final: 0.8124 (m-10) REVERT: B 607 ASN cc_start: 0.7857 (t0) cc_final: 0.7627 (t0) REVERT: B 615 GLU cc_start: 0.7135 (tm-30) cc_final: 0.6814 (tm-30) REVERT: B 711 GLN cc_start: 0.7546 (pm20) cc_final: 0.7177 (mp10) REVERT: B 792 ILE cc_start: 0.9062 (tt) cc_final: 0.8779 (pt) REVERT: B 832 LEU cc_start: 0.8774 (mt) cc_final: 0.8129 (mm) REVERT: B 842 ASN cc_start: 0.8653 (m-40) cc_final: 0.8320 (m-40) REVERT: B 848 ASP cc_start: 0.8238 (m-30) cc_final: 0.7676 (m-30) REVERT: B 855 ASP cc_start: 0.7886 (m-30) cc_final: 0.7632 (m-30) REVERT: B 867 GLN cc_start: 0.7290 (mm110) cc_final: 0.6985 (mm-40) REVERT: B 874 ASN cc_start: 0.8459 (m-40) cc_final: 0.7840 (p0) REVERT: B 887 ASN cc_start: 0.8820 (m-40) cc_final: 0.8614 (t0) REVERT: B 916 LYS cc_start: 0.8401 (pttt) cc_final: 0.8067 (ptmm) REVERT: B 999 ASP cc_start: 0.8141 (t0) cc_final: 0.7778 (t0) REVERT: B 1003 LYS cc_start: 0.9002 (mtpt) cc_final: 0.8560 (mtpp) REVERT: B 1004 ASN cc_start: 0.8224 (m-40) cc_final: 0.6418 (t0) REVERT: B 1006 LYS cc_start: 0.9195 (mmmm) cc_final: 0.8828 (mmmm) REVERT: B 1010 THR cc_start: 0.9083 (m) cc_final: 0.8813 (p) REVERT: B 1045 ASN cc_start: 0.8797 (t0) cc_final: 0.8526 (t0) REVERT: B 1054 LYS cc_start: 0.8796 (mttt) cc_final: 0.8388 (mmmm) REVERT: B 1075 GLN cc_start: 0.8189 (mm-40) cc_final: 0.7560 (mm-40) REVERT: B 1079 ASP cc_start: 0.8320 (m-30) cc_final: 0.7994 (m-30) REVERT: B 1095 GLN cc_start: 0.8068 (tm-30) cc_final: 0.6835 (tm-30) REVERT: B 1099 ASP cc_start: 0.8248 (m-30) cc_final: 0.7297 (m-30) REVERT: B 1126 ASN cc_start: 0.8194 (t0) cc_final: 0.7944 (t0) REVERT: B 1177 LYS cc_start: 0.8511 (ttmm) cc_final: 0.8307 (mmmm) REVERT: B 1189 MET cc_start: 0.8240 (mtt) cc_final: 0.7911 (mtt) REVERT: B 1199 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7331 (mm-30) REVERT: B 1208 PHE cc_start: 0.8989 (m-10) cc_final: 0.8581 (m-80) REVERT: B 1216 PHE cc_start: 0.7856 (m-10) cc_final: 0.7553 (m-80) REVERT: C 53 ASP cc_start: 0.7848 (m-30) cc_final: 0.7481 (m-30) REVERT: C 84 LYS cc_start: 0.8641 (mmmm) cc_final: 0.8377 (mmmt) REVERT: C 92 LYS cc_start: 0.9102 (mttt) cc_final: 0.8674 (mtpp) REVERT: C 140 GLN cc_start: 0.7472 (tm-30) cc_final: 0.7152 (tm-30) REVERT: C 226 LEU cc_start: 0.8606 (tp) cc_final: 0.8352 (tp) REVERT: C 262 SER cc_start: 0.7988 (t) cc_final: 0.7625 (p) REVERT: C 288 SER cc_start: 0.8668 (m) cc_final: 0.8204 (t) REVERT: C 293 LYS cc_start: 0.8837 (ttpt) cc_final: 0.8560 (ttpt) REVERT: C 331 LYS cc_start: 0.8949 (mttt) cc_final: 0.8406 (mtpp) REVERT: C 397 ARG cc_start: 0.8581 (mmt180) cc_final: 0.8262 (mmm-85) REVERT: C 437 ASN cc_start: 0.8586 (t0) cc_final: 0.8174 (t0) REVERT: C 439 TYR cc_start: 0.8128 (t80) cc_final: 0.7868 (t80) REVERT: C 446 ARG cc_start: 0.8545 (ttm110) cc_final: 0.7994 (mtm-85) REVERT: C 481 PHE cc_start: 0.6499 (t80) cc_final: 0.6244 (t80) REVERT: C 500 ASN cc_start: 0.7556 (m-40) cc_final: 0.7264 (m-40) REVERT: C 579 TYR cc_start: 0.8152 (p90) cc_final: 0.7799 (p90) REVERT: C 580 ASP cc_start: 0.7944 (t0) cc_final: 0.7739 (t0) REVERT: C 678 ARG cc_start: 0.7136 (ttm-80) cc_final: 0.6692 (ttm-80) REVERT: C 704 ASN cc_start: 0.7272 (p0) cc_final: 0.7017 (p0) REVERT: C 772 GLU cc_start: 0.7229 (mp0) cc_final: 0.6717 (mp0) REVERT: C 803 GLN cc_start: 0.7845 (tp-100) cc_final: 0.7295 (tp-100) REVERT: C 832 LEU cc_start: 0.9010 (mt) cc_final: 0.8592 (mm) REVERT: C 842 ASN cc_start: 0.8592 (m-40) cc_final: 0.8337 (m-40) REVERT: C 848 ASP cc_start: 0.8217 (m-30) cc_final: 0.7799 (m-30) REVERT: C 873 SER cc_start: 0.8865 (m) cc_final: 0.8646 (p) REVERT: C 874 ASN cc_start: 0.8563 (m-40) cc_final: 0.7880 (p0) REVERT: C 889 LYS cc_start: 0.9186 (ttpt) cc_final: 0.8802 (ttpp) REVERT: C 909 ASP cc_start: 0.8257 (m-30) cc_final: 0.7450 (m-30) REVERT: C 998 MET cc_start: 0.8707 (tpp) cc_final: 0.8126 (tpp) REVERT: C 999 ASP cc_start: 0.7940 (t70) cc_final: 0.7440 (t0) REVERT: C 1045 ASN cc_start: 0.8927 (t0) cc_final: 0.8663 (t0) REVERT: C 1075 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7137 (mm-40) REVERT: C 1079 ASP cc_start: 0.8149 (m-30) cc_final: 0.7729 (m-30) REVERT: C 1095 GLN cc_start: 0.8015 (tm-30) cc_final: 0.6895 (tm-30) REVERT: C 1099 ASP cc_start: 0.8223 (m-30) cc_final: 0.6560 (m-30) REVERT: C 1104 LYS cc_start: 0.8855 (tptt) cc_final: 0.8590 (ttmm) REVERT: C 1105 LEU cc_start: 0.8943 (mt) cc_final: 0.8635 (tt) REVERT: C 1112 GLU cc_start: 0.7986 (tp30) cc_final: 0.7613 (tp30) REVERT: C 1126 ASN cc_start: 0.8664 (m-40) cc_final: 0.8181 (t0) REVERT: C 1199 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7349 (mm-30) REVERT: C 1216 PHE cc_start: 0.7641 (m-10) cc_final: 0.7413 (m-80) outliers start: 49 outliers final: 24 residues processed: 558 average time/residue: 0.4297 time to fit residues: 372.9130 Evaluate side-chains 494 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 468 time to evaluate : 3.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 1003 LYS Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 293 LYS Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 608 ASP Chi-restraints excluded: chain B residue 909 ASP Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 1130 ASN Chi-restraints excluded: chain C residue 1159 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 180 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 269 optimal weight: 2.9990 chunk 220 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 324 optimal weight: 0.0470 chunk 350 optimal weight: 3.9990 chunk 289 optimal weight: 0.6980 chunk 322 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 260 optimal weight: 2.9990 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 HIS ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 ASN B 364 HIS ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 ASN B 589 ASN B 607 ASN B 858 GLN B1042 GLN C 364 HIS ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 589 ASN C1139 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30018 Z= 0.193 Angle : 0.568 11.459 40851 Z= 0.292 Chirality : 0.043 0.204 4842 Planarity : 0.004 0.062 5124 Dihedral : 7.016 59.969 5688 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.59 % Allowed : 12.78 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -0.64 (0.14), residues: 3573 helix: 1.77 (0.19), residues: 780 sheet: -0.27 (0.18), residues: 783 loop : -1.44 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 174 HIS 0.013 0.001 HIS B 142 PHE 0.016 0.001 PHE A 907 TYR 0.021 0.001 TYR B 713 ARG 0.006 0.000 ARG C 464 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 494 time to evaluate : 3.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 PHE cc_start: 0.7946 (t80) cc_final: 0.7715 (t80) REVERT: A 133 ASN cc_start: 0.8580 (p0) cc_final: 0.8241 (p0) REVERT: A 140 GLN cc_start: 0.7255 (tm-30) cc_final: 0.6420 (tm-30) REVERT: A 142 HIS cc_start: 0.8136 (m90) cc_final: 0.6992 (m90) REVERT: A 157 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7268 (mm-30) REVERT: A 175 HIS cc_start: 0.8454 (p-80) cc_final: 0.8184 (p-80) REVERT: A 186 LYS cc_start: 0.8266 (ttpp) cc_final: 0.7999 (ptmm) REVERT: A 289 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7798 (mm-30) REVERT: A 326 ASP cc_start: 0.7109 (t70) cc_final: 0.6769 (t0) REVERT: A 331 LYS cc_start: 0.8793 (mtpt) cc_final: 0.8447 (mtpp) REVERT: A 376 SER cc_start: 0.9054 (m) cc_final: 0.8600 (p) REVERT: A 384 LYS cc_start: 0.8427 (pttp) cc_final: 0.8078 (pttt) REVERT: A 437 ASN cc_start: 0.8786 (t0) cc_final: 0.8377 (t0) REVERT: A 553 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8015 (mm-30) REVERT: A 618 THR cc_start: 0.9204 (OUTLIER) cc_final: 0.8951 (m) REVERT: A 678 ARG cc_start: 0.7102 (mtm180) cc_final: 0.6835 (ttp-170) REVERT: A 704 ASN cc_start: 0.7643 (p0) cc_final: 0.7408 (p0) REVERT: A 711 GLN cc_start: 0.7679 (pm20) cc_final: 0.7311 (mp10) REVERT: A 772 GLU cc_start: 0.7607 (mp0) cc_final: 0.7348 (mp0) REVERT: A 805 GLU cc_start: 0.7350 (tm-30) cc_final: 0.7042 (tm-30) REVERT: A 842 ASN cc_start: 0.8707 (m-40) cc_final: 0.8396 (m-40) REVERT: A 844 ASN cc_start: 0.8826 (m-40) cc_final: 0.7721 (m-40) REVERT: A 848 ASP cc_start: 0.8054 (m-30) cc_final: 0.7613 (m-30) REVERT: A 849 GLU cc_start: 0.7839 (pp20) cc_final: 0.7603 (pp20) REVERT: A 858 GLN cc_start: 0.8215 (mm110) cc_final: 0.7926 (mm110) REVERT: A 874 ASN cc_start: 0.8510 (m-40) cc_final: 0.7997 (p0) REVERT: A 889 LYS cc_start: 0.9002 (ttpt) cc_final: 0.8640 (ttpp) REVERT: A 909 ASP cc_start: 0.8249 (m-30) cc_final: 0.7481 (m-30) REVERT: A 956 GLU cc_start: 0.7285 (pm20) cc_final: 0.7023 (pm20) REVERT: A 999 ASP cc_start: 0.8191 (t0) cc_final: 0.7717 (t0) REVERT: A 1054 LYS cc_start: 0.8824 (mttt) cc_final: 0.8520 (mtpp) REVERT: A 1068 ARG cc_start: 0.8576 (mtp85) cc_final: 0.8359 (mtp85) REVERT: A 1083 ASN cc_start: 0.8655 (m-40) cc_final: 0.8441 (m-40) REVERT: A 1095 GLN cc_start: 0.8003 (tm-30) cc_final: 0.7575 (tm-30) REVERT: A 1209 MET cc_start: 0.7851 (mtt) cc_final: 0.7574 (mtt) REVERT: B 69 LYS cc_start: 0.9001 (tmtt) cc_final: 0.8769 (tmmt) REVERT: B 88 LEU cc_start: 0.9160 (mp) cc_final: 0.8803 (tp) REVERT: B 107 LYS cc_start: 0.8646 (tttt) cc_final: 0.8343 (ttpp) REVERT: B 111 LEU cc_start: 0.8832 (mm) cc_final: 0.8412 (mt) REVERT: B 175 HIS cc_start: 0.8617 (p-80) cc_final: 0.8196 (p-80) REVERT: B 197 TRP cc_start: 0.8511 (m100) cc_final: 0.8091 (m100) REVERT: B 236 TYR cc_start: 0.7854 (t80) cc_final: 0.7592 (t80) REVERT: B 326 ASP cc_start: 0.6881 (t70) cc_final: 0.6047 (t0) REVERT: B 328 ASP cc_start: 0.7771 (m-30) cc_final: 0.7199 (m-30) REVERT: B 331 LYS cc_start: 0.8870 (mttt) cc_final: 0.8362 (mtpp) REVERT: B 384 LYS cc_start: 0.8592 (pttt) cc_final: 0.8244 (pttp) REVERT: B 397 ARG cc_start: 0.8437 (mmt180) cc_final: 0.7994 (mmm-85) REVERT: B 400 ASP cc_start: 0.7988 (m-30) cc_final: 0.7504 (m-30) REVERT: B 411 SER cc_start: 0.9242 (t) cc_final: 0.8804 (p) REVERT: B 417 ASP cc_start: 0.7877 (t70) cc_final: 0.7655 (t70) REVERT: B 446 ARG cc_start: 0.8791 (ttm110) cc_final: 0.8457 (ttm110) REVERT: B 587 ARG cc_start: 0.8031 (mtp85) cc_final: 0.7344 (mtp85) REVERT: B 607 ASN cc_start: 0.7866 (t0) cc_final: 0.7512 (t0) REVERT: B 711 GLN cc_start: 0.7626 (pm20) cc_final: 0.7243 (mp10) REVERT: B 781 ASP cc_start: 0.7635 (t0) cc_final: 0.7297 (t0) REVERT: B 792 ILE cc_start: 0.9059 (tt) cc_final: 0.8711 (pt) REVERT: B 832 LEU cc_start: 0.8781 (mt) cc_final: 0.8169 (mm) REVERT: B 842 ASN cc_start: 0.8588 (m-40) cc_final: 0.8280 (m-40) REVERT: B 848 ASP cc_start: 0.8207 (m-30) cc_final: 0.7701 (m-30) REVERT: B 849 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7771 (pp20) REVERT: B 855 ASP cc_start: 0.7877 (m-30) cc_final: 0.7614 (m-30) REVERT: B 874 ASN cc_start: 0.8587 (m-40) cc_final: 0.7870 (p0) REVERT: B 887 ASN cc_start: 0.8797 (m-40) cc_final: 0.8585 (t0) REVERT: B 889 LYS cc_start: 0.9044 (ttpt) cc_final: 0.8554 (ttmm) REVERT: B 914 LYS cc_start: 0.9124 (mmmt) cc_final: 0.8921 (mmmm) REVERT: B 916 LYS cc_start: 0.8406 (pttt) cc_final: 0.8058 (ptmm) REVERT: B 1006 LYS cc_start: 0.9162 (mmmm) cc_final: 0.8942 (mmmm) REVERT: B 1010 THR cc_start: 0.9080 (m) cc_final: 0.8819 (p) REVERT: B 1032 LYS cc_start: 0.8646 (mtpt) cc_final: 0.8426 (mtpt) REVERT: B 1045 ASN cc_start: 0.8752 (t0) cc_final: 0.8504 (t0) REVERT: B 1054 LYS cc_start: 0.8769 (mttt) cc_final: 0.8363 (mmmm) REVERT: B 1075 GLN cc_start: 0.8152 (mm-40) cc_final: 0.7499 (mm-40) REVERT: B 1079 ASP cc_start: 0.8228 (m-30) cc_final: 0.7886 (m-30) REVERT: B 1095 GLN cc_start: 0.8047 (tm-30) cc_final: 0.6821 (tm-30) REVERT: B 1099 ASP cc_start: 0.8248 (m-30) cc_final: 0.7274 (m-30) REVERT: B 1126 ASN cc_start: 0.8141 (t0) cc_final: 0.7864 (t0) REVERT: B 1189 MET cc_start: 0.8232 (mtt) cc_final: 0.7963 (mtt) REVERT: B 1199 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7266 (mm-30) REVERT: B 1208 PHE cc_start: 0.8693 (m-10) cc_final: 0.8381 (m-80) REVERT: B 1209 MET cc_start: 0.8077 (mpp) cc_final: 0.7410 (mpp) REVERT: B 1216 PHE cc_start: 0.7935 (m-10) cc_final: 0.7592 (m-80) REVERT: C 53 ASP cc_start: 0.7840 (m-30) cc_final: 0.7519 (m-30) REVERT: C 84 LYS cc_start: 0.8573 (mmmm) cc_final: 0.8301 (mmmt) REVERT: C 92 LYS cc_start: 0.9095 (mttt) cc_final: 0.8674 (mtpp) REVERT: C 111 LEU cc_start: 0.8533 (mt) cc_final: 0.8310 (mt) REVERT: C 147 GLU cc_start: 0.7838 (pp20) cc_final: 0.7593 (pp20) REVERT: C 218 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.7483 (mtp) REVERT: C 262 SER cc_start: 0.7915 (t) cc_final: 0.7516 (p) REVERT: C 288 SER cc_start: 0.8668 (m) cc_final: 0.8187 (t) REVERT: C 331 LYS cc_start: 0.8974 (mttt) cc_final: 0.8360 (mtpp) REVERT: C 384 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8334 (pttt) REVERT: C 397 ARG cc_start: 0.8537 (mmt180) cc_final: 0.8306 (mmm-85) REVERT: C 437 ASN cc_start: 0.8593 (t0) cc_final: 0.8230 (t0) REVERT: C 481 PHE cc_start: 0.6443 (t80) cc_final: 0.6200 (t80) REVERT: C 500 ASN cc_start: 0.7541 (m-40) cc_final: 0.7239 (m-40) REVERT: C 574 PHE cc_start: 0.8539 (m-80) cc_final: 0.8187 (m-80) REVERT: C 579 TYR cc_start: 0.8112 (p90) cc_final: 0.7858 (p90) REVERT: C 678 ARG cc_start: 0.7105 (ttm-80) cc_final: 0.6712 (ttm-80) REVERT: C 704 ASN cc_start: 0.7181 (p0) cc_final: 0.6942 (p0) REVERT: C 739 MET cc_start: 0.8505 (mmm) cc_final: 0.8183 (mmt) REVERT: C 772 GLU cc_start: 0.7203 (mp0) cc_final: 0.6942 (mp0) REVERT: C 803 GLN cc_start: 0.7900 (tp-100) cc_final: 0.7698 (tp-100) REVERT: C 832 LEU cc_start: 0.9017 (mt) cc_final: 0.8503 (mm) REVERT: C 842 ASN cc_start: 0.8571 (m-40) cc_final: 0.8321 (m-40) REVERT: C 848 ASP cc_start: 0.8201 (m-30) cc_final: 0.7790 (m-30) REVERT: C 858 GLN cc_start: 0.8202 (mt0) cc_final: 0.7907 (mm-40) REVERT: C 873 SER cc_start: 0.8898 (m) cc_final: 0.8650 (p) REVERT: C 874 ASN cc_start: 0.8507 (m-40) cc_final: 0.7818 (p0) REVERT: C 888 PHE cc_start: 0.8167 (m-10) cc_final: 0.7627 (m-10) REVERT: C 889 LYS cc_start: 0.9190 (ttpt) cc_final: 0.8956 (ttpp) REVERT: C 909 ASP cc_start: 0.8164 (m-30) cc_final: 0.7462 (m-30) REVERT: C 998 MET cc_start: 0.8819 (tpp) cc_final: 0.8181 (tpp) REVERT: C 999 ASP cc_start: 0.7994 (t70) cc_final: 0.7519 (t0) REVERT: C 1003 LYS cc_start: 0.8865 (ttpp) cc_final: 0.8623 (ttpp) REVERT: C 1045 ASN cc_start: 0.8899 (t0) cc_final: 0.8626 (t0) REVERT: C 1075 GLN cc_start: 0.8103 (mm-40) cc_final: 0.7087 (mm-40) REVERT: C 1079 ASP cc_start: 0.8105 (m-30) cc_final: 0.7698 (m-30) REVERT: C 1095 GLN cc_start: 0.7982 (tm-30) cc_final: 0.6833 (tm-30) REVERT: C 1099 ASP cc_start: 0.8215 (m-30) cc_final: 0.6503 (m-30) REVERT: C 1104 LYS cc_start: 0.8841 (tptt) cc_final: 0.8482 (tppt) REVERT: C 1105 LEU cc_start: 0.8923 (mt) cc_final: 0.8715 (tt) REVERT: C 1112 GLU cc_start: 0.7982 (tp30) cc_final: 0.7659 (tp30) REVERT: C 1126 ASN cc_start: 0.8679 (m-40) cc_final: 0.8118 (t0) REVERT: C 1199 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7325 (mm-30) REVERT: C 1209 MET cc_start: 0.7992 (mpp) cc_final: 0.7075 (mpp) REVERT: C 1216 PHE cc_start: 0.7745 (m-10) cc_final: 0.7435 (m-80) outliers start: 51 outliers final: 27 residues processed: 520 average time/residue: 0.4387 time to fit residues: 349.7783 Evaluate side-chains 493 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 462 time to evaluate : 2.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 632 GLN Chi-restraints excluded: chain A residue 780 ASN Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 608 ASP Chi-restraints excluded: chain B residue 909 ASP Chi-restraints excluded: chain B residue 940 CYS Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 608 ASP Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 1130 ASN Chi-restraints excluded: chain C residue 1172 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 320 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 chunk 168 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 218 optimal weight: 6.9990 chunk 325 optimal weight: 5.9990 chunk 345 optimal weight: 7.9990 chunk 170 optimal weight: 3.9990 chunk 308 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 945 ASN ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 858 GLN B1042 GLN B1053 ASN C 364 HIS ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 593 ASN ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 958 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.125 30018 Z= 0.519 Angle : 0.711 10.692 40851 Z= 0.371 Chirality : 0.047 0.271 4842 Planarity : 0.005 0.066 5124 Dihedral : 6.735 59.901 5688 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.33 % Allowed : 14.65 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -0.76 (0.14), residues: 3573 helix: 1.67 (0.19), residues: 765 sheet: -0.21 (0.19), residues: 738 loop : -1.54 (0.13), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 257 HIS 0.008 0.001 HIS C 201 PHE 0.025 0.002 PHE B 591 TYR 0.028 0.002 TYR A 717 ARG 0.010 0.001 ARG C 587 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 505 time to evaluate : 3.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ASN cc_start: 0.8872 (m-40) cc_final: 0.8561 (p0) REVERT: A 133 ASN cc_start: 0.8527 (p0) cc_final: 0.8295 (p0) REVERT: A 140 GLN cc_start: 0.7316 (tm-30) cc_final: 0.6764 (tm-30) REVERT: A 186 LYS cc_start: 0.8322 (ttpp) cc_final: 0.8113 (ptpp) REVERT: A 289 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7852 (mm-30) REVERT: A 326 ASP cc_start: 0.7071 (t70) cc_final: 0.6758 (t70) REVERT: A 331 LYS cc_start: 0.9029 (mtpt) cc_final: 0.8721 (mtpp) REVERT: A 376 SER cc_start: 0.9124 (m) cc_final: 0.8677 (p) REVERT: A 384 LYS cc_start: 0.8480 (pttp) cc_final: 0.8134 (pttt) REVERT: A 400 ASP cc_start: 0.8135 (m-30) cc_final: 0.7641 (m-30) REVERT: A 411 SER cc_start: 0.9027 (t) cc_final: 0.8644 (p) REVERT: A 553 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8177 (mm-30) REVERT: A 618 THR cc_start: 0.9262 (OUTLIER) cc_final: 0.8997 (m) REVERT: A 704 ASN cc_start: 0.7288 (p0) cc_final: 0.7043 (p0) REVERT: A 711 GLN cc_start: 0.7875 (pm20) cc_final: 0.7407 (mp10) REVERT: A 781 ASP cc_start: 0.7917 (m-30) cc_final: 0.7163 (m-30) REVERT: A 842 ASN cc_start: 0.8711 (m-40) cc_final: 0.8431 (m-40) REVERT: A 844 ASN cc_start: 0.8907 (m-40) cc_final: 0.7937 (m-40) REVERT: A 848 ASP cc_start: 0.8146 (m-30) cc_final: 0.7663 (m-30) REVERT: A 849 GLU cc_start: 0.7859 (pp20) cc_final: 0.7612 (pp20) REVERT: A 867 GLN cc_start: 0.7765 (mm-40) cc_final: 0.7506 (mm110) REVERT: A 873 SER cc_start: 0.8952 (m) cc_final: 0.8680 (p) REVERT: A 874 ASN cc_start: 0.8714 (m-40) cc_final: 0.8188 (p0) REVERT: A 889 LYS cc_start: 0.9092 (ttpt) cc_final: 0.8685 (ttpp) REVERT: A 909 ASP cc_start: 0.8378 (m-30) cc_final: 0.7596 (m-30) REVERT: A 956 GLU cc_start: 0.7383 (pm20) cc_final: 0.7065 (pm20) REVERT: A 999 ASP cc_start: 0.8377 (t0) cc_final: 0.7800 (t0) REVERT: A 1042 GLN cc_start: 0.8353 (tp-100) cc_final: 0.8106 (tp-100) REVERT: A 1054 LYS cc_start: 0.8863 (mttt) cc_final: 0.8403 (mtpp) REVERT: A 1083 ASN cc_start: 0.8711 (m-40) cc_final: 0.8497 (m-40) REVERT: A 1095 GLN cc_start: 0.8096 (tm-30) cc_final: 0.6670 (tm-30) REVERT: A 1099 ASP cc_start: 0.8306 (m-30) cc_final: 0.6941 (m-30) REVERT: A 1112 GLU cc_start: 0.7921 (tp30) cc_final: 0.7656 (tp30) REVERT: A 1177 LYS cc_start: 0.8518 (tppt) cc_final: 0.7997 (tppt) REVERT: A 1189 MET cc_start: 0.7983 (mtt) cc_final: 0.7755 (mtt) REVERT: B 18 PHE cc_start: 0.8033 (t80) cc_final: 0.7577 (t80) REVERT: B 60 THR cc_start: 0.8765 (OUTLIER) cc_final: 0.8524 (p) REVERT: B 69 LYS cc_start: 0.9047 (tmtt) cc_final: 0.8708 (tmmt) REVERT: B 88 LEU cc_start: 0.9312 (mp) cc_final: 0.8882 (tp) REVERT: B 111 LEU cc_start: 0.8923 (mm) cc_final: 0.8454 (mt) REVERT: B 131 ILE cc_start: 0.8852 (mp) cc_final: 0.8621 (tp) REVERT: B 175 HIS cc_start: 0.8674 (p-80) cc_final: 0.8207 (p-80) REVERT: B 197 TRP cc_start: 0.8651 (m100) cc_final: 0.8386 (m100) REVERT: B 236 TYR cc_start: 0.8107 (t80) cc_final: 0.7800 (t80) REVERT: B 293 LYS cc_start: 0.8850 (tttm) cc_final: 0.8555 (pttm) REVERT: B 326 ASP cc_start: 0.6900 (t70) cc_final: 0.6158 (t0) REVERT: B 328 ASP cc_start: 0.7887 (m-30) cc_final: 0.7463 (m-30) REVERT: B 331 LYS cc_start: 0.8954 (mttt) cc_final: 0.8554 (ttmm) REVERT: B 384 LYS cc_start: 0.8571 (pttt) cc_final: 0.8220 (pttp) REVERT: B 388 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8572 (mp) REVERT: B 397 ARG cc_start: 0.8577 (mmt180) cc_final: 0.8024 (mmm-85) REVERT: B 400 ASP cc_start: 0.8101 (m-30) cc_final: 0.7602 (m-30) REVERT: B 411 SER cc_start: 0.9235 (t) cc_final: 0.8766 (p) REVERT: B 450 PHE cc_start: 0.8397 (t80) cc_final: 0.8112 (t80) REVERT: B 537 LYS cc_start: 0.8325 (tppt) cc_final: 0.8100 (tppt) REVERT: B 587 ARG cc_start: 0.8257 (mtp85) cc_final: 0.7109 (ttm-80) REVERT: B 589 ASN cc_start: 0.8974 (OUTLIER) cc_final: 0.8432 (m-40) REVERT: B 607 ASN cc_start: 0.7716 (t0) cc_final: 0.7147 (t0) REVERT: B 711 GLN cc_start: 0.7751 (pm20) cc_final: 0.7337 (mp10) REVERT: B 781 ASP cc_start: 0.7832 (t0) cc_final: 0.7480 (m-30) REVERT: B 792 ILE cc_start: 0.9039 (tt) cc_final: 0.8615 (pt) REVERT: B 832 LEU cc_start: 0.8753 (mt) cc_final: 0.8240 (mm) REVERT: B 842 ASN cc_start: 0.8616 (m-40) cc_final: 0.8285 (m-40) REVERT: B 848 ASP cc_start: 0.8253 (m-30) cc_final: 0.7773 (m-30) REVERT: B 855 ASP cc_start: 0.7928 (m-30) cc_final: 0.7701 (m-30) REVERT: B 874 ASN cc_start: 0.8958 (m-40) cc_final: 0.8466 (p0) REVERT: B 881 PHE cc_start: 0.7469 (p90) cc_final: 0.6857 (p90) REVERT: B 887 ASN cc_start: 0.8823 (m-40) cc_final: 0.8567 (m-40) REVERT: B 889 LYS cc_start: 0.9179 (ttpt) cc_final: 0.8700 (ttmm) REVERT: B 914 LYS cc_start: 0.9153 (mmmt) cc_final: 0.8919 (mmmm) REVERT: B 916 LYS cc_start: 0.8592 (pttt) cc_final: 0.8272 (ptmm) REVERT: B 956 GLU cc_start: 0.7438 (pm20) cc_final: 0.6996 (pm20) REVERT: B 1004 ASN cc_start: 0.8364 (m-40) cc_final: 0.8026 (m-40) REVERT: B 1054 LYS cc_start: 0.8913 (mttt) cc_final: 0.8596 (mmmm) REVERT: B 1075 GLN cc_start: 0.8472 (mm-40) cc_final: 0.7715 (mm-40) REVERT: B 1079 ASP cc_start: 0.8299 (m-30) cc_final: 0.7937 (m-30) REVERT: B 1095 GLN cc_start: 0.8193 (tm-30) cc_final: 0.6951 (tm-30) REVERT: B 1099 ASP cc_start: 0.8322 (m-30) cc_final: 0.6761 (m-30) REVERT: B 1126 ASN cc_start: 0.8210 (t0) cc_final: 0.7869 (t0) REVERT: B 1177 LYS cc_start: 0.8362 (mmmm) cc_final: 0.7889 (mmmm) REVERT: B 1199 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7195 (mm-30) REVERT: B 1208 PHE cc_start: 0.8591 (m-80) cc_final: 0.8355 (m-80) REVERT: B 1209 MET cc_start: 0.8005 (mpp) cc_final: 0.7378 (mpp) REVERT: C 53 ASP cc_start: 0.8100 (m-30) cc_final: 0.7831 (t0) REVERT: C 60 THR cc_start: 0.8974 (OUTLIER) cc_final: 0.8676 (p) REVERT: C 84 LYS cc_start: 0.8624 (mmmm) cc_final: 0.8325 (mmmt) REVERT: C 92 LYS cc_start: 0.9075 (mttt) cc_final: 0.8693 (mtpp) REVERT: C 111 LEU cc_start: 0.8812 (mt) cc_final: 0.8466 (mt) REVERT: C 147 GLU cc_start: 0.7965 (pp20) cc_final: 0.7736 (pp20) REVERT: C 160 HIS cc_start: 0.7690 (t70) cc_final: 0.7443 (t-170) REVERT: C 330 ASP cc_start: 0.8060 (p0) cc_final: 0.7799 (p0) REVERT: C 331 LYS cc_start: 0.9041 (mttt) cc_final: 0.8656 (ttmm) REVERT: C 345 GLU cc_start: 0.7620 (tp30) cc_final: 0.7361 (tp30) REVERT: C 384 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8354 (pttt) REVERT: C 397 ARG cc_start: 0.8613 (mmt180) cc_final: 0.8329 (mmm-85) REVERT: C 464 ARG cc_start: 0.8596 (tpp80) cc_final: 0.8287 (tpp80) REVERT: C 473 PHE cc_start: 0.7881 (t80) cc_final: 0.7596 (t80) REVERT: C 481 PHE cc_start: 0.6647 (t80) cc_final: 0.6413 (t80) REVERT: C 500 ASN cc_start: 0.7489 (m-40) cc_final: 0.7205 (m-40) REVERT: C 537 LYS cc_start: 0.8310 (tppt) cc_final: 0.7797 (tppt) REVERT: C 772 GLU cc_start: 0.7406 (mp0) cc_final: 0.7178 (mp0) REVERT: C 832 LEU cc_start: 0.8969 (mt) cc_final: 0.8364 (mm) REVERT: C 842 ASN cc_start: 0.8538 (m-40) cc_final: 0.8268 (m-40) REVERT: C 844 ASN cc_start: 0.8908 (m-40) cc_final: 0.8631 (m-40) REVERT: C 858 GLN cc_start: 0.8254 (mt0) cc_final: 0.7893 (mm110) REVERT: C 873 SER cc_start: 0.9056 (m) cc_final: 0.8770 (p) REVERT: C 874 ASN cc_start: 0.8805 (m-40) cc_final: 0.8409 (p0) REVERT: C 882 ASP cc_start: 0.7980 (t0) cc_final: 0.7767 (m-30) REVERT: C 887 ASN cc_start: 0.8911 (t0) cc_final: 0.8560 (t0) REVERT: C 888 PHE cc_start: 0.8214 (m-10) cc_final: 0.7867 (m-10) REVERT: C 889 LYS cc_start: 0.9225 (ttpt) cc_final: 0.8712 (ttmm) REVERT: C 909 ASP cc_start: 0.8077 (m-30) cc_final: 0.7363 (m-30) REVERT: C 956 GLU cc_start: 0.7303 (mm-30) cc_final: 0.7075 (mm-30) REVERT: C 998 MET cc_start: 0.8772 (tpp) cc_final: 0.7956 (mpp) REVERT: C 999 ASP cc_start: 0.8013 (t70) cc_final: 0.7569 (t0) REVERT: C 1045 ASN cc_start: 0.8930 (t0) cc_final: 0.8662 (t0) REVERT: C 1075 GLN cc_start: 0.8279 (mm110) cc_final: 0.7433 (mm-40) REVERT: C 1079 ASP cc_start: 0.8176 (m-30) cc_final: 0.7788 (m-30) REVERT: C 1095 GLN cc_start: 0.8053 (tm-30) cc_final: 0.6897 (tm-30) REVERT: C 1099 ASP cc_start: 0.8298 (m-30) cc_final: 0.6635 (m-30) REVERT: C 1105 LEU cc_start: 0.8880 (mt) cc_final: 0.8666 (tt) REVERT: C 1112 GLU cc_start: 0.8016 (tp30) cc_final: 0.7647 (tp30) REVERT: C 1209 MET cc_start: 0.7973 (mpp) cc_final: 0.7161 (mpp) REVERT: C 1216 PHE cc_start: 0.8294 (m-10) cc_final: 0.7937 (m-80) outliers start: 75 outliers final: 44 residues processed: 553 average time/residue: 0.4361 time to fit residues: 374.3208 Evaluate side-chains 518 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 468 time to evaluate : 3.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 444 TRP Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 780 ASN Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 589 ASN Chi-restraints excluded: chain B residue 608 ASP Chi-restraints excluded: chain B residue 909 ASP Chi-restraints excluded: chain B residue 940 CYS Chi-restraints excluded: chain B residue 1036 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 305 ASP Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 406 SER Chi-restraints excluded: chain C residue 608 ASP Chi-restraints excluded: chain C residue 703 LEU Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 885 ASN Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 1102 LEU Chi-restraints excluded: chain C residue 1130 ASN Chi-restraints excluded: chain C residue 1167 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 287 optimal weight: 9.9990 chunk 195 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 256 optimal weight: 0.5980 chunk 142 optimal weight: 4.9990 chunk 294 optimal weight: 0.6980 chunk 238 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 176 optimal weight: 0.9990 chunk 309 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 GLN ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 858 GLN B1053 ASN B1178 GLN C 364 HIS C 395 ASN ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 30018 Z= 0.187 Angle : 0.577 10.022 40851 Z= 0.298 Chirality : 0.043 0.298 4842 Planarity : 0.004 0.059 5124 Dihedral : 6.119 59.796 5688 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.71 % Allowed : 16.29 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.66 (0.14), residues: 3573 helix: 1.88 (0.19), residues: 777 sheet: -0.21 (0.18), residues: 759 loop : -1.54 (0.13), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 257 HIS 0.005 0.001 HIS A 160 PHE 0.023 0.001 PHE A 473 TYR 0.019 0.001 TYR A 439 ARG 0.004 0.000 ARG C 206 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 483 time to evaluate : 3.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 PHE cc_start: 0.8003 (t80) cc_final: 0.7786 (t80) REVERT: A 114 ASN cc_start: 0.8855 (m-40) cc_final: 0.8637 (m110) REVERT: A 133 ASN cc_start: 0.8461 (p0) cc_final: 0.8241 (p0) REVERT: A 140 GLN cc_start: 0.7341 (tm-30) cc_final: 0.6654 (tm-30) REVERT: A 157 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7563 (mm-30) REVERT: A 186 LYS cc_start: 0.8237 (ttpp) cc_final: 0.8001 (ptpp) REVERT: A 326 ASP cc_start: 0.7075 (t70) cc_final: 0.6776 (t0) REVERT: A 331 LYS cc_start: 0.8957 (mtpt) cc_final: 0.8655 (mtpp) REVERT: A 376 SER cc_start: 0.9057 (m) cc_final: 0.8605 (p) REVERT: A 384 LYS cc_start: 0.8486 (pttp) cc_final: 0.8097 (pttt) REVERT: A 411 SER cc_start: 0.9004 (t) cc_final: 0.8708 (p) REVERT: A 415 LYS cc_start: 0.8701 (tmtt) cc_final: 0.8434 (tmtt) REVERT: A 437 ASN cc_start: 0.8568 (t0) cc_final: 0.8213 (t0) REVERT: A 446 ARG cc_start: 0.8511 (ttm-80) cc_final: 0.8119 (ttm-80) REVERT: A 553 GLU cc_start: 0.8522 (mm-30) cc_final: 0.7934 (mm-30) REVERT: A 704 ASN cc_start: 0.7001 (p0) cc_final: 0.6629 (p0) REVERT: A 711 GLN cc_start: 0.7919 (pm20) cc_final: 0.7424 (mp10) REVERT: A 781 ASP cc_start: 0.7819 (m-30) cc_final: 0.7050 (m-30) REVERT: A 792 ILE cc_start: 0.9068 (tp) cc_final: 0.8722 (pt) REVERT: A 842 ASN cc_start: 0.8711 (m-40) cc_final: 0.8347 (m-40) REVERT: A 844 ASN cc_start: 0.8850 (m-40) cc_final: 0.7751 (m-40) REVERT: A 848 ASP cc_start: 0.8098 (m-30) cc_final: 0.7614 (m-30) REVERT: A 849 GLU cc_start: 0.7844 (pp20) cc_final: 0.7572 (pp20) REVERT: A 858 GLN cc_start: 0.8226 (mm110) cc_final: 0.7977 (mm110) REVERT: A 867 GLN cc_start: 0.7695 (mm-40) cc_final: 0.7386 (mm110) REVERT: A 873 SER cc_start: 0.8830 (m) cc_final: 0.8613 (p) REVERT: A 874 ASN cc_start: 0.8612 (m-40) cc_final: 0.8117 (p0) REVERT: A 889 LYS cc_start: 0.9020 (ttpt) cc_final: 0.8654 (ttpp) REVERT: A 909 ASP cc_start: 0.8250 (m-30) cc_final: 0.7533 (m-30) REVERT: A 956 GLU cc_start: 0.7315 (pm20) cc_final: 0.7013 (pm20) REVERT: A 998 MET cc_start: 0.8760 (tpp) cc_final: 0.8128 (tpp) REVERT: A 999 ASP cc_start: 0.8323 (t0) cc_final: 0.7730 (t0) REVERT: A 1042 GLN cc_start: 0.8335 (tp-100) cc_final: 0.8050 (tp-100) REVERT: A 1075 GLN cc_start: 0.8333 (mm-40) cc_final: 0.7438 (mm-40) REVERT: A 1079 ASP cc_start: 0.8343 (m-30) cc_final: 0.7734 (m-30) REVERT: A 1083 ASN cc_start: 0.8682 (m-40) cc_final: 0.8473 (m-40) REVERT: A 1095 GLN cc_start: 0.8008 (tm-30) cc_final: 0.6584 (tm-30) REVERT: A 1099 ASP cc_start: 0.8252 (m-30) cc_final: 0.6834 (m-30) REVERT: A 1112 GLU cc_start: 0.7845 (tp30) cc_final: 0.7606 (tp30) REVERT: B 18 PHE cc_start: 0.7955 (t80) cc_final: 0.7577 (t80) REVERT: B 69 LYS cc_start: 0.9039 (tmtt) cc_final: 0.8711 (tmmt) REVERT: B 88 LEU cc_start: 0.9254 (mp) cc_final: 0.8839 (tp) REVERT: B 111 LEU cc_start: 0.8947 (mm) cc_final: 0.8404 (mt) REVERT: B 142 HIS cc_start: 0.8009 (m-70) cc_final: 0.7758 (m-70) REVERT: B 175 HIS cc_start: 0.8646 (p-80) cc_final: 0.8211 (p-80) REVERT: B 271 ASP cc_start: 0.7252 (p0) cc_final: 0.7020 (p0) REVERT: B 273 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7465 (mtp-110) REVERT: B 293 LYS cc_start: 0.8833 (tttm) cc_final: 0.8588 (pttm) REVERT: B 326 ASP cc_start: 0.6883 (t70) cc_final: 0.6378 (t70) REVERT: B 328 ASP cc_start: 0.7884 (m-30) cc_final: 0.7603 (m-30) REVERT: B 331 LYS cc_start: 0.8911 (mttt) cc_final: 0.8472 (ttmm) REVERT: B 384 LYS cc_start: 0.8529 (pttt) cc_final: 0.8037 (pttp) REVERT: B 397 ARG cc_start: 0.8493 (mmt180) cc_final: 0.8067 (mmm-85) REVERT: B 400 ASP cc_start: 0.8050 (m-30) cc_final: 0.7695 (m-30) REVERT: B 411 SER cc_start: 0.9205 (t) cc_final: 0.8756 (p) REVERT: B 448 TYR cc_start: 0.8528 (m-10) cc_final: 0.8317 (m-10) REVERT: B 450 PHE cc_start: 0.8222 (t80) cc_final: 0.7959 (t80) REVERT: B 536 LYS cc_start: 0.7941 (mmtp) cc_final: 0.7579 (mmtt) REVERT: B 537 LYS cc_start: 0.8329 (tppt) cc_final: 0.7958 (tptt) REVERT: B 563 TYR cc_start: 0.8549 (m-80) cc_final: 0.8341 (m-80) REVERT: B 587 ARG cc_start: 0.8264 (mtp85) cc_final: 0.7216 (ttm-80) REVERT: B 711 GLN cc_start: 0.7797 (pm20) cc_final: 0.7343 (mp10) REVERT: B 781 ASP cc_start: 0.7893 (t0) cc_final: 0.7499 (m-30) REVERT: B 792 ILE cc_start: 0.9066 (tt) cc_final: 0.8685 (pt) REVERT: B 832 LEU cc_start: 0.8777 (mt) cc_final: 0.7580 (mt) REVERT: B 842 ASN cc_start: 0.8600 (m-40) cc_final: 0.8286 (m-40) REVERT: B 848 ASP cc_start: 0.8211 (m-30) cc_final: 0.7753 (m-30) REVERT: B 849 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7677 (pp20) REVERT: B 855 ASP cc_start: 0.7880 (m-30) cc_final: 0.7494 (m-30) REVERT: B 881 PHE cc_start: 0.7466 (p90) cc_final: 0.7203 (p90) REVERT: B 887 ASN cc_start: 0.8839 (m-40) cc_final: 0.8624 (m-40) REVERT: B 889 LYS cc_start: 0.9109 (ttpt) cc_final: 0.8673 (ttmm) REVERT: B 914 LYS cc_start: 0.9106 (mmmt) cc_final: 0.8872 (mmmm) REVERT: B 916 LYS cc_start: 0.8489 (pttt) cc_final: 0.8156 (ptmm) REVERT: B 956 GLU cc_start: 0.7284 (pm20) cc_final: 0.6879 (pm20) REVERT: B 1004 ASN cc_start: 0.8243 (m-40) cc_final: 0.7894 (m-40) REVERT: B 1054 LYS cc_start: 0.8855 (mttt) cc_final: 0.8465 (mmmm) REVERT: B 1075 GLN cc_start: 0.8351 (mm-40) cc_final: 0.7366 (mm-40) REVERT: B 1079 ASP cc_start: 0.8218 (m-30) cc_final: 0.7795 (m-30) REVERT: B 1095 GLN cc_start: 0.8095 (tm-30) cc_final: 0.6860 (tm-30) REVERT: B 1099 ASP cc_start: 0.8279 (m-30) cc_final: 0.6629 (m-30) REVERT: B 1126 ASN cc_start: 0.8172 (t0) cc_final: 0.7802 (t0) REVERT: B 1177 LYS cc_start: 0.8427 (mmmm) cc_final: 0.7824 (mmmm) REVERT: C 17 ASP cc_start: 0.7460 (p0) cc_final: 0.7078 (p0) REVERT: C 53 ASP cc_start: 0.8056 (m-30) cc_final: 0.7829 (t0) REVERT: C 84 LYS cc_start: 0.8587 (mmmm) cc_final: 0.8291 (mmmt) REVERT: C 111 LEU cc_start: 0.8799 (mt) cc_final: 0.8447 (mt) REVERT: C 147 GLU cc_start: 0.7956 (pp20) cc_final: 0.7737 (pp20) REVERT: C 293 LYS cc_start: 0.8856 (ttpt) cc_final: 0.8447 (ptpp) REVERT: C 330 ASP cc_start: 0.7972 (p0) cc_final: 0.7606 (p0) REVERT: C 331 LYS cc_start: 0.9017 (mttt) cc_final: 0.8592 (ttmm) REVERT: C 384 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8289 (pttt) REVERT: C 397 ARG cc_start: 0.8553 (mmt180) cc_final: 0.8279 (mmm-85) REVERT: C 473 PHE cc_start: 0.7715 (t80) cc_final: 0.7507 (t80) REVERT: C 481 PHE cc_start: 0.6585 (t80) cc_final: 0.6353 (t80) REVERT: C 500 ASN cc_start: 0.7484 (m-40) cc_final: 0.7203 (m-40) REVERT: C 537 LYS cc_start: 0.8318 (tppt) cc_final: 0.8052 (tppt) REVERT: C 678 ARG cc_start: 0.7423 (ttm170) cc_final: 0.7188 (ttm-80) REVERT: C 739 MET cc_start: 0.8527 (mmm) cc_final: 0.8156 (mmt) REVERT: C 772 GLU cc_start: 0.7370 (mp0) cc_final: 0.7114 (mp0) REVERT: C 832 LEU cc_start: 0.8972 (mt) cc_final: 0.8359 (mm) REVERT: C 842 ASN cc_start: 0.8585 (m-40) cc_final: 0.8321 (m-40) REVERT: C 844 ASN cc_start: 0.8904 (m-40) cc_final: 0.7557 (m-40) REVERT: C 848 ASP cc_start: 0.8289 (t0) cc_final: 0.7974 (m-30) REVERT: C 850 VAL cc_start: 0.9288 (OUTLIER) cc_final: 0.8840 (p) REVERT: C 855 ASP cc_start: 0.7874 (m-30) cc_final: 0.7664 (m-30) REVERT: C 858 GLN cc_start: 0.8263 (mt0) cc_final: 0.7890 (mt0) REVERT: C 873 SER cc_start: 0.9024 (m) cc_final: 0.8752 (p) REVERT: C 874 ASN cc_start: 0.8721 (m-40) cc_final: 0.8271 (p0) REVERT: C 882 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7172 (t0) REVERT: C 888 PHE cc_start: 0.8161 (m-10) cc_final: 0.7753 (m-10) REVERT: C 889 LYS cc_start: 0.9150 (ttpt) cc_final: 0.8771 (ttpp) REVERT: C 909 ASP cc_start: 0.8013 (m-30) cc_final: 0.7307 (m-30) REVERT: C 956 GLU cc_start: 0.7227 (mm-30) cc_final: 0.7007 (mm-30) REVERT: C 998 MET cc_start: 0.8726 (tpp) cc_final: 0.7821 (mpp) REVERT: C 999 ASP cc_start: 0.7969 (t70) cc_final: 0.7530 (t0) REVERT: C 1045 ASN cc_start: 0.8892 (t0) cc_final: 0.8627 (t0) REVERT: C 1075 GLN cc_start: 0.8176 (mm110) cc_final: 0.7268 (mm-40) REVERT: C 1079 ASP cc_start: 0.8082 (m-30) cc_final: 0.7666 (m-30) REVERT: C 1095 GLN cc_start: 0.8011 (tm-30) cc_final: 0.6822 (tm-30) REVERT: C 1099 ASP cc_start: 0.8216 (m-30) cc_final: 0.6482 (m-30) REVERT: C 1104 LYS cc_start: 0.8822 (tptp) cc_final: 0.8560 (ttmm) REVERT: C 1105 LEU cc_start: 0.8845 (mt) cc_final: 0.8631 (tt) REVERT: C 1112 GLU cc_start: 0.7985 (tp30) cc_final: 0.7662 (tp30) REVERT: C 1153 LYS cc_start: 0.8423 (tptp) cc_final: 0.8179 (tptp) REVERT: C 1199 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7229 (mm-30) REVERT: C 1209 MET cc_start: 0.7947 (mpp) cc_final: 0.7192 (mpp) outliers start: 55 outliers final: 32 residues processed: 515 average time/residue: 0.4485 time to fit residues: 356.3428 Evaluate side-chains 500 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 463 time to evaluate : 3.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 444 TRP Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 535 GLN Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 608 ASP Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1036 VAL Chi-restraints excluded: chain B residue 1186 ASP Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 186 LYS Chi-restraints excluded: chain C residue 305 ASP Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 608 ASP Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 882 ASP Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 1130 ASN Chi-restraints excluded: chain C residue 1159 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 116 optimal weight: 4.9990 chunk 310 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 202 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 345 optimal weight: 0.8980 chunk 286 optimal weight: 0.0970 chunk 159 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 181 optimal weight: 3.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 GLN B 372 ASN ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 858 GLN B 958 GLN ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 364 HIS C 424 GLN ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 30018 Z= 0.264 Angle : 0.579 9.973 40851 Z= 0.301 Chirality : 0.043 0.235 4842 Planarity : 0.004 0.059 5124 Dihedral : 5.793 58.259 5688 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.18 % Allowed : 16.54 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -0.65 (0.14), residues: 3573 helix: 1.87 (0.19), residues: 783 sheet: -0.21 (0.18), residues: 768 loop : -1.52 (0.13), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 257 HIS 0.007 0.001 HIS C 160 PHE 0.019 0.001 PHE B 714 TYR 0.023 0.001 TYR B 236 ARG 0.007 0.001 ARG A 464 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 485 time to evaluate : 3.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ASN cc_start: 0.8910 (m-40) cc_final: 0.8597 (p0) REVERT: A 133 ASN cc_start: 0.8438 (p0) cc_final: 0.8226 (p0) REVERT: A 135 TYR cc_start: 0.8748 (m-80) cc_final: 0.8448 (m-80) REVERT: A 140 GLN cc_start: 0.7268 (tm-30) cc_final: 0.6441 (tm-30) REVERT: A 142 HIS cc_start: 0.7781 (m90) cc_final: 0.6568 (m90) REVERT: A 157 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7718 (mm-30) REVERT: A 289 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7766 (mm-30) REVERT: A 331 LYS cc_start: 0.8989 (mtpt) cc_final: 0.8697 (mtpp) REVERT: A 376 SER cc_start: 0.9070 (m) cc_final: 0.8629 (p) REVERT: A 384 LYS cc_start: 0.8500 (pttp) cc_final: 0.8104 (pttt) REVERT: A 411 SER cc_start: 0.9021 (t) cc_final: 0.8719 (p) REVERT: A 415 LYS cc_start: 0.8729 (tmtt) cc_final: 0.8379 (tmtt) REVERT: A 446 ARG cc_start: 0.8514 (ttm-80) cc_final: 0.8079 (ttm-80) REVERT: A 553 GLU cc_start: 0.8507 (mm-30) cc_final: 0.7917 (mm-30) REVERT: A 609 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8709 (tt) REVERT: A 618 THR cc_start: 0.9280 (OUTLIER) cc_final: 0.9010 (m) REVERT: A 704 ASN cc_start: 0.6842 (p0) cc_final: 0.6515 (p0) REVERT: A 711 GLN cc_start: 0.7939 (pm20) cc_final: 0.7437 (mp10) REVERT: A 792 ILE cc_start: 0.9092 (tp) cc_final: 0.8758 (pt) REVERT: A 842 ASN cc_start: 0.8700 (m-40) cc_final: 0.8367 (m-40) REVERT: A 844 ASN cc_start: 0.8867 (m-40) cc_final: 0.7750 (m-40) REVERT: A 848 ASP cc_start: 0.8104 (m-30) cc_final: 0.7677 (m-30) REVERT: A 849 GLU cc_start: 0.7867 (pp20) cc_final: 0.7593 (pp20) REVERT: A 858 GLN cc_start: 0.8252 (mm110) cc_final: 0.8043 (mm110) REVERT: A 867 GLN cc_start: 0.7770 (mm-40) cc_final: 0.7450 (mm110) REVERT: A 873 SER cc_start: 0.8861 (m) cc_final: 0.8610 (p) REVERT: A 874 ASN cc_start: 0.8634 (m-40) cc_final: 0.8122 (p0) REVERT: A 889 LYS cc_start: 0.9030 (ttpt) cc_final: 0.8662 (ttpp) REVERT: A 909 ASP cc_start: 0.8303 (m-30) cc_final: 0.7603 (m-30) REVERT: A 956 GLU cc_start: 0.7313 (pm20) cc_final: 0.6975 (pm20) REVERT: A 998 MET cc_start: 0.8798 (tpp) cc_final: 0.8132 (tpp) REVERT: A 999 ASP cc_start: 0.8311 (t0) cc_final: 0.7756 (t0) REVERT: A 1064 GLU cc_start: 0.8144 (tp30) cc_final: 0.7534 (tp30) REVERT: A 1083 ASN cc_start: 0.8696 (m-40) cc_final: 0.8494 (m-40) REVERT: A 1095 GLN cc_start: 0.8041 (tm-30) cc_final: 0.6579 (tm-30) REVERT: A 1099 ASP cc_start: 0.8289 (m-30) cc_final: 0.6881 (m-30) REVERT: A 1112 GLU cc_start: 0.7881 (tp30) cc_final: 0.7555 (tp30) REVERT: A 1177 LYS cc_start: 0.8462 (tppt) cc_final: 0.7948 (tppt) REVERT: A 1178 GLN cc_start: 0.8633 (tt0) cc_final: 0.8319 (tt0) REVERT: B 18 PHE cc_start: 0.8027 (t80) cc_final: 0.7704 (t80) REVERT: B 53 ASP cc_start: 0.7891 (m-30) cc_final: 0.7677 (m-30) REVERT: B 69 LYS cc_start: 0.9050 (tmtt) cc_final: 0.8724 (tmmt) REVERT: B 88 LEU cc_start: 0.9248 (mp) cc_final: 0.8808 (tp) REVERT: B 111 LEU cc_start: 0.8983 (mm) cc_final: 0.8479 (mt) REVERT: B 142 HIS cc_start: 0.8130 (m-70) cc_final: 0.7273 (m-70) REVERT: B 175 HIS cc_start: 0.8643 (p-80) cc_final: 0.8169 (p-80) REVERT: B 293 LYS cc_start: 0.8843 (tttm) cc_final: 0.8592 (tmmt) REVERT: B 326 ASP cc_start: 0.6849 (t70) cc_final: 0.6348 (t70) REVERT: B 328 ASP cc_start: 0.7933 (m-30) cc_final: 0.7663 (m-30) REVERT: B 331 LYS cc_start: 0.8926 (mttt) cc_final: 0.8500 (ttmm) REVERT: B 388 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8454 (mp) REVERT: B 397 ARG cc_start: 0.8516 (mmt180) cc_final: 0.8139 (mmm-85) REVERT: B 400 ASP cc_start: 0.8096 (m-30) cc_final: 0.7750 (m-30) REVERT: B 411 SER cc_start: 0.9208 (t) cc_final: 0.8744 (p) REVERT: B 446 ARG cc_start: 0.8624 (ttm110) cc_final: 0.8189 (ttm110) REVERT: B 536 LYS cc_start: 0.8029 (mmtp) cc_final: 0.7635 (mmtt) REVERT: B 537 LYS cc_start: 0.8346 (tppt) cc_final: 0.8092 (tppt) REVERT: B 587 ARG cc_start: 0.8273 (mtp85) cc_final: 0.7154 (ttm-80) REVERT: B 711 GLN cc_start: 0.7806 (pm20) cc_final: 0.7342 (mp10) REVERT: B 781 ASP cc_start: 0.7902 (t0) cc_final: 0.7502 (m-30) REVERT: B 792 ILE cc_start: 0.9052 (tt) cc_final: 0.8690 (pt) REVERT: B 832 LEU cc_start: 0.8775 (mt) cc_final: 0.8020 (mm) REVERT: B 842 ASN cc_start: 0.8575 (m-40) cc_final: 0.8301 (m-40) REVERT: B 848 ASP cc_start: 0.8224 (m-30) cc_final: 0.7755 (m-30) REVERT: B 850 VAL cc_start: 0.9212 (OUTLIER) cc_final: 0.9003 (p) REVERT: B 855 ASP cc_start: 0.7888 (m-30) cc_final: 0.7471 (m-30) REVERT: B 881 PHE cc_start: 0.7514 (p90) cc_final: 0.7230 (p90) REVERT: B 887 ASN cc_start: 0.8839 (m-40) cc_final: 0.8634 (m-40) REVERT: B 889 LYS cc_start: 0.9121 (ttpt) cc_final: 0.8680 (ttmm) REVERT: B 914 LYS cc_start: 0.9102 (mmmt) cc_final: 0.8801 (mmmm) REVERT: B 916 LYS cc_start: 0.8533 (pttt) cc_final: 0.8228 (ptmm) REVERT: B 956 GLU cc_start: 0.7337 (pm20) cc_final: 0.6861 (pm20) REVERT: B 1004 ASN cc_start: 0.8260 (m-40) cc_final: 0.7970 (m-40) REVERT: B 1034 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8268 (mp10) REVERT: B 1042 GLN cc_start: 0.8461 (mm-40) cc_final: 0.8003 (tp-100) REVERT: B 1054 LYS cc_start: 0.8887 (mttt) cc_final: 0.8566 (mmmm) REVERT: B 1073 GLU cc_start: 0.7455 (pm20) cc_final: 0.7244 (pm20) REVERT: B 1075 GLN cc_start: 0.8384 (mm-40) cc_final: 0.7578 (mm-40) REVERT: B 1079 ASP cc_start: 0.8243 (m-30) cc_final: 0.7859 (m-30) REVERT: B 1095 GLN cc_start: 0.8103 (tm-30) cc_final: 0.6860 (tm-30) REVERT: B 1099 ASP cc_start: 0.8287 (m-30) cc_final: 0.6661 (m-30) REVERT: B 1126 ASN cc_start: 0.8231 (t0) cc_final: 0.7835 (t0) REVERT: C 17 ASP cc_start: 0.7506 (p0) cc_final: 0.7077 (p0) REVERT: C 53 ASP cc_start: 0.8079 (m-30) cc_final: 0.7836 (t0) REVERT: C 60 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8624 (p) REVERT: C 84 LYS cc_start: 0.8630 (mmmm) cc_final: 0.8115 (tptt) REVERT: C 147 GLU cc_start: 0.7988 (pp20) cc_final: 0.7710 (pp20) REVERT: C 330 ASP cc_start: 0.8057 (p0) cc_final: 0.7703 (p0) REVERT: C 331 LYS cc_start: 0.9030 (mttt) cc_final: 0.8623 (ttmm) REVERT: C 384 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8200 (pttp) REVERT: C 397 ARG cc_start: 0.8608 (mmt180) cc_final: 0.8315 (mmm-85) REVERT: C 473 PHE cc_start: 0.7803 (t80) cc_final: 0.7559 (t80) REVERT: C 481 PHE cc_start: 0.6624 (t80) cc_final: 0.6374 (t80) REVERT: C 500 ASN cc_start: 0.7489 (m-40) cc_final: 0.7228 (m-40) REVERT: C 739 MET cc_start: 0.8564 (mmm) cc_final: 0.8178 (mmt) REVERT: C 772 GLU cc_start: 0.7439 (mp0) cc_final: 0.7173 (mp0) REVERT: C 832 LEU cc_start: 0.8992 (mt) cc_final: 0.8310 (mm) REVERT: C 842 ASN cc_start: 0.8587 (m-40) cc_final: 0.8316 (m-40) REVERT: C 855 ASP cc_start: 0.7895 (m-30) cc_final: 0.7571 (m-30) REVERT: C 858 GLN cc_start: 0.8253 (mt0) cc_final: 0.7850 (mm110) REVERT: C 873 SER cc_start: 0.9050 (m) cc_final: 0.8777 (p) REVERT: C 874 ASN cc_start: 0.8760 (m-40) cc_final: 0.8373 (p0) REVERT: C 882 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7211 (t0) REVERT: C 888 PHE cc_start: 0.8231 (m-10) cc_final: 0.7787 (m-10) REVERT: C 889 LYS cc_start: 0.9150 (ttpt) cc_final: 0.8732 (ttpp) REVERT: C 909 ASP cc_start: 0.7995 (m-30) cc_final: 0.7757 (m-30) REVERT: C 956 GLU cc_start: 0.7271 (mm-30) cc_final: 0.7034 (mm-30) REVERT: C 971 MET cc_start: 0.7341 (ttt) cc_final: 0.7105 (ttt) REVERT: C 998 MET cc_start: 0.8506 (tpp) cc_final: 0.7991 (tpp) REVERT: C 999 ASP cc_start: 0.7955 (t70) cc_final: 0.7560 (t0) REVERT: C 1045 ASN cc_start: 0.8895 (t0) cc_final: 0.8635 (t0) REVERT: C 1075 GLN cc_start: 0.8249 (mm110) cc_final: 0.7414 (mm-40) REVERT: C 1079 ASP cc_start: 0.8115 (m-30) cc_final: 0.7696 (m-30) REVERT: C 1095 GLN cc_start: 0.8025 (tm-30) cc_final: 0.6827 (tm-30) REVERT: C 1099 ASP cc_start: 0.8224 (m-30) cc_final: 0.6504 (m-30) REVERT: C 1112 GLU cc_start: 0.7994 (tp30) cc_final: 0.7632 (tp30) REVERT: C 1153 LYS cc_start: 0.8477 (tptp) cc_final: 0.8236 (tptp) REVERT: C 1199 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7232 (mm-30) REVERT: C 1209 MET cc_start: 0.7991 (mpp) cc_final: 0.7283 (mpp) outliers start: 70 outliers final: 46 residues processed: 530 average time/residue: 0.4572 time to fit residues: 377.5977 Evaluate side-chains 528 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 473 time to evaluate : 3.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 444 TRP Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 780 ASN Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1186 ASP Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 535 GLN Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 608 ASP Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1034 GLN Chi-restraints excluded: chain B residue 1186 ASP Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 305 ASP Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 406 SER Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 589 ASN Chi-restraints excluded: chain C residue 608 ASP Chi-restraints excluded: chain C residue 699 CYS Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 882 ASP Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 1130 ASN Chi-restraints excluded: chain C residue 1167 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 333 optimal weight: 0.4980 chunk 38 optimal weight: 0.1980 chunk 196 optimal weight: 3.9990 chunk 252 optimal weight: 6.9990 chunk 195 optimal weight: 0.2980 chunk 290 optimal weight: 7.9990 chunk 192 optimal weight: 0.9980 chunk 344 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 209 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 GLN ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 858 GLN B 958 GLN ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 364 HIS C 424 GLN ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1139 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30018 Z= 0.181 Angle : 0.571 9.500 40851 Z= 0.295 Chirality : 0.043 0.301 4842 Planarity : 0.004 0.057 5124 Dihedral : 5.555 56.948 5688 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.08 % Allowed : 17.72 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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 (0.14), residues: 3573 helix: 2.13 (0.19), residues: 768 sheet: -0.06 (0.18), residues: 756 loop : -1.53 (0.13), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 646 HIS 0.008 0.001 HIS B 142 PHE 0.023 0.001 PHE B 714 TYR 0.017 0.001 TYR A 439 ARG 0.009 0.000 ARG A 464 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 491 time to evaluate : 3.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASN cc_start: 0.8844 (p0) cc_final: 0.8551 (p0) REVERT: A 114 ASN cc_start: 0.8909 (m-40) cc_final: 0.8589 (p0) REVERT: A 135 TYR cc_start: 0.8744 (m-80) cc_final: 0.8470 (m-80) REVERT: A 140 GLN cc_start: 0.7309 (tm-30) cc_final: 0.6609 (tm-30) REVERT: A 142 HIS cc_start: 0.8110 (m90) cc_final: 0.6606 (m90) REVERT: A 157 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7669 (mm-30) REVERT: A 175 HIS cc_start: 0.8542 (p-80) cc_final: 0.8219 (p-80) REVERT: A 288 SER cc_start: 0.8700 (m) cc_final: 0.8278 (t) REVERT: A 319 ARG cc_start: 0.8346 (mmm160) cc_final: 0.7969 (mmm-85) REVERT: A 331 LYS cc_start: 0.8951 (mtpt) cc_final: 0.8655 (mtpp) REVERT: A 376 SER cc_start: 0.9038 (m) cc_final: 0.8587 (p) REVERT: A 384 LYS cc_start: 0.8489 (pttp) cc_final: 0.8119 (pttt) REVERT: A 398 ARG cc_start: 0.8731 (tpt-90) cc_final: 0.8480 (tpt90) REVERT: A 411 SER cc_start: 0.9005 (t) cc_final: 0.8715 (p) REVERT: A 415 LYS cc_start: 0.8737 (tmtt) cc_final: 0.8478 (tmtt) REVERT: A 446 ARG cc_start: 0.8451 (ttm-80) cc_final: 0.8049 (ttm-80) REVERT: A 553 GLU cc_start: 0.8502 (mm-30) cc_final: 0.7902 (mm-30) REVERT: A 609 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8773 (tt) REVERT: A 618 THR cc_start: 0.9243 (OUTLIER) cc_final: 0.9013 (m) REVERT: A 711 GLN cc_start: 0.7963 (pm20) cc_final: 0.7452 (mp10) REVERT: A 792 ILE cc_start: 0.9046 (tp) cc_final: 0.8750 (pt) REVERT: A 805 GLU cc_start: 0.7408 (tm-30) cc_final: 0.7134 (tm-30) REVERT: A 842 ASN cc_start: 0.8730 (m-40) cc_final: 0.8444 (m-40) REVERT: A 844 ASN cc_start: 0.8852 (m-40) cc_final: 0.7686 (m-40) REVERT: A 848 ASP cc_start: 0.8094 (m-30) cc_final: 0.7646 (m-30) REVERT: A 849 GLU cc_start: 0.7865 (pp20) cc_final: 0.7588 (pp20) REVERT: A 858 GLN cc_start: 0.8258 (mm110) cc_final: 0.8019 (mm110) REVERT: A 867 GLN cc_start: 0.7763 (mm-40) cc_final: 0.7434 (mm110) REVERT: A 873 SER cc_start: 0.8798 (m) cc_final: 0.8583 (p) REVERT: A 874 ASN cc_start: 0.8613 (m-40) cc_final: 0.8161 (p0) REVERT: A 889 LYS cc_start: 0.8995 (ttpt) cc_final: 0.8643 (ttpp) REVERT: A 909 ASP cc_start: 0.8164 (m-30) cc_final: 0.7591 (m-30) REVERT: A 956 GLU cc_start: 0.7280 (pm20) cc_final: 0.6960 (pm20) REVERT: A 998 MET cc_start: 0.8772 (tpp) cc_final: 0.8116 (tpp) REVERT: A 999 ASP cc_start: 0.8300 (t0) cc_final: 0.7750 (t0) REVERT: A 1075 GLN cc_start: 0.8446 (mm-40) cc_final: 0.7296 (mm-40) REVERT: A 1079 ASP cc_start: 0.8363 (m-30) cc_final: 0.7769 (m-30) REVERT: A 1095 GLN cc_start: 0.8000 (tm-30) cc_final: 0.6578 (tm-30) REVERT: A 1099 ASP cc_start: 0.8260 (m-30) cc_final: 0.6804 (m-30) REVERT: A 1112 GLU cc_start: 0.7821 (tp30) cc_final: 0.7511 (tp30) REVERT: A 1177 LYS cc_start: 0.8448 (tppt) cc_final: 0.7889 (tppt) REVERT: B 18 PHE cc_start: 0.7995 (t80) cc_final: 0.7681 (t80) REVERT: B 69 LYS cc_start: 0.9047 (tmtt) cc_final: 0.8695 (tmmt) REVERT: B 88 LEU cc_start: 0.9220 (mp) cc_final: 0.8806 (tp) REVERT: B 111 LEU cc_start: 0.8951 (mm) cc_final: 0.8439 (mt) REVERT: B 142 HIS cc_start: 0.7888 (m-70) cc_final: 0.7325 (m90) REVERT: B 147 GLU cc_start: 0.6192 (mp0) cc_final: 0.5482 (mp0) REVERT: B 175 HIS cc_start: 0.8631 (p-80) cc_final: 0.8206 (p-80) REVERT: B 293 LYS cc_start: 0.8797 (tttm) cc_final: 0.8544 (tmmt) REVERT: B 326 ASP cc_start: 0.6772 (t70) cc_final: 0.6273 (t70) REVERT: B 328 ASP cc_start: 0.7943 (m-30) cc_final: 0.7677 (m-30) REVERT: B 331 LYS cc_start: 0.8899 (mttt) cc_final: 0.8477 (ttmm) REVERT: B 384 LYS cc_start: 0.8561 (pttt) cc_final: 0.8214 (pmtt) REVERT: B 397 ARG cc_start: 0.8550 (mmt180) cc_final: 0.8161 (mmm-85) REVERT: B 400 ASP cc_start: 0.8028 (m-30) cc_final: 0.7652 (m-30) REVERT: B 411 SER cc_start: 0.9184 (t) cc_final: 0.8723 (p) REVERT: B 446 ARG cc_start: 0.8550 (ttm110) cc_final: 0.8122 (ttm110) REVERT: B 536 LYS cc_start: 0.8072 (mmtp) cc_final: 0.7693 (mmtt) REVERT: B 537 LYS cc_start: 0.8349 (tppt) cc_final: 0.8139 (tppt) REVERT: B 615 GLU cc_start: 0.7004 (tm-30) cc_final: 0.6775 (tm-30) REVERT: B 711 GLN cc_start: 0.7873 (pm20) cc_final: 0.7404 (mp10) REVERT: B 781 ASP cc_start: 0.7742 (t0) cc_final: 0.7262 (t0) REVERT: B 792 ILE cc_start: 0.9056 (tt) cc_final: 0.8797 (pt) REVERT: B 832 LEU cc_start: 0.8777 (mt) cc_final: 0.7605 (mm) REVERT: B 835 GLU cc_start: 0.7606 (mp0) cc_final: 0.7290 (mp0) REVERT: B 842 ASN cc_start: 0.8568 (m-40) cc_final: 0.8247 (m-40) REVERT: B 848 ASP cc_start: 0.8230 (m-30) cc_final: 0.7751 (m-30) REVERT: B 850 VAL cc_start: 0.9159 (OUTLIER) cc_final: 0.8903 (t) REVERT: B 855 ASP cc_start: 0.7890 (m-30) cc_final: 0.7474 (m-30) REVERT: B 867 GLN cc_start: 0.7526 (mm110) cc_final: 0.7216 (mm-40) REVERT: B 887 ASN cc_start: 0.8823 (m-40) cc_final: 0.8610 (t0) REVERT: B 889 LYS cc_start: 0.9082 (ttpt) cc_final: 0.8650 (ttmm) REVERT: B 914 LYS cc_start: 0.9099 (mmmt) cc_final: 0.8859 (mmmm) REVERT: B 916 LYS cc_start: 0.8531 (pttt) cc_final: 0.8218 (ptmm) REVERT: B 956 GLU cc_start: 0.7299 (pm20) cc_final: 0.6749 (pm20) REVERT: B 1004 ASN cc_start: 0.8275 (m-40) cc_final: 0.7965 (m-40) REVERT: B 1034 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8315 (mp10) REVERT: B 1054 LYS cc_start: 0.8859 (mttt) cc_final: 0.8539 (mmmm) REVERT: B 1075 GLN cc_start: 0.8327 (mm-40) cc_final: 0.7414 (mm-40) REVERT: B 1079 ASP cc_start: 0.8204 (m-30) cc_final: 0.7815 (m-30) REVERT: B 1095 GLN cc_start: 0.8075 (tm-30) cc_final: 0.6805 (tm-30) REVERT: B 1099 ASP cc_start: 0.8275 (m-30) cc_final: 0.6557 (m-30) REVERT: B 1126 ASN cc_start: 0.8187 (t0) cc_final: 0.7800 (t0) REVERT: B 1218 LYS cc_start: 0.8514 (mtpp) cc_final: 0.8136 (mmmm) REVERT: C 17 ASP cc_start: 0.7447 (p0) cc_final: 0.7046 (p0) REVERT: C 18 PHE cc_start: 0.8057 (t80) cc_final: 0.7645 (t80) REVERT: C 53 ASP cc_start: 0.8050 (m-30) cc_final: 0.7839 (t0) REVERT: C 84 LYS cc_start: 0.8608 (mmmm) cc_final: 0.8109 (tptt) REVERT: C 147 GLU cc_start: 0.8003 (pp20) cc_final: 0.7739 (pp20) REVERT: C 288 SER cc_start: 0.8664 (m) cc_final: 0.8229 (t) REVERT: C 330 ASP cc_start: 0.8029 (p0) cc_final: 0.7655 (p0) REVERT: C 331 LYS cc_start: 0.9030 (mttt) cc_final: 0.8604 (ttmm) REVERT: C 384 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8162 (pttp) REVERT: C 397 ARG cc_start: 0.8592 (mmt180) cc_final: 0.8315 (mmm-85) REVERT: C 448 TYR cc_start: 0.8540 (m-80) cc_final: 0.8074 (m-80) REVERT: C 481 PHE cc_start: 0.6561 (t80) cc_final: 0.6299 (t80) REVERT: C 500 ASN cc_start: 0.7437 (m-40) cc_final: 0.7175 (m-40) REVERT: C 529 ASP cc_start: 0.7964 (t70) cc_final: 0.7425 (t0) REVERT: C 739 MET cc_start: 0.8544 (mmm) cc_final: 0.8166 (mmt) REVERT: C 772 GLU cc_start: 0.7441 (mp0) cc_final: 0.7181 (mp0) REVERT: C 832 LEU cc_start: 0.8962 (mt) cc_final: 0.8247 (mm) REVERT: C 842 ASN cc_start: 0.8569 (m-40) cc_final: 0.8312 (m-40) REVERT: C 849 GLU cc_start: 0.7847 (pp20) cc_final: 0.7613 (pp20) REVERT: C 855 ASP cc_start: 0.7880 (m-30) cc_final: 0.7552 (m-30) REVERT: C 858 GLN cc_start: 0.8240 (mt0) cc_final: 0.7814 (mm110) REVERT: C 873 SER cc_start: 0.8899 (m) cc_final: 0.8559 (p) REVERT: C 874 ASN cc_start: 0.8795 (m-40) cc_final: 0.8381 (p0) REVERT: C 882 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7125 (t0) REVERT: C 888 PHE cc_start: 0.8176 (m-10) cc_final: 0.7484 (m-10) REVERT: C 889 LYS cc_start: 0.9123 (ttpt) cc_final: 0.8725 (ttpp) REVERT: C 909 ASP cc_start: 0.8025 (m-30) cc_final: 0.7534 (m-30) REVERT: C 971 MET cc_start: 0.7316 (ttt) cc_final: 0.7070 (ttt) REVERT: C 999 ASP cc_start: 0.7919 (t70) cc_final: 0.7665 (t0) REVERT: C 1045 ASN cc_start: 0.8867 (t0) cc_final: 0.8608 (t0) REVERT: C 1075 GLN cc_start: 0.8191 (mm110) cc_final: 0.7235 (mm-40) REVERT: C 1079 ASP cc_start: 0.8056 (m-30) cc_final: 0.7645 (m-30) REVERT: C 1095 GLN cc_start: 0.8023 (tm-30) cc_final: 0.6841 (tm-30) REVERT: C 1099 ASP cc_start: 0.8218 (m-30) cc_final: 0.6616 (m-30) REVERT: C 1112 GLU cc_start: 0.7911 (tp30) cc_final: 0.7548 (tp30) REVERT: C 1153 LYS cc_start: 0.8413 (tptp) cc_final: 0.8171 (tptp) REVERT: C 1199 GLU cc_start: 0.7501 (mm-30) cc_final: 0.7292 (mm-30) REVERT: C 1206 VAL cc_start: 0.9077 (t) cc_final: 0.8785 (p) REVERT: C 1209 MET cc_start: 0.7963 (mpp) cc_final: 0.7230 (mpp) outliers start: 67 outliers final: 44 residues processed: 535 average time/residue: 0.4333 time to fit residues: 358.5406 Evaluate side-chains 520 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 469 time to evaluate : 3.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1186 ASP Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 535 GLN Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 608 ASP Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1034 GLN Chi-restraints excluded: chain B residue 1036 VAL Chi-restraints excluded: chain B residue 1148 MET Chi-restraints excluded: chain B residue 1186 ASP Chi-restraints excluded: chain B residue 1204 LYS Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 305 ASP Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 588 CYS Chi-restraints excluded: chain C residue 589 ASN Chi-restraints excluded: chain C residue 597 ASN Chi-restraints excluded: chain C residue 608 ASP Chi-restraints excluded: chain C residue 699 CYS Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 882 ASP Chi-restraints excluded: chain C residue 1130 ASN Chi-restraints excluded: chain C residue 1167 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 212 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 205 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 218 optimal weight: 0.8980 chunk 234 optimal weight: 2.9990 chunk 170 optimal weight: 0.0030 chunk 32 optimal weight: 0.0770 chunk 270 optimal weight: 0.0870 overall best weight: 0.8128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 GLN ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 858 GLN B 958 GLN ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 364 HIS C 424 GLN ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30018 Z= 0.184 Angle : 0.572 9.176 40851 Z= 0.296 Chirality : 0.043 0.484 4842 Planarity : 0.004 0.057 5124 Dihedral : 5.432 56.026 5688 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.25 % Favored : 95.72 % Rotamer: Outliers : 1.87 % Allowed : 18.31 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -0.48 (0.14), residues: 3573 helix: 2.16 (0.19), residues: 771 sheet: -0.03 (0.18), residues: 762 loop : -1.50 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 174 HIS 0.006 0.001 HIS C 160 PHE 0.030 0.001 PHE A 473 TYR 0.027 0.001 TYR B 675 ARG 0.006 0.000 ARG A 464 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 498 time to evaluate : 3.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASN cc_start: 0.8832 (p0) cc_final: 0.8514 (p0) REVERT: A 114 ASN cc_start: 0.8923 (m-40) cc_final: 0.8608 (p0) REVERT: A 135 TYR cc_start: 0.8795 (m-80) cc_final: 0.8493 (m-80) REVERT: A 140 GLN cc_start: 0.7273 (tm-30) cc_final: 0.6575 (tm-30) REVERT: A 142 HIS cc_start: 0.8086 (m90) cc_final: 0.6579 (m90) REVERT: A 157 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7764 (mm-30) REVERT: A 175 HIS cc_start: 0.8545 (p-80) cc_final: 0.8214 (p-80) REVERT: A 273 ARG cc_start: 0.7619 (mpp80) cc_final: 0.7390 (mtp85) REVERT: A 288 SER cc_start: 0.8690 (m) cc_final: 0.8255 (t) REVERT: A 289 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7761 (mm-30) REVERT: A 319 ARG cc_start: 0.8337 (mmm160) cc_final: 0.7829 (mmm-85) REVERT: A 331 LYS cc_start: 0.8941 (mtpt) cc_final: 0.8638 (mtpp) REVERT: A 376 SER cc_start: 0.9035 (m) cc_final: 0.8569 (p) REVERT: A 384 LYS cc_start: 0.8495 (pttp) cc_final: 0.8126 (pttt) REVERT: A 398 ARG cc_start: 0.8739 (tpt-90) cc_final: 0.8526 (tpt90) REVERT: A 411 SER cc_start: 0.9001 (t) cc_final: 0.8706 (p) REVERT: A 415 LYS cc_start: 0.8746 (tmtt) cc_final: 0.8436 (tmtt) REVERT: A 446 ARG cc_start: 0.8400 (ttm-80) cc_final: 0.7802 (mtm-85) REVERT: A 553 GLU cc_start: 0.8484 (mm-30) cc_final: 0.7913 (mm-30) REVERT: A 587 ARG cc_start: 0.8261 (mtp85) cc_final: 0.7638 (ttm-80) REVERT: A 609 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8776 (tt) REVERT: A 618 THR cc_start: 0.9232 (OUTLIER) cc_final: 0.9007 (m) REVERT: A 711 GLN cc_start: 0.7987 (pm20) cc_final: 0.7478 (mp10) REVERT: A 792 ILE cc_start: 0.9024 (tp) cc_final: 0.8741 (pt) REVERT: A 842 ASN cc_start: 0.8740 (m-40) cc_final: 0.8453 (m-40) REVERT: A 844 ASN cc_start: 0.8856 (m-40) cc_final: 0.7692 (m-40) REVERT: A 848 ASP cc_start: 0.8092 (m-30) cc_final: 0.7644 (m-30) REVERT: A 849 GLU cc_start: 0.7873 (pp20) cc_final: 0.7598 (pp20) REVERT: A 858 GLN cc_start: 0.8256 (mm110) cc_final: 0.7995 (mm110) REVERT: A 867 GLN cc_start: 0.7769 (mm-40) cc_final: 0.7440 (mm110) REVERT: A 873 SER cc_start: 0.8784 (m) cc_final: 0.8544 (p) REVERT: A 889 LYS cc_start: 0.9003 (ttpt) cc_final: 0.8639 (ttpp) REVERT: A 909 ASP cc_start: 0.8175 (m-30) cc_final: 0.7667 (m-30) REVERT: A 956 GLU cc_start: 0.7332 (pm20) cc_final: 0.6968 (pm20) REVERT: A 998 MET cc_start: 0.8772 (tpp) cc_final: 0.8105 (tpp) REVERT: A 999 ASP cc_start: 0.8305 (t0) cc_final: 0.7773 (t0) REVERT: A 1075 GLN cc_start: 0.8434 (mm-40) cc_final: 0.7595 (mm-40) REVERT: A 1079 ASP cc_start: 0.8301 (m-30) cc_final: 0.7895 (m-30) REVERT: A 1095 GLN cc_start: 0.7989 (tm-30) cc_final: 0.6515 (tm-30) REVERT: A 1099 ASP cc_start: 0.8264 (m-30) cc_final: 0.6728 (m-30) REVERT: A 1112 GLU cc_start: 0.7830 (tp30) cc_final: 0.7507 (tp30) REVERT: A 1177 LYS cc_start: 0.8471 (tppt) cc_final: 0.7902 (tppt) REVERT: A 1178 GLN cc_start: 0.8566 (tt0) cc_final: 0.8264 (tt0) REVERT: B 18 PHE cc_start: 0.7999 (t80) cc_final: 0.7708 (t80) REVERT: B 69 LYS cc_start: 0.9045 (tmtt) cc_final: 0.8688 (tmmt) REVERT: B 88 LEU cc_start: 0.9193 (mp) cc_final: 0.8785 (tp) REVERT: B 111 LEU cc_start: 0.8951 (mm) cc_final: 0.8400 (mt) REVERT: B 175 HIS cc_start: 0.8629 (p-80) cc_final: 0.8166 (p-80) REVERT: B 218 MET cc_start: 0.7775 (mmm) cc_final: 0.7402 (tpt) REVERT: B 293 LYS cc_start: 0.8791 (tttm) cc_final: 0.8532 (pttm) REVERT: B 319 ARG cc_start: 0.8612 (mmm-85) cc_final: 0.8338 (mmm-85) REVERT: B 326 ASP cc_start: 0.6759 (t70) cc_final: 0.6262 (t70) REVERT: B 328 ASP cc_start: 0.7956 (m-30) cc_final: 0.7685 (m-30) REVERT: B 331 LYS cc_start: 0.8896 (mttt) cc_final: 0.8472 (ttmm) REVERT: B 384 LYS cc_start: 0.8530 (pttt) cc_final: 0.8060 (pttp) REVERT: B 388 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8412 (mp) REVERT: B 397 ARG cc_start: 0.8550 (mmt180) cc_final: 0.8155 (mmm-85) REVERT: B 400 ASP cc_start: 0.8031 (m-30) cc_final: 0.7654 (m-30) REVERT: B 411 SER cc_start: 0.9197 (t) cc_final: 0.8741 (p) REVERT: B 446 ARG cc_start: 0.8593 (ttm110) cc_final: 0.8122 (ttm110) REVERT: B 529 ASP cc_start: 0.8020 (t70) cc_final: 0.7455 (t0) REVERT: B 536 LYS cc_start: 0.8074 (mmtp) cc_final: 0.7812 (mptt) REVERT: B 537 LYS cc_start: 0.8210 (tppt) cc_final: 0.7778 (tptt) REVERT: B 615 GLU cc_start: 0.7041 (tm-30) cc_final: 0.6772 (tm-30) REVERT: B 711 GLN cc_start: 0.7886 (pm20) cc_final: 0.7592 (mp10) REVERT: B 781 ASP cc_start: 0.7812 (t0) cc_final: 0.7065 (t0) REVERT: B 792 ILE cc_start: 0.9061 (tt) cc_final: 0.8800 (pt) REVERT: B 832 LEU cc_start: 0.8779 (mt) cc_final: 0.7550 (mm) REVERT: B 835 GLU cc_start: 0.7594 (mp0) cc_final: 0.7299 (mp0) REVERT: B 842 ASN cc_start: 0.8578 (m-40) cc_final: 0.8264 (m-40) REVERT: B 848 ASP cc_start: 0.8215 (m-30) cc_final: 0.7717 (m-30) REVERT: B 850 VAL cc_start: 0.9109 (OUTLIER) cc_final: 0.8884 (t) REVERT: B 855 ASP cc_start: 0.7908 (m-30) cc_final: 0.7479 (m-30) REVERT: B 867 GLN cc_start: 0.7539 (mm110) cc_final: 0.7177 (mm-40) REVERT: B 887 ASN cc_start: 0.8823 (m-40) cc_final: 0.8622 (t0) REVERT: B 889 LYS cc_start: 0.9081 (ttpt) cc_final: 0.8618 (ttmm) REVERT: B 914 LYS cc_start: 0.9213 (mmmt) cc_final: 0.8896 (mmmm) REVERT: B 916 LYS cc_start: 0.8519 (pttt) cc_final: 0.8208 (ptmm) REVERT: B 956 GLU cc_start: 0.7335 (pm20) cc_final: 0.6939 (pm20) REVERT: B 1004 ASN cc_start: 0.8281 (m-40) cc_final: 0.7974 (m-40) REVERT: B 1034 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8286 (mp10) REVERT: B 1054 LYS cc_start: 0.8839 (mttt) cc_final: 0.8464 (mmmm) REVERT: B 1075 GLN cc_start: 0.8311 (mm-40) cc_final: 0.7422 (mm-40) REVERT: B 1079 ASP cc_start: 0.8209 (m-30) cc_final: 0.7813 (m-30) REVERT: B 1095 GLN cc_start: 0.8059 (tm-30) cc_final: 0.6787 (tm-30) REVERT: B 1099 ASP cc_start: 0.8286 (m-30) cc_final: 0.6540 (m-30) REVERT: B 1112 GLU cc_start: 0.7737 (tp30) cc_final: 0.7493 (tp30) REVERT: B 1126 ASN cc_start: 0.8211 (t0) cc_final: 0.7800 (t0) REVERT: B 1218 LYS cc_start: 0.8517 (mtpp) cc_final: 0.8051 (mmmm) REVERT: C 17 ASP cc_start: 0.7424 (p0) cc_final: 0.7102 (p0) REVERT: C 18 PHE cc_start: 0.8052 (t80) cc_final: 0.7680 (t80) REVERT: C 53 ASP cc_start: 0.8048 (m-30) cc_final: 0.7836 (t0) REVERT: C 60 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8624 (p) REVERT: C 76 ASP cc_start: 0.7459 (t0) cc_final: 0.7064 (t0) REVERT: C 84 LYS cc_start: 0.8607 (mmmm) cc_final: 0.8116 (tptt) REVERT: C 147 GLU cc_start: 0.8003 (pp20) cc_final: 0.7774 (pp20) REVERT: C 288 SER cc_start: 0.8685 (m) cc_final: 0.8215 (t) REVERT: C 330 ASP cc_start: 0.8055 (p0) cc_final: 0.7695 (p0) REVERT: C 331 LYS cc_start: 0.8995 (mttt) cc_final: 0.8569 (ttmm) REVERT: C 384 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8150 (pttp) REVERT: C 397 ARG cc_start: 0.8610 (mmt180) cc_final: 0.8324 (mmm-85) REVERT: C 448 TYR cc_start: 0.8418 (m-80) cc_final: 0.8182 (m-80) REVERT: C 460 VAL cc_start: 0.8948 (t) cc_final: 0.8691 (p) REVERT: C 481 PHE cc_start: 0.6580 (t80) cc_final: 0.6313 (t80) REVERT: C 500 ASN cc_start: 0.7414 (m-40) cc_final: 0.7173 (m-40) REVERT: C 529 ASP cc_start: 0.7951 (t70) cc_final: 0.7412 (t0) REVERT: C 537 LYS cc_start: 0.8097 (tppt) cc_final: 0.7837 (tppt) REVERT: C 678 ARG cc_start: 0.7436 (ttm170) cc_final: 0.7098 (ttm-80) REVERT: C 739 MET cc_start: 0.8531 (mmm) cc_final: 0.8179 (mmt) REVERT: C 832 LEU cc_start: 0.8963 (mt) cc_final: 0.8252 (mm) REVERT: C 842 ASN cc_start: 0.8555 (m-40) cc_final: 0.8295 (m-40) REVERT: C 849 GLU cc_start: 0.7820 (pp20) cc_final: 0.7484 (pp20) REVERT: C 858 GLN cc_start: 0.8232 (mt0) cc_final: 0.7783 (mm110) REVERT: C 873 SER cc_start: 0.8939 (m) cc_final: 0.8551 (p) REVERT: C 874 ASN cc_start: 0.8807 (m-40) cc_final: 0.8459 (p0) REVERT: C 882 ASP cc_start: 0.7889 (t0) cc_final: 0.7167 (t0) REVERT: C 888 PHE cc_start: 0.8174 (m-10) cc_final: 0.7469 (m-10) REVERT: C 889 LYS cc_start: 0.9107 (ttpt) cc_final: 0.8704 (ttpp) REVERT: C 909 ASP cc_start: 0.8024 (m-30) cc_final: 0.7405 (m-30) REVERT: C 916 LYS cc_start: 0.8469 (pttt) cc_final: 0.7906 (ptmm) REVERT: C 971 MET cc_start: 0.7344 (ttt) cc_final: 0.7082 (ttt) REVERT: C 999 ASP cc_start: 0.7913 (t70) cc_final: 0.7667 (t0) REVERT: C 1045 ASN cc_start: 0.8859 (t0) cc_final: 0.8606 (t0) REVERT: C 1075 GLN cc_start: 0.8195 (mm110) cc_final: 0.7208 (mm-40) REVERT: C 1079 ASP cc_start: 0.8049 (m-30) cc_final: 0.7651 (m-30) REVERT: C 1095 GLN cc_start: 0.7989 (tm-30) cc_final: 0.6826 (tm-30) REVERT: C 1099 ASP cc_start: 0.8228 (m-30) cc_final: 0.6591 (m-30) REVERT: C 1112 GLU cc_start: 0.7984 (tp30) cc_final: 0.7670 (tp30) REVERT: C 1189 MET cc_start: 0.8458 (mtt) cc_final: 0.7993 (mtt) REVERT: C 1206 VAL cc_start: 0.9063 (t) cc_final: 0.8754 (p) REVERT: C 1209 MET cc_start: 0.7975 (mpp) cc_final: 0.7261 (mpp) outliers start: 60 outliers final: 42 residues processed: 540 average time/residue: 0.4382 time to fit residues: 367.9234 Evaluate side-chains 532 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 482 time to evaluate : 3.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1186 ASP Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 535 GLN Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 608 ASP Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1034 GLN Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1148 MET Chi-restraints excluded: chain B residue 1186 ASP Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 588 CYS Chi-restraints excluded: chain C residue 589 ASN Chi-restraints excluded: chain C residue 608 ASP Chi-restraints excluded: chain C residue 621 CYS Chi-restraints excluded: chain C residue 699 CYS Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 1130 ASN Chi-restraints excluded: chain C residue 1167 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 313 optimal weight: 4.9990 chunk 329 optimal weight: 0.6980 chunk 300 optimal weight: 3.9990 chunk 320 optimal weight: 0.5980 chunk 192 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 251 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 289 optimal weight: 1.9990 chunk 303 optimal weight: 7.9990 chunk 319 optimal weight: 4.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 858 GLN B 958 GLN ** B1126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 364 HIS ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 30018 Z= 0.303 Angle : 0.615 9.563 40851 Z= 0.319 Chirality : 0.044 0.491 4842 Planarity : 0.004 0.059 5124 Dihedral : 5.460 57.526 5688 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.35 % Favored : 94.63 % Rotamer: Outliers : 2.18 % Allowed : 18.66 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -0.55 (0.14), residues: 3573 helix: 2.02 (0.19), residues: 774 sheet: -0.10 (0.18), residues: 798 loop : -1.51 (0.13), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 174 HIS 0.007 0.001 HIS C 160 PHE 0.038 0.001 PHE B 714 TYR 0.029 0.002 TYR B 675 ARG 0.008 0.001 ARG C 587 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 492 time to evaluate : 3.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASN cc_start: 0.8830 (p0) cc_final: 0.8515 (p0) REVERT: A 114 ASN cc_start: 0.8973 (m-40) cc_final: 0.8646 (p0) REVERT: A 135 TYR cc_start: 0.8923 (m-80) cc_final: 0.8546 (m-80) REVERT: A 140 GLN cc_start: 0.7303 (tm-30) cc_final: 0.6908 (tm-30) REVERT: A 157 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7844 (mm-30) REVERT: A 288 SER cc_start: 0.8725 (m) cc_final: 0.8312 (t) REVERT: A 319 ARG cc_start: 0.8370 (mmm160) cc_final: 0.8013 (mmm-85) REVERT: A 331 LYS cc_start: 0.8983 (mtpt) cc_final: 0.8718 (mtpp) REVERT: A 376 SER cc_start: 0.9079 (m) cc_final: 0.8619 (p) REVERT: A 384 LYS cc_start: 0.8521 (pttp) cc_final: 0.8170 (pttt) REVERT: A 398 ARG cc_start: 0.8775 (tpt-90) cc_final: 0.8545 (tpt90) REVERT: A 411 SER cc_start: 0.9022 (t) cc_final: 0.8721 (p) REVERT: A 415 LYS cc_start: 0.8773 (tmtt) cc_final: 0.8397 (tmtt) REVERT: A 446 ARG cc_start: 0.8468 (ttm-80) cc_final: 0.7869 (mtm-85) REVERT: A 553 GLU cc_start: 0.8530 (mm-30) cc_final: 0.7869 (mm-30) REVERT: A 587 ARG cc_start: 0.8291 (mtp85) cc_final: 0.7793 (ttt90) REVERT: A 609 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8693 (tt) REVERT: A 618 THR cc_start: 0.9262 (OUTLIER) cc_final: 0.9000 (m) REVERT: A 711 GLN cc_start: 0.7959 (pm20) cc_final: 0.7461 (mp10) REVERT: A 792 ILE cc_start: 0.9053 (tp) cc_final: 0.8739 (pt) REVERT: A 805 GLU cc_start: 0.7405 (tm-30) cc_final: 0.7144 (tm-30) REVERT: A 842 ASN cc_start: 0.8738 (m-40) cc_final: 0.8473 (m-40) REVERT: A 844 ASN cc_start: 0.8882 (m-40) cc_final: 0.7711 (m-40) REVERT: A 848 ASP cc_start: 0.8111 (m-30) cc_final: 0.7667 (m-30) REVERT: A 849 GLU cc_start: 0.7884 (pp20) cc_final: 0.7648 (pp20) REVERT: A 867 GLN cc_start: 0.7783 (mm-40) cc_final: 0.7436 (mm110) REVERT: A 873 SER cc_start: 0.8935 (m) cc_final: 0.8659 (p) REVERT: A 889 LYS cc_start: 0.9084 (ttpt) cc_final: 0.8738 (ttpp) REVERT: A 909 ASP cc_start: 0.8204 (m-30) cc_final: 0.7621 (m-30) REVERT: A 956 GLU cc_start: 0.7287 (pm20) cc_final: 0.6943 (pm20) REVERT: A 998 MET cc_start: 0.8774 (tpp) cc_final: 0.8055 (tpp) REVERT: A 999 ASP cc_start: 0.8315 (t0) cc_final: 0.7811 (t0) REVERT: A 1064 GLU cc_start: 0.8175 (tp30) cc_final: 0.7600 (tp30) REVERT: A 1075 GLN cc_start: 0.8501 (mm-40) cc_final: 0.7191 (mm-40) REVERT: A 1079 ASP cc_start: 0.8344 (m-30) cc_final: 0.7812 (m-30) REVERT: A 1095 GLN cc_start: 0.8048 (tm-30) cc_final: 0.6589 (tm-30) REVERT: A 1099 ASP cc_start: 0.8275 (m-30) cc_final: 0.6813 (m-30) REVERT: A 1112 GLU cc_start: 0.7900 (tp30) cc_final: 0.7664 (tp30) REVERT: A 1177 LYS cc_start: 0.8486 (tppt) cc_final: 0.7922 (tppt) REVERT: A 1178 GLN cc_start: 0.8610 (tt0) cc_final: 0.8301 (tt0) REVERT: B 18 PHE cc_start: 0.8095 (t80) cc_final: 0.7771 (t80) REVERT: B 69 LYS cc_start: 0.9046 (tmtt) cc_final: 0.8671 (tmmt) REVERT: B 88 LEU cc_start: 0.9213 (mp) cc_final: 0.8817 (tp) REVERT: B 111 LEU cc_start: 0.8969 (mm) cc_final: 0.8479 (mt) REVERT: B 175 HIS cc_start: 0.8621 (p-80) cc_final: 0.8133 (p-80) REVERT: B 218 MET cc_start: 0.7754 (mmm) cc_final: 0.7408 (tpt) REVERT: B 289 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7724 (mm-30) REVERT: B 319 ARG cc_start: 0.8653 (mmm-85) cc_final: 0.8372 (mmm-85) REVERT: B 326 ASP cc_start: 0.6793 (t70) cc_final: 0.6298 (t70) REVERT: B 328 ASP cc_start: 0.8001 (m-30) cc_final: 0.7714 (m-30) REVERT: B 331 LYS cc_start: 0.8944 (mttt) cc_final: 0.8527 (ttmm) REVERT: B 384 LYS cc_start: 0.8559 (pttt) cc_final: 0.8214 (pttt) REVERT: B 388 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8462 (mp) REVERT: B 397 ARG cc_start: 0.8579 (mmt180) cc_final: 0.8195 (mmm-85) REVERT: B 400 ASP cc_start: 0.8062 (m-30) cc_final: 0.7618 (m-30) REVERT: B 411 SER cc_start: 0.9200 (t) cc_final: 0.8727 (p) REVERT: B 446 ARG cc_start: 0.8545 (ttm110) cc_final: 0.8109 (ttm110) REVERT: B 529 ASP cc_start: 0.8091 (t70) cc_final: 0.7520 (t0) REVERT: B 536 LYS cc_start: 0.8087 (mmtp) cc_final: 0.7829 (mptt) REVERT: B 537 LYS cc_start: 0.8220 (tppt) cc_final: 0.7988 (tppt) REVERT: B 615 GLU cc_start: 0.7040 (tm-30) cc_final: 0.6770 (tm-30) REVERT: B 711 GLN cc_start: 0.7854 (pm20) cc_final: 0.7377 (mp10) REVERT: B 781 ASP cc_start: 0.7849 (t0) cc_final: 0.7082 (t0) REVERT: B 792 ILE cc_start: 0.9041 (tt) cc_final: 0.8767 (pt) REVERT: B 832 LEU cc_start: 0.8793 (mt) cc_final: 0.7570 (mm) REVERT: B 835 GLU cc_start: 0.7653 (mp0) cc_final: 0.7290 (mp0) REVERT: B 842 ASN cc_start: 0.8579 (m-40) cc_final: 0.8268 (m-40) REVERT: B 848 ASP cc_start: 0.8222 (m-30) cc_final: 0.7755 (m-30) REVERT: B 850 VAL cc_start: 0.9123 (OUTLIER) cc_final: 0.8902 (t) REVERT: B 855 ASP cc_start: 0.7921 (m-30) cc_final: 0.7515 (m-30) REVERT: B 867 GLN cc_start: 0.7595 (mm110) cc_final: 0.7209 (mm-40) REVERT: B 887 ASN cc_start: 0.8776 (m-40) cc_final: 0.8536 (m-40) REVERT: B 889 LYS cc_start: 0.9130 (ttpt) cc_final: 0.8645 (ttmm) REVERT: B 914 LYS cc_start: 0.9167 (mmmt) cc_final: 0.8884 (mmmm) REVERT: B 916 LYS cc_start: 0.8581 (pttt) cc_final: 0.8095 (ptmm) REVERT: B 956 GLU cc_start: 0.7380 (pm20) cc_final: 0.6969 (pm20) REVERT: B 1004 ASN cc_start: 0.8361 (m-40) cc_final: 0.7995 (m-40) REVERT: B 1034 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8316 (mp10) REVERT: B 1054 LYS cc_start: 0.8882 (mttt) cc_final: 0.8587 (mmmm) REVERT: B 1075 GLN cc_start: 0.8395 (mm-40) cc_final: 0.7400 (mm-40) REVERT: B 1079 ASP cc_start: 0.8222 (m-30) cc_final: 0.7862 (m-30) REVERT: B 1095 GLN cc_start: 0.8078 (tm-30) cc_final: 0.6816 (tm-30) REVERT: B 1099 ASP cc_start: 0.8296 (m-30) cc_final: 0.6630 (m-30) REVERT: B 1112 GLU cc_start: 0.7749 (tp30) cc_final: 0.7517 (tp30) REVERT: B 1126 ASN cc_start: 0.8216 (t0) cc_final: 0.7866 (t0) REVERT: B 1182 ILE cc_start: 0.9014 (mp) cc_final: 0.8807 (pt) REVERT: B 1218 LYS cc_start: 0.8549 (mtpp) cc_final: 0.8140 (mmmm) REVERT: C 17 ASP cc_start: 0.7576 (p0) cc_final: 0.7238 (p0) REVERT: C 18 PHE cc_start: 0.8178 (t80) cc_final: 0.7789 (t80) REVERT: C 53 ASP cc_start: 0.8121 (m-30) cc_final: 0.7815 (t0) REVERT: C 60 THR cc_start: 0.8976 (OUTLIER) cc_final: 0.8660 (p) REVERT: C 84 LYS cc_start: 0.8619 (mmmm) cc_final: 0.8135 (tptt) REVERT: C 149 THR cc_start: 0.8656 (p) cc_final: 0.8434 (p) REVERT: C 288 SER cc_start: 0.8651 (m) cc_final: 0.8211 (t) REVERT: C 330 ASP cc_start: 0.8112 (p0) cc_final: 0.7785 (p0) REVERT: C 331 LYS cc_start: 0.9042 (mttt) cc_final: 0.8644 (ttmm) REVERT: C 384 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8211 (pttp) REVERT: C 397 ARG cc_start: 0.8638 (mmt180) cc_final: 0.8348 (mmm-85) REVERT: C 448 TYR cc_start: 0.8501 (m-80) cc_final: 0.8260 (m-80) REVERT: C 481 PHE cc_start: 0.6784 (t80) cc_final: 0.6504 (t80) REVERT: C 500 ASN cc_start: 0.7427 (m-40) cc_final: 0.7200 (m-40) REVERT: C 529 ASP cc_start: 0.7985 (t70) cc_final: 0.7458 (t0) REVERT: C 537 LYS cc_start: 0.8177 (tppt) cc_final: 0.7960 (tppt) REVERT: C 832 LEU cc_start: 0.8974 (mt) cc_final: 0.8281 (mm) REVERT: C 842 ASN cc_start: 0.8576 (m-40) cc_final: 0.8336 (m-40) REVERT: C 849 GLU cc_start: 0.7799 (pp20) cc_final: 0.7461 (pp20) REVERT: C 858 GLN cc_start: 0.8236 (mt0) cc_final: 0.7947 (mt0) REVERT: C 873 SER cc_start: 0.8991 (m) cc_final: 0.8593 (p) REVERT: C 874 ASN cc_start: 0.8855 (m-40) cc_final: 0.8510 (p0) REVERT: C 882 ASP cc_start: 0.7930 (t0) cc_final: 0.7259 (t0) REVERT: C 889 LYS cc_start: 0.9152 (ttpt) cc_final: 0.8743 (ttpp) REVERT: C 916 LYS cc_start: 0.8548 (pttt) cc_final: 0.8000 (ptmm) REVERT: C 999 ASP cc_start: 0.7978 (t70) cc_final: 0.7594 (t0) REVERT: C 1042 GLN cc_start: 0.8635 (tt0) cc_final: 0.8262 (tm-30) REVERT: C 1045 ASN cc_start: 0.8885 (t0) cc_final: 0.8640 (t0) REVERT: C 1075 GLN cc_start: 0.8256 (mm110) cc_final: 0.7261 (mm-40) REVERT: C 1079 ASP cc_start: 0.8122 (m-30) cc_final: 0.7720 (m-30) REVERT: C 1095 GLN cc_start: 0.8012 (tm-30) cc_final: 0.7559 (tm-30) REVERT: C 1104 LYS cc_start: 0.8853 (tptt) cc_final: 0.8637 (tptp) REVERT: C 1112 GLU cc_start: 0.8079 (tp30) cc_final: 0.7739 (tp30) REVERT: C 1116 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7254 (mm-30) REVERT: C 1153 LYS cc_start: 0.8791 (tmmt) cc_final: 0.8479 (tmmt) REVERT: C 1209 MET cc_start: 0.7985 (mpp) cc_final: 0.7263 (mpp) outliers start: 70 outliers final: 49 residues processed: 537 average time/residue: 0.4344 time to fit residues: 360.9157 Evaluate side-chains 533 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 476 time to evaluate : 3.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1186 ASP Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 535 GLN Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 608 ASP Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 940 CYS Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1034 GLN Chi-restraints excluded: chain B residue 1036 VAL Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1148 MET Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 406 SER Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 588 CYS Chi-restraints excluded: chain C residue 589 ASN Chi-restraints excluded: chain C residue 597 ASN Chi-restraints excluded: chain C residue 608 ASP Chi-restraints excluded: chain C residue 699 CYS Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 1064 GLU Chi-restraints excluded: chain C residue 1167 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 210 optimal weight: 3.9990 chunk 339 optimal weight: 0.8980 chunk 206 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 235 optimal weight: 2.9990 chunk 355 optimal weight: 1.9990 chunk 327 optimal weight: 1.9990 chunk 283 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 218 optimal weight: 10.0000 chunk 173 optimal weight: 10.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 HIS ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 858 GLN B 958 GLN ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 364 HIS ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 30018 Z= 0.282 Angle : 0.622 9.596 40851 Z= 0.323 Chirality : 0.045 0.508 4842 Planarity : 0.004 0.065 5124 Dihedral : 5.512 55.565 5688 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.32 % Favored : 94.65 % Rotamer: Outliers : 2.05 % Allowed : 18.94 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -0.56 (0.14), residues: 3573 helix: 1.96 (0.19), residues: 777 sheet: -0.05 (0.18), residues: 789 loop : -1.53 (0.13), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 174 HIS 0.006 0.001 HIS C 160 PHE 0.038 0.001 PHE B 714 TYR 0.026 0.001 TYR B 675 ARG 0.006 0.000 ARG B 206 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 487 time to evaluate : 3.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASN cc_start: 0.8793 (p0) cc_final: 0.8472 (p0) REVERT: A 114 ASN cc_start: 0.8974 (m-40) cc_final: 0.8709 (p0) REVERT: A 135 TYR cc_start: 0.8927 (m-80) cc_final: 0.8645 (m-80) REVERT: A 140 GLN cc_start: 0.7315 (tm-30) cc_final: 0.6906 (tm-30) REVERT: A 157 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7688 (mm-30) REVERT: A 288 SER cc_start: 0.8708 (m) cc_final: 0.8274 (t) REVERT: A 289 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7789 (mm-30) REVERT: A 319 ARG cc_start: 0.8365 (mmm160) cc_final: 0.7858 (mmm-85) REVERT: A 331 LYS cc_start: 0.8982 (mtpt) cc_final: 0.8734 (mtpp) REVERT: A 376 SER cc_start: 0.9071 (m) cc_final: 0.8630 (p) REVERT: A 384 LYS cc_start: 0.8529 (pttp) cc_final: 0.8168 (pttt) REVERT: A 398 ARG cc_start: 0.8772 (tpt-90) cc_final: 0.8528 (tpt90) REVERT: A 411 SER cc_start: 0.9020 (t) cc_final: 0.8713 (p) REVERT: A 415 LYS cc_start: 0.8776 (tmtt) cc_final: 0.8424 (tmtt) REVERT: A 446 ARG cc_start: 0.8433 (ttm-80) cc_final: 0.7846 (mtm-85) REVERT: A 587 ARG cc_start: 0.8294 (mtp85) cc_final: 0.7797 (ttt90) REVERT: A 609 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8673 (tt) REVERT: A 618 THR cc_start: 0.9259 (OUTLIER) cc_final: 0.8999 (m) REVERT: A 711 GLN cc_start: 0.7948 (pm20) cc_final: 0.7446 (mp10) REVERT: A 805 GLU cc_start: 0.7370 (tm-30) cc_final: 0.7127 (tm-30) REVERT: A 842 ASN cc_start: 0.8734 (m-40) cc_final: 0.8465 (m-40) REVERT: A 844 ASN cc_start: 0.8874 (m-40) cc_final: 0.7698 (m-40) REVERT: A 848 ASP cc_start: 0.8107 (m-30) cc_final: 0.7676 (m-30) REVERT: A 849 GLU cc_start: 0.7853 (pp20) cc_final: 0.7623 (pp20) REVERT: A 858 GLN cc_start: 0.8189 (mm110) cc_final: 0.7987 (mm110) REVERT: A 867 GLN cc_start: 0.7797 (mm-40) cc_final: 0.7432 (mm110) REVERT: A 873 SER cc_start: 0.8908 (m) cc_final: 0.8638 (p) REVERT: A 889 LYS cc_start: 0.9083 (ttpt) cc_final: 0.8733 (ttpp) REVERT: A 909 ASP cc_start: 0.8195 (m-30) cc_final: 0.7604 (m-30) REVERT: A 956 GLU cc_start: 0.7277 (pm20) cc_final: 0.6917 (pm20) REVERT: A 998 MET cc_start: 0.8793 (tpp) cc_final: 0.8062 (tpp) REVERT: A 999 ASP cc_start: 0.8305 (t0) cc_final: 0.7789 (t0) REVERT: A 1075 GLN cc_start: 0.8510 (mm-40) cc_final: 0.7151 (mm-40) REVERT: A 1079 ASP cc_start: 0.8341 (m-30) cc_final: 0.7800 (m-30) REVERT: A 1095 GLN cc_start: 0.8044 (tm-30) cc_final: 0.6546 (tm-30) REVERT: A 1099 ASP cc_start: 0.8275 (m-30) cc_final: 0.6767 (m-30) REVERT: A 1112 GLU cc_start: 0.7894 (tp30) cc_final: 0.7627 (tp30) REVERT: A 1177 LYS cc_start: 0.8466 (tppt) cc_final: 0.7903 (tppt) REVERT: A 1178 GLN cc_start: 0.8602 (tt0) cc_final: 0.8292 (tt0) REVERT: A 1199 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7134 (mm-30) REVERT: A 1208 PHE cc_start: 0.8755 (m-80) cc_final: 0.8543 (m-80) REVERT: B 18 PHE cc_start: 0.8037 (t80) cc_final: 0.7790 (t80) REVERT: B 69 LYS cc_start: 0.9054 (tmtt) cc_final: 0.8680 (tmmt) REVERT: B 88 LEU cc_start: 0.9215 (mp) cc_final: 0.8815 (tp) REVERT: B 111 LEU cc_start: 0.8973 (mm) cc_final: 0.8452 (mt) REVERT: B 175 HIS cc_start: 0.8608 (p-80) cc_final: 0.8155 (p-80) REVERT: B 218 MET cc_start: 0.7796 (mmm) cc_final: 0.7475 (tpt) REVERT: B 271 ASP cc_start: 0.7232 (p0) cc_final: 0.7028 (p0) REVERT: B 289 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7716 (mm-30) REVERT: B 319 ARG cc_start: 0.8647 (mmm-85) cc_final: 0.8358 (mmm-85) REVERT: B 326 ASP cc_start: 0.6786 (t70) cc_final: 0.6282 (t70) REVERT: B 328 ASP cc_start: 0.7973 (m-30) cc_final: 0.7699 (m-30) REVERT: B 331 LYS cc_start: 0.8931 (mttt) cc_final: 0.8521 (ttmm) REVERT: B 384 LYS cc_start: 0.8565 (pttt) cc_final: 0.8062 (pttp) REVERT: B 388 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8478 (mp) REVERT: B 397 ARG cc_start: 0.8565 (mmt180) cc_final: 0.8188 (mmm-85) REVERT: B 398 ARG cc_start: 0.8677 (tpp80) cc_final: 0.8444 (tpt-90) REVERT: B 400 ASP cc_start: 0.8055 (m-30) cc_final: 0.7619 (m-30) REVERT: B 411 SER cc_start: 0.9191 (t) cc_final: 0.8732 (p) REVERT: B 446 ARG cc_start: 0.8508 (ttm110) cc_final: 0.8064 (ttm110) REVERT: B 529 ASP cc_start: 0.8091 (t70) cc_final: 0.7518 (t0) REVERT: B 536 LYS cc_start: 0.8075 (mmtp) cc_final: 0.7642 (mmtt) REVERT: B 537 LYS cc_start: 0.8228 (tppt) cc_final: 0.7798 (tptt) REVERT: B 615 GLU cc_start: 0.7033 (tm-30) cc_final: 0.6757 (tm-30) REVERT: B 711 GLN cc_start: 0.7837 (pm20) cc_final: 0.7367 (mp10) REVERT: B 781 ASP cc_start: 0.7865 (t0) cc_final: 0.7078 (t0) REVERT: B 792 ILE cc_start: 0.9045 (tt) cc_final: 0.8782 (pt) REVERT: B 832 LEU cc_start: 0.8793 (mt) cc_final: 0.7392 (mt) REVERT: B 835 GLU cc_start: 0.7657 (mp0) cc_final: 0.7309 (mp0) REVERT: B 842 ASN cc_start: 0.8584 (m-40) cc_final: 0.8278 (m-40) REVERT: B 848 ASP cc_start: 0.8214 (m-30) cc_final: 0.7765 (m-30) REVERT: B 850 VAL cc_start: 0.9116 (OUTLIER) cc_final: 0.8904 (t) REVERT: B 855 ASP cc_start: 0.7887 (m-30) cc_final: 0.7493 (m-30) REVERT: B 867 GLN cc_start: 0.7571 (mm110) cc_final: 0.7229 (mm-40) REVERT: B 887 ASN cc_start: 0.8772 (m-40) cc_final: 0.8548 (m-40) REVERT: B 889 LYS cc_start: 0.9139 (ttpt) cc_final: 0.8681 (ttmm) REVERT: B 914 LYS cc_start: 0.9279 (mmmt) cc_final: 0.8958 (mmmm) REVERT: B 916 LYS cc_start: 0.8607 (pttt) cc_final: 0.8116 (ptmm) REVERT: B 956 GLU cc_start: 0.7358 (pm20) cc_final: 0.6954 (pm20) REVERT: B 1004 ASN cc_start: 0.8376 (m-40) cc_final: 0.7948 (m-40) REVERT: B 1034 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8310 (mp10) REVERT: B 1054 LYS cc_start: 0.8883 (mttt) cc_final: 0.8588 (mmmm) REVERT: B 1075 GLN cc_start: 0.8382 (mm-40) cc_final: 0.7355 (mm-40) REVERT: B 1079 ASP cc_start: 0.8215 (m-30) cc_final: 0.7861 (m-30) REVERT: B 1095 GLN cc_start: 0.8100 (tm-30) cc_final: 0.6861 (tm-30) REVERT: B 1099 ASP cc_start: 0.8294 (m-30) cc_final: 0.6625 (m-30) REVERT: B 1112 GLU cc_start: 0.7742 (tp30) cc_final: 0.7491 (tp30) REVERT: B 1126 ASN cc_start: 0.8228 (t0) cc_final: 0.7842 (t0) REVERT: B 1182 ILE cc_start: 0.9019 (mp) cc_final: 0.8813 (pt) REVERT: B 1204 LYS cc_start: 0.8930 (mttt) cc_final: 0.8709 (mtpt) REVERT: C 17 ASP cc_start: 0.7616 (p0) cc_final: 0.7273 (p0) REVERT: C 18 PHE cc_start: 0.8169 (t80) cc_final: 0.7768 (t80) REVERT: C 53 ASP cc_start: 0.8160 (m-30) cc_final: 0.7859 (t0) REVERT: C 60 THR cc_start: 0.8968 (OUTLIER) cc_final: 0.8658 (p) REVERT: C 76 ASP cc_start: 0.7452 (t0) cc_final: 0.7197 (t0) REVERT: C 84 LYS cc_start: 0.8622 (mmmm) cc_final: 0.8140 (tptt) REVERT: C 149 THR cc_start: 0.8578 (p) cc_final: 0.8333 (p) REVERT: C 288 SER cc_start: 0.8645 (m) cc_final: 0.8194 (t) REVERT: C 289 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7545 (mm-30) REVERT: C 330 ASP cc_start: 0.8124 (p0) cc_final: 0.7785 (p0) REVERT: C 331 LYS cc_start: 0.9042 (mttt) cc_final: 0.8668 (ttmm) REVERT: C 384 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8198 (pttp) REVERT: C 397 ARG cc_start: 0.8638 (mmt180) cc_final: 0.8391 (mmm-85) REVERT: C 481 PHE cc_start: 0.6820 (t80) cc_final: 0.6531 (t80) REVERT: C 500 ASN cc_start: 0.7383 (m-40) cc_final: 0.7170 (m-40) REVERT: C 529 ASP cc_start: 0.7998 (t70) cc_final: 0.7473 (t0) REVERT: C 832 LEU cc_start: 0.8976 (mt) cc_final: 0.8199 (mm) REVERT: C 842 ASN cc_start: 0.8591 (m-40) cc_final: 0.8347 (m-40) REVERT: C 849 GLU cc_start: 0.7783 (pp20) cc_final: 0.7506 (pp20) REVERT: C 858 GLN cc_start: 0.8228 (mt0) cc_final: 0.7955 (mt0) REVERT: C 873 SER cc_start: 0.8986 (m) cc_final: 0.8594 (p) REVERT: C 874 ASN cc_start: 0.8852 (m-40) cc_final: 0.8491 (p0) REVERT: C 882 ASP cc_start: 0.7874 (t0) cc_final: 0.7279 (t0) REVERT: C 889 LYS cc_start: 0.9164 (ttpt) cc_final: 0.8754 (ttpp) REVERT: C 909 ASP cc_start: 0.8021 (m-30) cc_final: 0.7597 (m-30) REVERT: C 916 LYS cc_start: 0.8548 (pttt) cc_final: 0.8006 (ptmm) REVERT: C 999 ASP cc_start: 0.7981 (t70) cc_final: 0.7731 (t0) REVERT: C 1042 GLN cc_start: 0.8634 (tt0) cc_final: 0.8141 (tm-30) REVERT: C 1045 ASN cc_start: 0.8882 (t0) cc_final: 0.8649 (t0) REVERT: C 1075 GLN cc_start: 0.8217 (mm110) cc_final: 0.7301 (mm-40) REVERT: C 1079 ASP cc_start: 0.8119 (m-30) cc_final: 0.7707 (m-30) REVERT: C 1095 GLN cc_start: 0.7995 (tm-30) cc_final: 0.7523 (tm-30) REVERT: C 1104 LYS cc_start: 0.8856 (tptt) cc_final: 0.8630 (tptp) REVERT: C 1112 GLU cc_start: 0.8000 (tp30) cc_final: 0.7746 (tp30) REVERT: C 1116 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7206 (mm-30) REVERT: C 1153 LYS cc_start: 0.8772 (tmmt) cc_final: 0.8421 (tmmt) REVERT: C 1209 MET cc_start: 0.7952 (mpp) cc_final: 0.7235 (mpp) outliers start: 66 outliers final: 52 residues processed: 530 average time/residue: 0.4442 time to fit residues: 365.4493 Evaluate side-chains 538 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 478 time to evaluate : 3.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1186 ASP Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 535 GLN Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 608 ASP Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 881 PHE Chi-restraints excluded: chain B residue 940 CYS Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1034 GLN Chi-restraints excluded: chain B residue 1036 VAL Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1148 MET Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 406 SER Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 589 ASN Chi-restraints excluded: chain C residue 608 ASP Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 699 CYS Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 1064 GLU Chi-restraints excluded: chain C residue 1167 CYS Chi-restraints excluded: chain C residue 1206 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 224 optimal weight: 3.9990 chunk 301 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 261 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 78 optimal weight: 0.0980 chunk 283 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 291 optimal weight: 0.0060 chunk 35 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 858 GLN B 958 GLN ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 364 HIS ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.101348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.080248 restraints weight = 62620.005| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 3.80 r_work: 0.2916 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 30018 Z= 0.210 Angle : 0.607 10.526 40851 Z= 0.313 Chirality : 0.044 0.481 4842 Planarity : 0.004 0.057 5124 Dihedral : 5.365 56.177 5688 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.90 % Favored : 95.07 % Rotamer: Outliers : 1.99 % Allowed : 19.12 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -0.48 (0.14), residues: 3573 helix: 2.04 (0.19), residues: 777 sheet: 0.05 (0.18), residues: 789 loop : -1.51 (0.13), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 174 HIS 0.006 0.001 HIS C 160 PHE 0.034 0.001 PHE B 714 TYR 0.025 0.001 TYR B 675 ARG 0.008 0.000 ARG C 464 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7208.11 seconds wall clock time: 131 minutes 54.94 seconds (7914.94 seconds total)