Starting phenix.real_space_refine on Sat Apr 13 22:08:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwl_32869/04_2024/7wwl_32869.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwl_32869/04_2024/7wwl_32869.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwl_32869/04_2024/7wwl_32869.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwl_32869/04_2024/7wwl_32869.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwl_32869/04_2024/7wwl_32869.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwl_32869/04_2024/7wwl_32869.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 126 5.16 5 C 18859 2.51 5 N 4890 2.21 5 O 5829 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ASP 228": "OD1" <-> "OD2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A GLU 725": "OE1" <-> "OE2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A ARG 1107": "NH1" <-> "NH2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B ARG 408": "NH1" <-> "NH2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B GLU 748": "OE1" <-> "OE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B GLU 918": "OE1" <-> "OE2" Residue "B GLU 1072": "OE1" <-> "OE2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C GLU 516": "OE1" <-> "OE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C GLU 725": "OE1" <-> "OE2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C GLU 1031": "OE1" <-> "OE2" Residue "C GLU 1072": "OE1" <-> "OE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 100": "NH1" <-> "NH2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 100": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "J ARG 100": "NH1" <-> "NH2" Residue "N GLU 27": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 29704 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 7765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7765 Classifications: {'peptide': 994} Link IDs: {'PTRANS': 53, 'TRANS': 940} Chain breaks: 8 Chain: "B" Number of atoms: 7759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7759 Classifications: {'peptide': 993} Link IDs: {'PTRANS': 53, 'TRANS': 939} Chain breaks: 8 Chain: "C" Number of atoms: 7759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7759 Classifications: {'peptide': 993} Link IDs: {'PTRANS': 53, 'TRANS': 939} Chain breaks: 8 Chain: "H" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 967 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "L" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 842 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 99} Chain: "I" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 967 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "M" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 842 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 99} Chain: "J" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 967 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "N" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 842 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 99} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: 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: "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: "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: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 15.43, per 1000 atoms: 0.52 Number of scatterers: 29704 At special positions: 0 Unit cell: (134.788, 153.267, 200.008, 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 126 16.00 O 5829 8.00 N 4890 7.00 C 18859 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.31 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.17 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.63 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=1.75 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.17 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.53 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.05 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.05 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.12 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.10 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.17 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.52 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.05 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=1.98 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 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 K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " 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 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 e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 603 " " NAG A1407 " - " ASN A 616 " " NAG A1408 " - " ASN A 657 " " NAG A1409 " - " ASN A 709 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 282 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 616 " " NAG B1408 " - " ASN B 657 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 282 " " NAG C1406 " - " ASN C 603 " " NAG C1407 " - " ASN C 616 " " NAG C1408 " - " ASN C 657 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A 343 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1074 " " NAG O 1 " - " ASN A1098 " " NAG P 1 " - " ASN A1134 " " NAG Q 1 " - " ASN B 331 " " NAG R 1 " - " ASN B 343 " " NAG S 1 " - " ASN B 709 " " NAG T 1 " - " ASN B 717 " " NAG U 1 " - " ASN B 801 " " NAG V 1 " - " ASN B1098 " " NAG W 1 " - " ASN B1134 " " NAG X 1 " - " ASN C 331 " " NAG Y 1 " - " ASN C 343 " " NAG Z 1 " - " ASN C 709 " " NAG a 1 " - " ASN C 717 " " NAG b 1 " - " ASN C 801 " " NAG c 1 " - " ASN C1074 " " NAG d 1 " - " ASN C1098 " " NAG e 1 " - " ASN C1134 " " NAG f 1 " - " ASN B1074 " Time building additional restraints: 11.51 Conformation dependent library (CDL) restraints added in 5.0 seconds 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6836 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 60 sheets defined 19.1% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.41 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.578A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.630A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.773A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.634A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 815' Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.774A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.573A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.993A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.626A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.879A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.632A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.647A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.578A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 removed outlier: 3.694A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.964A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.545A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.603A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.009A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.245A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.578A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 572 removed outlier: 3.849A pdb=" N THR C 572 " --> pdb=" O ILE C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.717A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.560A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.698A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.590A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.355A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.221A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'H' and resid 103 through 107 removed outlier: 3.563A pdb=" N ILE H 106 " --> pdb=" O TRP H 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 103 through 107 removed outlier: 3.563A pdb=" N ILE I 106 " --> pdb=" O TRP I 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 107 removed outlier: 3.563A pdb=" N ILE J 106 " --> pdb=" O TRP J 103 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.858A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.012A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.524A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 653 through 655 Processing sheet with id=AB2, first strand: chain 'A' and resid 664 through 667 removed outlier: 6.417A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.505A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.713A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.857A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC2, first strand: chain 'B' and resid 116 through 121 removed outlier: 3.732A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.037A pdb=" N GLY B 311 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.554A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N THR B 573 " --> pdb=" O ASP B 568 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASP B 568 " --> pdb=" O THR B 573 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.526A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.264A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.541A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.541A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.579A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.061A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 49 through 55 removed outlier: 3.858A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD8, first strand: chain 'C' and resid 116 through 121 removed outlier: 3.731A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.908A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.525A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.851A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.592A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.592A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.569A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF1, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AF2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.606A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.632A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.574A pdb=" N LEU L 11 " --> pdb=" O LYS L 104 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 46 through 48 removed outlier: 6.666A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AF7, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.606A pdb=" N ALA I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 5 through 6 Processing sheet with id=AF9, first strand: chain 'M' and resid 10 through 13 removed outlier: 3.574A pdb=" N LEU M 11 " --> pdb=" O LYS M 104 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 46 through 48 removed outlier: 6.666A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AG3, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.606A pdb=" N ALA J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 5 through 6 removed outlier: 3.632A pdb=" N ASP N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'N' and resid 10 through 13 removed outlier: 3.574A pdb=" N LEU N 11 " --> pdb=" O LYS N 104 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 46 through 48 removed outlier: 6.665A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) 1038 hydrogen bonds defined for protein. 2805 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: 12.77 Time building geometry restraints manager: 12.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6613 1.33 - 1.45: 7696 1.45 - 1.58: 15896 1.58 - 1.70: 0 1.70 - 1.83: 159 Bond restraints: 30364 Sorted by residual: bond pdb=" CA SER A 698 " pdb=" C SER A 698 " ideal model delta sigma weight residual 1.522 1.444 0.078 1.20e-02 6.94e+03 4.26e+01 bond pdb=" C HIS B1088 " pdb=" N PHE B1089 " ideal model delta sigma weight residual 1.331 1.264 0.068 1.59e-02 3.96e+03 1.80e+01 bond pdb=" N PRO A 589 " pdb=" CD PRO A 589 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.80e+01 bond pdb=" N PRO B 589 " pdb=" CD PRO B 589 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.77e+01 bond pdb=" N PRO C 589 " pdb=" CD PRO C 589 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.77e+01 ... (remaining 30359 not shown) Histogram of bond angle deviations from ideal: 97.53 - 105.76: 658 105.76 - 113.99: 17549 113.99 - 122.23: 17592 122.23 - 130.46: 5395 130.46 - 138.70: 102 Bond angle restraints: 41296 Sorted by residual: angle pdb=" C PHE C 86 " pdb=" N ASN C 87 " pdb=" CA ASN C 87 " ideal model delta sigma weight residual 121.54 132.73 -11.19 1.91e+00 2.74e-01 3.43e+01 angle pdb=" C PHE A 86 " pdb=" N ASN A 87 " pdb=" CA ASN A 87 " ideal model delta sigma weight residual 121.54 132.73 -11.19 1.91e+00 2.74e-01 3.43e+01 angle pdb=" C PHE B 86 " pdb=" N ASN B 87 " pdb=" CA ASN B 87 " ideal model delta sigma weight residual 121.54 132.72 -11.18 1.91e+00 2.74e-01 3.43e+01 angle pdb=" N PHE B 565 " pdb=" CA PHE B 565 " pdb=" C PHE B 565 " ideal model delta sigma weight residual 108.86 116.78 -7.92 1.41e+00 5.03e-01 3.15e+01 angle pdb=" C SER C 31 " pdb=" N PHE C 32 " pdb=" CA PHE C 32 " ideal model delta sigma weight residual 122.56 115.23 7.33 1.50e+00 4.44e-01 2.39e+01 ... (remaining 41291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 16409 17.93 - 35.87: 1795 35.87 - 53.80: 581 53.80 - 71.74: 154 71.74 - 89.67: 52 Dihedral angle restraints: 18991 sinusoidal: 8350 harmonic: 10641 Sorted by residual: dihedral pdb=" CB CYS I 22 " pdb=" SG CYS I 22 " pdb=" SG CYS I 96 " pdb=" CB CYS I 96 " ideal model delta sinusoidal sigma weight residual -86.00 -171.51 85.51 1 1.00e+01 1.00e-02 8.85e+01 dihedral pdb=" CB CYS J 22 " pdb=" SG CYS J 22 " pdb=" SG CYS J 96 " pdb=" CB CYS J 96 " ideal model delta sinusoidal sigma weight residual -86.00 -171.50 85.50 1 1.00e+01 1.00e-02 8.85e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual -86.00 -171.50 85.50 1 1.00e+01 1.00e-02 8.85e+01 ... (remaining 18988 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.329: 4835 0.329 - 0.659: 3 0.659 - 0.988: 5 0.988 - 1.318: 0 1.318 - 1.647: 1 Chirality restraints: 4844 Sorted by residual: chirality pdb=" C1 NAG f 2 " pdb=" O4 NAG f 1 " pdb=" C2 NAG f 2 " pdb=" O5 NAG f 2 " both_signs ideal model delta sigma weight residual False -2.40 -3.08 0.68 2.00e-02 2.50e+03 1.17e+03 chirality pdb=" C1 NAG e 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG e 1 " pdb=" O5 NAG e 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.75 -1.65 2.00e-01 2.50e+01 6.78e+01 chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.64 -0.76 2.00e-01 2.50e+01 1.44e+01 ... (remaining 4841 not shown) Planarity restraints: 5304 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " 0.077 2.00e-02 2.50e+03 1.03e-01 1.33e+02 pdb=" CG ASN B 331 " -0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " -0.180 2.00e-02 2.50e+03 pdb=" C1 NAG Q 1 " 0.117 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 709 " -0.047 2.00e-02 2.50e+03 5.80e-02 4.20e+01 pdb=" CG ASN A 709 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 709 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN A 709 " 0.099 2.00e-02 2.50e+03 pdb=" C1 NAG A1409 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " -0.053 2.00e-02 2.50e+03 5.69e-02 4.05e+01 pdb=" CG ASN C 331 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " 0.091 2.00e-02 2.50e+03 pdb=" C1 NAG X 1 " -0.068 2.00e-02 2.50e+03 ... (remaining 5301 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 228 2.51 - 3.11: 20919 3.11 - 3.70: 42180 3.70 - 4.30: 63969 4.30 - 4.90: 107487 Nonbonded interactions: 234783 Sorted by model distance: nonbonded pdb=" O VAL A 227 " pdb=" OD1 ASP A 228 " model vdw 1.911 3.040 nonbonded pdb=" OD1 ASN A 532 " pdb=" N LEU A 533 " model vdw 2.043 2.520 nonbonded pdb=" O GLY M 64 " pdb=" OG SER M 65 " model vdw 2.067 2.440 nonbonded pdb=" O ILE B 332 " pdb=" OG1 THR B 333 " model vdw 2.080 2.440 nonbonded pdb=" O THR B 523 " pdb=" O VAL B 524 " model vdw 2.090 3.040 ... (remaining 234778 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' and (resid 27 through 939 or resid 944 through 1146 or resid 1401 thr \ ough 1408)) selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'K' selection = chain 'O' selection = chain 'P' 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 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 1.460 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: 0.020 Extract box with map and model: 7.190 Check model and map are aligned: 0.500 Set scattering table: 0.300 Process input model: 79.470 Find NCS groups from input model: 2.260 Set up NCS constraints: 0.490 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:11.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 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 : 0.010 0.117 30364 Z= 0.637 Angle : 1.018 13.697 41296 Z= 0.585 Chirality : 0.072 1.647 4844 Planarity : 0.007 0.096 5256 Dihedral : 17.166 89.673 12020 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 20.05 Ramachandran Plot: Outliers : 2.30 % Allowed : 9.48 % Favored : 88.22 % Rotamer: Outliers : 9.75 % Allowed : 15.91 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.96 (0.11), residues: 3607 helix: -2.34 (0.16), residues: 677 sheet: -1.76 (0.15), residues: 1015 loop : -3.32 (0.11), residues: 1915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP H 103 HIS 0.009 0.002 HIS A1048 PHE 0.025 0.003 PHE A 898 TYR 0.027 0.002 TYR B1067 ARG 0.008 0.001 ARG M 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 312 poor density : 472 time to evaluate : 3.297 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: A 116 SER cc_start: 0.6367 (OUTLIER) cc_final: 0.6043 (m) REVERT: A 164 ASN cc_start: 0.5162 (OUTLIER) cc_final: 0.4704 (OUTLIER) REVERT: A 389 ASP cc_start: 0.5828 (OUTLIER) cc_final: 0.5053 (m-30) REVERT: A 444 LYS cc_start: 0.6508 (pttt) cc_final: 0.5627 (tttp) REVERT: A 529 LYS cc_start: 0.6692 (OUTLIER) cc_final: 0.5697 (mtpt) REVERT: A 530 SER cc_start: 0.5179 (OUTLIER) cc_final: 0.4565 (t) REVERT: A 531 THR cc_start: 0.8786 (OUTLIER) cc_final: 0.8315 (p) REVERT: A 1039 ARG cc_start: 0.9234 (OUTLIER) cc_final: 0.8792 (mtp180) REVERT: B 403 ARG cc_start: 0.7271 (ttp-170) cc_final: 0.6961 (ttp80) REVERT: B 523 THR cc_start: 0.3941 (OUTLIER) cc_final: 0.3730 (p) REVERT: B 554 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7325 (mp0) REVERT: B 599 THR cc_start: 0.8942 (OUTLIER) cc_final: 0.8678 (t) REVERT: B 811 LYS cc_start: 0.6393 (OUTLIER) cc_final: 0.5701 (mtpp) REVERT: C 195 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8830 (ptmt) REVERT: C 324 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6974 (pm20) REVERT: C 354 ASN cc_start: 0.7076 (t0) cc_final: 0.6828 (t0) REVERT: J 51 ILE cc_start: 0.1272 (OUTLIER) cc_final: 0.0601 (tp) outliers start: 312 outliers final: 82 residues processed: 729 average time/residue: 1.1422 time to fit residues: 1010.8885 Evaluate side-chains 340 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 245 time to evaluate : 3.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain I residue 27 PHE Chi-restraints excluded: chain J residue 31 ASN Chi-restraints excluded: chain J residue 51 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 306 optimal weight: 4.9990 chunk 275 optimal weight: 0.7980 chunk 152 optimal weight: 0.0270 chunk 93 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 284 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 chunk 173 optimal weight: 1.9990 chunk 211 optimal weight: 4.9990 chunk 329 optimal weight: 6.9990 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 137 ASN A 188 ASN A 317 ASN A 422 ASN A 498 GLN A 519 HIS A 540 ASN A 644 GLN A 703 ASN A 762 GLN A 804 GLN A 901 GLN A 914 ASN A 919 ASN A 926 GLN A 955 ASN A 969 ASN A 992 GLN A1010 GLN A1058 HIS ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN B 498 GLN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 644 GLN B 703 ASN B 901 GLN B 914 ASN B 919 ASN B 920 GLN B 926 GLN B 954 GLN B 992 GLN B1054 GLN C 137 ASN C 422 ASN C 440 ASN C 448 ASN C 450 ASN C 519 HIS C 542 ASN C 644 GLN C 703 ASN C 751 ASN C 784 GLN C 901 GLN C 914 ASN C 926 GLN C 969 ASN C 992 GLN C1010 GLN C1071 GLN C1101 HIS ** H 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 ASN L 37 GLN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30364 Z= 0.210 Angle : 0.714 13.675 41296 Z= 0.359 Chirality : 0.050 0.761 4844 Planarity : 0.005 0.062 5256 Dihedral : 9.757 60.000 5591 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.07 % Favored : 92.71 % Rotamer: Outliers : 6.31 % Allowed : 20.82 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.13), residues: 3607 helix: -0.10 (0.20), residues: 653 sheet: -1.43 (0.15), residues: 1051 loop : -2.65 (0.12), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP I 103 HIS 0.005 0.001 HIS H 112 PHE 0.022 0.002 PHE A 559 TYR 0.029 0.001 TYR B 200 ARG 0.008 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 273 time to evaluate : 3.244 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: A 164 ASN cc_start: 0.4732 (OUTLIER) cc_final: 0.4481 (OUTLIER) REVERT: A 190 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.6969 (mtt90) REVERT: A 389 ASP cc_start: 0.6145 (OUTLIER) cc_final: 0.5764 (m-30) REVERT: A 529 LYS cc_start: 0.6366 (OUTLIER) cc_final: 0.5679 (mtpt) REVERT: A 531 THR cc_start: 0.8581 (OUTLIER) cc_final: 0.8233 (p) REVERT: A 544 ASN cc_start: 0.6645 (p0) cc_final: 0.6348 (p0) REVERT: A 572 THR cc_start: 0.8349 (OUTLIER) cc_final: 0.7845 (p) REVERT: B 324 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6832 (pt0) REVERT: B 403 ARG cc_start: 0.7444 (ttp-170) cc_final: 0.7073 (ttp80) REVERT: B 506 GLN cc_start: 0.7042 (mt0) cc_final: 0.5965 (mp10) REVERT: B 544 ASN cc_start: 0.6647 (p0) cc_final: 0.6121 (p0) REVERT: B 599 THR cc_start: 0.9043 (OUTLIER) cc_final: 0.8762 (t) REVERT: B 787 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7168 (mm-40) REVERT: C 354 ASN cc_start: 0.7049 (t0) cc_final: 0.6784 (t0) REVERT: C 368 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8455 (mp) REVERT: C 457 ARG cc_start: 0.6510 (ttt-90) cc_final: 0.6241 (ttt-90) REVERT: C 493 GLN cc_start: 0.7439 (OUTLIER) cc_final: 0.6970 (tt0) REVERT: C 756 TYR cc_start: 0.8761 (m-80) cc_final: 0.8491 (m-80) REVERT: H 54 ASP cc_start: 0.6731 (OUTLIER) cc_final: 0.6453 (m-30) REVERT: H 99 ASP cc_start: 0.7763 (t70) cc_final: 0.7500 (t0) REVERT: H 112 HIS cc_start: 0.6436 (t-90) cc_final: 0.6236 (t-90) REVERT: I 83 MET cc_start: -0.0985 (tpt) cc_final: -0.1401 (mpp) REVERT: J 71 SER cc_start: 0.6389 (p) cc_final: 0.6012 (m) outliers start: 202 outliers final: 81 residues processed: 439 average time/residue: 1.1340 time to fit residues: 609.9754 Evaluate side-chains 313 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 221 time to evaluate : 3.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain L residue 101 GLN Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain M residue 10 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 183 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 274 optimal weight: 0.5980 chunk 224 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 330 optimal weight: 10.0000 chunk 356 optimal weight: 8.9990 chunk 294 optimal weight: 0.5980 chunk 327 optimal weight: 20.0000 chunk 112 optimal weight: 6.9990 chunk 264 optimal weight: 0.3980 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1010 GLN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN B 498 GLN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1106 GLN C 501 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 HIS H 77 ASN ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 28 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 30364 Z= 0.294 Angle : 0.706 14.512 41296 Z= 0.351 Chirality : 0.050 0.608 4844 Planarity : 0.005 0.065 5256 Dihedral : 8.357 59.805 5503 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.60 % Favored : 92.24 % Rotamer: Outliers : 6.16 % Allowed : 22.10 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -1.98 (0.13), residues: 3607 helix: 0.60 (0.21), residues: 653 sheet: -0.92 (0.16), residues: 1015 loop : -2.29 (0.12), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP I 103 HIS 0.006 0.001 HIS B 49 PHE 0.025 0.002 PHE I 95 TYR 0.020 0.002 TYR A1067 ARG 0.007 0.001 ARG I 100 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 249 time to evaluate : 3.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ASN cc_start: -0.0230 (OUTLIER) cc_final: -0.0574 (p0) REVERT: A 164 ASN cc_start: 0.4904 (OUTLIER) cc_final: 0.4603 (OUTLIER) REVERT: A 324 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6983 (pm20) REVERT: A 389 ASP cc_start: 0.5835 (OUTLIER) cc_final: 0.5519 (m-30) REVERT: A 529 LYS cc_start: 0.6462 (OUTLIER) cc_final: 0.5887 (mtpt) REVERT: A 531 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.8265 (p) REVERT: A 787 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8437 (mt0) REVERT: B 331 ASN cc_start: 0.7070 (OUTLIER) cc_final: 0.6157 (m-40) REVERT: B 811 LYS cc_start: 0.6871 (OUTLIER) cc_final: 0.6489 (mtpp) REVERT: C 135 PHE cc_start: 0.6483 (m-80) cc_final: 0.6239 (m-80) REVERT: C 200 TYR cc_start: 0.6370 (OUTLIER) cc_final: 0.5977 (t80) REVERT: C 368 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8490 (mp) REVERT: C 408 ARG cc_start: 0.7391 (ptp-170) cc_final: 0.7151 (ptp-170) REVERT: C 493 GLN cc_start: 0.7528 (OUTLIER) cc_final: 0.7036 (tt0) REVERT: C 988 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6754 (tm-30) REVERT: H 19 ARG cc_start: 0.6892 (ttt-90) cc_final: 0.6654 (ttt-90) REVERT: H 67 ARG cc_start: 0.7645 (ttp-110) cc_final: 0.7238 (ttp80) REVERT: H 112 HIS cc_start: 0.6538 (t-90) cc_final: 0.6299 (t-90) REVERT: L 27 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7398 (mt-10) REVERT: L 48 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8492 (mt) REVERT: L 98 THR cc_start: 0.9046 (m) cc_final: 0.8729 (p) REVERT: J 51 ILE cc_start: 0.1198 (OUTLIER) cc_final: 0.0646 (tp) outliers start: 197 outliers final: 81 residues processed: 408 average time/residue: 1.0392 time to fit residues: 528.6345 Evaluate side-chains 292 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 197 time to evaluate : 3.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain J residue 51 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 326 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 157 optimal weight: 6.9990 chunk 221 optimal weight: 5.9990 chunk 331 optimal weight: 10.0000 chunk 350 optimal weight: 10.0000 chunk 173 optimal weight: 4.9990 chunk 314 optimal weight: 0.0980 chunk 94 optimal weight: 0.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 493 GLN A1010 GLN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B1005 GLN C 81 ASN C 115 GLN H 77 ASN ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 ASN L 53 ASN J 74 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 30364 Z= 0.282 Angle : 0.684 13.099 41296 Z= 0.336 Chirality : 0.050 0.629 4844 Planarity : 0.004 0.054 5256 Dihedral : 7.816 59.544 5479 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.68 % Favored : 93.18 % Rotamer: Outliers : 5.78 % Allowed : 22.76 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -1.79 (0.13), residues: 3607 helix: 0.78 (0.21), residues: 661 sheet: -0.87 (0.16), residues: 1044 loop : -2.15 (0.12), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP J 103 HIS 0.034 0.001 HIS B 207 PHE 0.018 0.002 PHE C 86 TYR 0.018 0.001 TYR C1067 ARG 0.005 0.001 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 224 time to evaluate : 3.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 ASN cc_start: 0.4802 (OUTLIER) cc_final: 0.4512 (OUTLIER) REVERT: A 319 ARG cc_start: 0.7146 (ttp-110) cc_final: 0.6927 (mtm180) REVERT: A 324 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7046 (pm20) REVERT: A 389 ASP cc_start: 0.5757 (OUTLIER) cc_final: 0.5432 (m-30) REVERT: A 480 CYS cc_start: 0.2442 (OUTLIER) cc_final: 0.1888 (t) REVERT: A 529 LYS cc_start: 0.6579 (OUTLIER) cc_final: 0.5921 (mtpt) REVERT: A 531 THR cc_start: 0.8606 (OUTLIER) cc_final: 0.8318 (p) REVERT: A 869 MET cc_start: 0.8573 (mtt) cc_final: 0.8344 (mtt) REVERT: B 132 GLU cc_start: 0.2908 (OUTLIER) cc_final: 0.2667 (tt0) REVERT: B 444 LYS cc_start: 0.7048 (OUTLIER) cc_final: 0.6845 (ptpp) REVERT: B 787 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7519 (mt0) REVERT: B 811 LYS cc_start: 0.7059 (OUTLIER) cc_final: 0.6645 (mtpp) REVERT: C 200 TYR cc_start: 0.6377 (OUTLIER) cc_final: 0.5927 (t80) REVERT: C 493 GLN cc_start: 0.7443 (OUTLIER) cc_final: 0.6985 (tt0) REVERT: C 529 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8010 (ttpt) REVERT: C 878 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8715 (mp) REVERT: C 988 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.6867 (tm-30) REVERT: H 112 HIS cc_start: 0.6472 (t-90) cc_final: 0.6219 (t-90) REVERT: L 18 ARG cc_start: 0.8034 (mmm160) cc_final: 0.7737 (mtp-110) REVERT: L 98 THR cc_start: 0.9091 (m) cc_final: 0.8775 (p) REVERT: I 83 MET cc_start: -0.1459 (tmt) cc_final: -0.2109 (mmt) REVERT: J 51 ILE cc_start: 0.1379 (OUTLIER) cc_final: 0.0729 (tp) REVERT: J 71 SER cc_start: 0.6799 (p) cc_final: 0.6463 (m) REVERT: J 106 ILE cc_start: 0.6124 (OUTLIER) cc_final: 0.5787 (mm) outliers start: 185 outliers final: 97 residues processed: 378 average time/residue: 1.1111 time to fit residues: 516.8256 Evaluate side-chains 308 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 195 time to evaluate : 3.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 106 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 292 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 261 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 299 optimal weight: 8.9990 chunk 242 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 179 optimal weight: 4.9990 chunk 314 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN A1010 GLN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 81 ASN C 239 GLN C 751 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 ASN ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN J 74 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 30364 Z= 0.335 Angle : 0.696 13.671 41296 Z= 0.343 Chirality : 0.050 0.651 4844 Planarity : 0.005 0.057 5256 Dihedral : 7.740 58.506 5477 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.93 % Favored : 92.93 % Rotamer: Outliers : 6.38 % Allowed : 22.82 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -1.67 (0.13), residues: 3607 helix: 0.88 (0.21), residues: 665 sheet: -0.80 (0.16), residues: 1039 loop : -2.09 (0.12), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 113 HIS 0.005 0.001 HIS H 112 PHE 0.021 0.002 PHE M 99 TYR 0.019 0.001 TYR C1067 ARG 0.006 0.001 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 212 time to evaluate : 3.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 ASN cc_start: 0.4929 (OUTLIER) cc_final: 0.4557 (OUTLIER) REVERT: A 202 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8238 (mttt) REVERT: A 314 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8654 (tm-30) REVERT: A 319 ARG cc_start: 0.7279 (ttp-110) cc_final: 0.7059 (mtm180) REVERT: A 324 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7139 (pm20) REVERT: A 389 ASP cc_start: 0.5645 (OUTLIER) cc_final: 0.5208 (m-30) REVERT: A 480 CYS cc_start: 0.2425 (OUTLIER) cc_final: 0.1920 (t) REVERT: A 529 LYS cc_start: 0.6619 (OUTLIER) cc_final: 0.5932 (mtpt) REVERT: A 531 THR cc_start: 0.8624 (OUTLIER) cc_final: 0.8341 (p) REVERT: A 787 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8370 (mt0) REVERT: A 869 MET cc_start: 0.8583 (mtt) cc_final: 0.8341 (mtt) REVERT: B 200 TYR cc_start: 0.7112 (OUTLIER) cc_final: 0.6184 (m-80) REVERT: B 231 ILE cc_start: 0.6363 (mp) cc_final: 0.6158 (mp) REVERT: B 331 ASN cc_start: 0.7067 (OUTLIER) cc_final: 0.6271 (m-40) REVERT: B 444 LYS cc_start: 0.7224 (OUTLIER) cc_final: 0.6993 (ptpp) REVERT: B 452 ARG cc_start: 0.6754 (OUTLIER) cc_final: 0.6261 (mtt180) REVERT: B 787 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7542 (mt0) REVERT: C 200 TYR cc_start: 0.6370 (OUTLIER) cc_final: 0.5803 (t80) REVERT: C 493 GLN cc_start: 0.7439 (OUTLIER) cc_final: 0.6988 (tt0) REVERT: C 529 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8029 (ttpt) REVERT: C 878 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8732 (mp) REVERT: C 988 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6892 (tm-30) REVERT: H 99 ASP cc_start: 0.7792 (t70) cc_final: 0.7550 (t70) REVERT: H 112 HIS cc_start: 0.6530 (t-90) cc_final: 0.6299 (t-90) REVERT: L 18 ARG cc_start: 0.8156 (mmm160) cc_final: 0.7943 (mtp-110) REVERT: L 48 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8392 (mt) REVERT: L 74 THR cc_start: 0.7660 (m) cc_final: 0.7456 (t) REVERT: L 98 THR cc_start: 0.9094 (m) cc_final: 0.8855 (p) REVERT: I 83 MET cc_start: -0.1301 (tmt) cc_final: -0.2111 (mmt) REVERT: J 51 ILE cc_start: 0.1498 (OUTLIER) cc_final: 0.0235 (mt) REVERT: J 71 SER cc_start: 0.6856 (p) cc_final: 0.6565 (m) REVERT: J 106 ILE cc_start: 0.6404 (OUTLIER) cc_final: 0.6030 (mm) outliers start: 204 outliers final: 110 residues processed: 382 average time/residue: 1.0611 time to fit residues: 505.4191 Evaluate side-chains 328 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 197 time to evaluate : 3.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 106 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 118 optimal weight: 7.9990 chunk 315 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 206 optimal weight: 7.9990 chunk 86 optimal weight: 0.9990 chunk 351 optimal weight: 10.0000 chunk 291 optimal weight: 2.9990 chunk 162 optimal weight: 0.6980 chunk 29 optimal weight: 8.9990 chunk 116 optimal weight: 6.9990 chunk 184 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1010 GLN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1106 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 ASN ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 ASN I 31 ASN ** I 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 30364 Z= 0.209 Angle : 0.641 14.862 41296 Z= 0.315 Chirality : 0.048 0.577 4844 Planarity : 0.004 0.053 5256 Dihedral : 7.412 58.743 5473 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.27 % Favored : 93.57 % Rotamer: Outliers : 5.28 % Allowed : 23.94 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -1.39 (0.13), residues: 3607 helix: 1.30 (0.21), residues: 653 sheet: -0.66 (0.16), residues: 1056 loop : -1.93 (0.13), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 33 HIS 0.004 0.001 HIS I 59 PHE 0.022 0.001 PHE A 855 TYR 0.017 0.001 TYR C1067 ARG 0.004 0.000 ARG J 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 220 time to evaluate : 3.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 SER cc_start: 0.6527 (OUTLIER) cc_final: 0.6075 (t) REVERT: A 164 ASN cc_start: 0.4790 (OUTLIER) cc_final: 0.4534 (OUTLIER) REVERT: A 202 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8106 (mtpp) REVERT: A 324 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7121 (pm20) REVERT: A 329 PHE cc_start: 0.6926 (m-80) cc_final: 0.6129 (m-10) REVERT: A 480 CYS cc_start: 0.2375 (OUTLIER) cc_final: 0.1926 (t) REVERT: A 529 LYS cc_start: 0.6565 (OUTLIER) cc_final: 0.5818 (mtpt) REVERT: A 787 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8369 (mt0) REVERT: B 331 ASN cc_start: 0.7190 (OUTLIER) cc_final: 0.6317 (m-40) REVERT: B 428 ASP cc_start: 0.7686 (OUTLIER) cc_final: 0.7352 (p0) REVERT: B 444 LYS cc_start: 0.7445 (ptpp) cc_final: 0.7187 (ptpp) REVERT: B 787 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.7517 (mt0) REVERT: B 858 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8148 (mt) REVERT: B 1113 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7768 (mt0) REVERT: C 200 TYR cc_start: 0.6322 (OUTLIER) cc_final: 0.5796 (t80) REVERT: C 493 GLN cc_start: 0.7424 (OUTLIER) cc_final: 0.7013 (tt0) REVERT: C 529 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8057 (ttpt) REVERT: C 985 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7213 (m-30) REVERT: L 18 ARG cc_start: 0.8147 (mmm160) cc_final: 0.7902 (mtp-110) REVERT: L 98 THR cc_start: 0.9085 (m) cc_final: 0.8859 (p) REVERT: I 34 MET cc_start: 0.2205 (mtt) cc_final: -0.1111 (mmm) REVERT: I 83 MET cc_start: -0.1375 (tmt) cc_final: -0.2019 (mmt) REVERT: J 51 ILE cc_start: 0.1579 (OUTLIER) cc_final: 0.0314 (mt) REVERT: J 71 SER cc_start: 0.6675 (p) cc_final: 0.6423 (m) REVERT: J 106 ILE cc_start: 0.6441 (OUTLIER) cc_final: 0.6110 (mm) REVERT: N 77 SER cc_start: 0.5093 (p) cc_final: 0.4517 (m) outliers start: 169 outliers final: 86 residues processed: 362 average time/residue: 1.0883 time to fit residues: 492.4439 Evaluate side-chains 303 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 200 time to evaluate : 3.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 106 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 338 optimal weight: 5.9990 chunk 39 optimal weight: 20.0000 chunk 200 optimal weight: 8.9990 chunk 256 optimal weight: 0.5980 chunk 198 optimal weight: 10.0000 chunk 295 optimal weight: 5.9990 chunk 196 optimal weight: 0.0370 chunk 349 optimal weight: 2.9990 chunk 218 optimal weight: 0.9980 chunk 213 optimal weight: 3.9990 chunk 161 optimal weight: 8.9990 overall best weight: 1.7262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1010 GLN B 115 GLN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 ASN ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30364 Z= 0.225 Angle : 0.642 13.045 41296 Z= 0.315 Chirality : 0.048 0.548 4844 Planarity : 0.004 0.053 5256 Dihedral : 7.208 59.549 5465 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.68 % Favored : 93.15 % Rotamer: Outliers : 4.81 % Allowed : 24.51 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -1.21 (0.14), residues: 3607 helix: 1.56 (0.22), residues: 635 sheet: -0.56 (0.16), residues: 1043 loop : -1.82 (0.13), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 36 HIS 0.010 0.001 HIS I 59 PHE 0.030 0.001 PHE C 133 TYR 0.018 0.001 TYR C1067 ARG 0.005 0.000 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 213 time to evaluate : 3.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 SER cc_start: 0.6486 (OUTLIER) cc_final: 0.6070 (t) REVERT: A 164 ASN cc_start: 0.4772 (OUTLIER) cc_final: 0.4529 (OUTLIER) REVERT: A 202 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8099 (mtpp) REVERT: A 324 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.6939 (pm20) REVERT: A 389 ASP cc_start: 0.5795 (OUTLIER) cc_final: 0.5415 (m-30) REVERT: A 480 CYS cc_start: 0.2443 (OUTLIER) cc_final: 0.1959 (t) REVERT: A 523 THR cc_start: 0.3616 (OUTLIER) cc_final: 0.3408 (t) REVERT: A 529 LYS cc_start: 0.6823 (OUTLIER) cc_final: 0.6035 (mtpt) REVERT: B 200 TYR cc_start: 0.7143 (OUTLIER) cc_final: 0.6206 (m-80) REVERT: B 331 ASN cc_start: 0.7176 (OUTLIER) cc_final: 0.6299 (m-40) REVERT: B 335 LEU cc_start: 0.8196 (mm) cc_final: 0.7982 (tt) REVERT: B 444 LYS cc_start: 0.7646 (ptpp) cc_final: 0.7361 (ptpp) REVERT: B 787 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7550 (mt0) REVERT: B 858 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8196 (mt) REVERT: C 200 TYR cc_start: 0.6333 (OUTLIER) cc_final: 0.5867 (t80) REVERT: C 493 GLN cc_start: 0.7436 (OUTLIER) cc_final: 0.7000 (tt0) REVERT: C 529 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8054 (ttpt) REVERT: C 985 ASP cc_start: 0.7581 (OUTLIER) cc_final: 0.7232 (p0) REVERT: L 61 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.7069 (ttp-110) REVERT: L 98 THR cc_start: 0.9102 (m) cc_final: 0.8825 (p) REVERT: I 34 MET cc_start: 0.2211 (mtt) cc_final: 0.1716 (pmm) REVERT: J 51 ILE cc_start: 0.1819 (OUTLIER) cc_final: 0.0514 (mt) REVERT: J 71 SER cc_start: 0.6566 (p) cc_final: 0.6279 (m) REVERT: J 106 ILE cc_start: 0.6377 (OUTLIER) cc_final: 0.6030 (mm) REVERT: N 77 SER cc_start: 0.4900 (p) cc_final: 0.4401 (m) outliers start: 154 outliers final: 100 residues processed: 343 average time/residue: 1.0601 time to fit residues: 452.9192 Evaluate side-chains 314 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 196 time to evaluate : 3.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 106 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 216 optimal weight: 2.9990 chunk 139 optimal weight: 9.9990 chunk 208 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 68 optimal weight: 0.0170 chunk 67 optimal weight: 0.9980 chunk 222 optimal weight: 0.6980 chunk 238 optimal weight: 7.9990 chunk 172 optimal weight: 3.9990 chunk 32 optimal weight: 0.0270 chunk 275 optimal weight: 0.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN B 134 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 422 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN H 39 GLN H 77 ASN ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN J 74 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 30364 Z= 0.153 Angle : 0.609 11.757 41296 Z= 0.297 Chirality : 0.047 0.636 4844 Planarity : 0.004 0.049 5256 Dihedral : 6.792 59.045 5462 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.96 % Favored : 93.90 % Rotamer: Outliers : 4.10 % Allowed : 25.63 % Favored : 70.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.97 (0.14), residues: 3607 helix: 1.83 (0.22), residues: 640 sheet: -0.43 (0.16), residues: 1060 loop : -1.70 (0.13), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP I 33 HIS 0.003 0.000 HIS I 59 PHE 0.011 0.001 PHE A 92 TYR 0.017 0.001 TYR B1067 ARG 0.005 0.000 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 206 time to evaluate : 3.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 SER cc_start: 0.6253 (OUTLIER) cc_final: 0.5916 (t) REVERT: A 202 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8045 (mtpp) REVERT: A 324 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6944 (pm20) REVERT: A 346 ARG cc_start: 0.7145 (mpt-90) cc_final: 0.6911 (ttm170) REVERT: A 529 LYS cc_start: 0.6927 (OUTLIER) cc_final: 0.6043 (mtpt) REVERT: B 200 TYR cc_start: 0.7130 (OUTLIER) cc_final: 0.6213 (m-80) REVERT: B 331 ASN cc_start: 0.7186 (OUTLIER) cc_final: 0.6294 (m-40) REVERT: B 396 TYR cc_start: 0.7839 (m-80) cc_final: 0.7355 (m-80) REVERT: B 444 LYS cc_start: 0.7686 (ptpp) cc_final: 0.7413 (ptpp) REVERT: B 787 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7498 (mt0) REVERT: B 978 ASN cc_start: 0.7639 (m-40) cc_final: 0.7439 (m-40) REVERT: C 493 GLN cc_start: 0.7484 (OUTLIER) cc_final: 0.7082 (tt0) REVERT: C 529 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8064 (ttpt) REVERT: C 985 ASP cc_start: 0.7483 (OUTLIER) cc_final: 0.6979 (p0) REVERT: L 61 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.7274 (ttp-110) REVERT: I 34 MET cc_start: 0.2130 (mtt) cc_final: -0.0838 (mmm) REVERT: J 51 ILE cc_start: 0.1550 (OUTLIER) cc_final: 0.0288 (mt) REVERT: J 71 SER cc_start: 0.6683 (p) cc_final: 0.6404 (m) REVERT: J 106 ILE cc_start: 0.6296 (OUTLIER) cc_final: 0.5949 (mm) outliers start: 131 outliers final: 68 residues processed: 318 average time/residue: 1.0993 time to fit residues: 432.3875 Evaluate side-chains 271 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 190 time to evaluate : 3.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 106 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 318 optimal weight: 0.3980 chunk 335 optimal weight: 5.9990 chunk 305 optimal weight: 20.0000 chunk 326 optimal weight: 9.9990 chunk 196 optimal weight: 3.9990 chunk 142 optimal weight: 0.4980 chunk 256 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 294 optimal weight: 0.5980 chunk 308 optimal weight: 3.9990 chunk 324 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 926 GLN A1005 GLN A1010 GLN B 121 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 498 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN H 39 GLN H 77 ASN ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.5116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30364 Z= 0.200 Angle : 0.626 11.951 41296 Z= 0.307 Chirality : 0.048 0.585 4844 Planarity : 0.004 0.055 5256 Dihedral : 6.718 58.381 5460 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.46 % Favored : 93.37 % Rotamer: Outliers : 3.63 % Allowed : 26.04 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.94 (0.14), residues: 3607 helix: 1.86 (0.22), residues: 638 sheet: -0.33 (0.16), residues: 1024 loop : -1.71 (0.13), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP I 33 HIS 0.003 0.001 HIS I 59 PHE 0.024 0.001 PHE C 133 TYR 0.019 0.001 TYR C1067 ARG 0.007 0.000 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 199 time to evaluate : 3.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 SER cc_start: 0.6228 (OUTLIER) cc_final: 0.5896 (t) REVERT: A 202 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8121 (mtpp) REVERT: A 216 LEU cc_start: 0.5169 (OUTLIER) cc_final: 0.4967 (tt) REVERT: A 324 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6924 (pm20) REVERT: A 346 ARG cc_start: 0.7163 (mpt-90) cc_final: 0.6920 (ttm170) REVERT: A 389 ASP cc_start: 0.5723 (OUTLIER) cc_final: 0.5489 (m-30) REVERT: A 529 LYS cc_start: 0.6947 (OUTLIER) cc_final: 0.6117 (mtpt) REVERT: B 200 TYR cc_start: 0.7189 (OUTLIER) cc_final: 0.6330 (m-80) REVERT: B 331 ASN cc_start: 0.7181 (OUTLIER) cc_final: 0.6300 (m-40) REVERT: B 444 LYS cc_start: 0.7710 (ptpp) cc_final: 0.7444 (ptpp) REVERT: B 787 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7545 (mt0) REVERT: B 858 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8183 (mt) REVERT: B 1113 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7840 (mt0) REVERT: C 200 TYR cc_start: 0.6160 (OUTLIER) cc_final: 0.5456 (t80) REVERT: C 493 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.7086 (tt0) REVERT: C 529 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8049 (ttpt) REVERT: H 11 LEU cc_start: 0.6799 (tm) cc_final: 0.6373 (mm) REVERT: L 38 GLN cc_start: 0.8294 (tp40) cc_final: 0.8090 (tm-30) REVERT: L 48 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8340 (mt) REVERT: L 61 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.7263 (ttp-110) REVERT: J 51 ILE cc_start: 0.1777 (OUTLIER) cc_final: 0.0514 (mt) REVERT: J 71 SER cc_start: 0.6510 (p) cc_final: 0.6228 (m) REVERT: J 106 ILE cc_start: 0.6369 (OUTLIER) cc_final: 0.6040 (mm) outliers start: 116 outliers final: 73 residues processed: 299 average time/residue: 1.1236 time to fit residues: 418.4121 Evaluate side-chains 280 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 189 time to evaluate : 3.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 214 optimal weight: 1.9990 chunk 344 optimal weight: 2.9990 chunk 210 optimal weight: 0.9990 chunk 163 optimal weight: 7.9990 chunk 239 optimal weight: 9.9990 chunk 361 optimal weight: 7.9990 chunk 332 optimal weight: 8.9990 chunk 287 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 222 optimal weight: 3.9990 chunk 176 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 926 GLN A 955 ASN A1005 GLN A1010 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 ASN J 74 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.5302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 30364 Z= 0.258 Angle : 0.658 12.623 41296 Z= 0.323 Chirality : 0.049 0.588 4844 Planarity : 0.004 0.053 5256 Dihedral : 6.803 58.649 5458 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.65 % Favored : 93.21 % Rotamer: Outliers : 3.34 % Allowed : 26.45 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -1.03 (0.14), residues: 3607 helix: 1.71 (0.22), residues: 636 sheet: -0.42 (0.16), residues: 1032 loop : -1.71 (0.13), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP I 33 HIS 0.004 0.001 HIS I 59 PHE 0.018 0.002 PHE C 86 TYR 0.018 0.001 TYR C1067 ARG 0.007 0.001 ARG H 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 205 time to evaluate : 3.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 SER cc_start: 0.6078 (OUTLIER) cc_final: 0.5814 (t) REVERT: A 216 LEU cc_start: 0.5296 (OUTLIER) cc_final: 0.5059 (tt) REVERT: A 324 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.6825 (pm20) REVERT: A 346 ARG cc_start: 0.7248 (mpt-90) cc_final: 0.7033 (ttm170) REVERT: A 529 LYS cc_start: 0.6953 (OUTLIER) cc_final: 0.6076 (mtpt) REVERT: A 1010 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7825 (pt0) REVERT: B 331 ASN cc_start: 0.7190 (OUTLIER) cc_final: 0.6313 (m-40) REVERT: B 396 TYR cc_start: 0.7908 (m-80) cc_final: 0.7455 (m-80) REVERT: B 421 TYR cc_start: 0.7418 (p90) cc_final: 0.7185 (p90) REVERT: B 444 LYS cc_start: 0.7742 (ptpp) cc_final: 0.7481 (ptpp) REVERT: B 787 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7595 (mt0) REVERT: B 858 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8260 (mt) REVERT: B 1113 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7761 (mt0) REVERT: C 493 GLN cc_start: 0.7514 (OUTLIER) cc_final: 0.7035 (tt0) REVERT: C 529 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8011 (ttpt) REVERT: H 11 LEU cc_start: 0.7091 (tm) cc_final: 0.6589 (mm) REVERT: L 48 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8369 (mt) REVERT: L 81 GLU cc_start: 0.6980 (pt0) cc_final: 0.6568 (pp20) REVERT: I 34 MET cc_start: 0.1986 (mtt) cc_final: -0.1315 (mmm) REVERT: J 51 ILE cc_start: 0.2026 (OUTLIER) cc_final: 0.0755 (mt) REVERT: J 71 SER cc_start: 0.6718 (p) cc_final: 0.6476 (m) REVERT: J 106 ILE cc_start: 0.6493 (OUTLIER) cc_final: 0.6187 (mm) REVERT: N 77 SER cc_start: 0.5102 (p) cc_final: 0.4682 (m) outliers start: 107 outliers final: 76 residues processed: 297 average time/residue: 1.1008 time to fit residues: 403.5422 Evaluate side-chains 278 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 188 time to evaluate : 3.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 228 optimal weight: 0.9980 chunk 306 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 265 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 288 optimal weight: 0.0870 chunk 120 optimal weight: 4.9990 chunk 296 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN A1010 GLN A1142 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN B 501 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 969 ASN B1005 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 ASN J 74 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.163845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.111343 restraints weight = 45026.150| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.51 r_work: 0.3138 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.5417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 30364 Z= 0.154 Angle : 0.610 12.301 41296 Z= 0.299 Chirality : 0.047 0.544 4844 Planarity : 0.004 0.050 5256 Dihedral : 6.472 57.196 5456 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.93 % Favored : 93.93 % Rotamer: Outliers : 2.88 % Allowed : 26.95 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.84 (0.14), residues: 3607 helix: 1.88 (0.22), residues: 636 sheet: -0.21 (0.16), residues: 1068 loop : -1.67 (0.13), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP I 33 HIS 0.003 0.000 HIS I 59 PHE 0.027 0.001 PHE B 135 TYR 0.017 0.001 TYR B1067 ARG 0.006 0.000 ARG H 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9782.02 seconds wall clock time: 177 minutes 18.16 seconds (10638.16 seconds total)