Starting phenix.real_space_refine on Sat Apr 13 16:10:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dx5_30896/04_2024/7dx5_30896.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dx5_30896/04_2024/7dx5_30896.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dx5_30896/04_2024/7dx5_30896.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dx5_30896/04_2024/7dx5_30896.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dx5_30896/04_2024/7dx5_30896.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dx5_30896/04_2024/7dx5_30896.pdb" } resolution = 3.3 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= 0.004 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 133 5.16 5 C 18475 2.51 5 N 4720 2.21 5 O 5717 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 GLU 156": "OE1" <-> "OE2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A ARG 408": "NH1" <-> "NH2" 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 GLU 988": "OE1" <-> "OE2" Residue "A ARG 1107": "NH1" <-> "NH2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B ARG 246": "NH1" <-> "NH2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" 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 GLU 156": "OE1" <-> "OE2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C ARG 246": "NH1" <-> "NH2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C ARG 408": "NH1" <-> "NH2" 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 "D GLU 23": "OE1" <-> "OE2" Residue "D GLU 56": "OE1" <-> "OE2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D GLU 227": "OE1" <-> "OE2" Residue "D ARG 245": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "D ARG 306": "NH1" <-> "NH2" Residue "D GLU 329": "OE1" <-> "OE2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D GLU 435": "OE1" <-> "OE2" Residue "D ARG 518": "NH1" <-> "NH2" Residue "D GLU 527": "OE1" <-> "OE2" Residue "D GLU 549": "OE1" <-> "OE2" Residue "D GLU 564": "OE1" <-> "OE2" Residue "D TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 29045 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 7872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 7872 Classifications: {'peptide': 1007} Link IDs: {'PTRANS': 50, 'TRANS': 956} Chain breaks: 8 Chain: "B" Number of atoms: 7584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 7584 Classifications: {'peptide': 971} Link IDs: {'PTRANS': 48, 'TRANS': 922} Chain breaks: 9 Chain: "C" Number of atoms: 7584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 7584 Classifications: {'peptide': 971} Link IDs: {'PTRANS': 48, 'TRANS': 922} Chain breaks: 9 Chain: "D" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 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: "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: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 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 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 14.19, per 1000 atoms: 0.49 Number of scatterers: 29045 At special positions: 0 Unit cell: (138.049, 193.486, 204.356, 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 133 16.00 O 5717 8.00 N 4720 7.00 C 18475 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, 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=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.17 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.11 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=2.56 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=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.12 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.12 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.44 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.17 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.12 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.45 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=2.04 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 D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.17 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B1406 " - " NAG B1407 " " NAG B1411 " - " NAG B1412 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG 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-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 343 " " NAG B1408 " - " ASN B 603 " " NAG B1409 " - " ASN B 616 " " NAG B1410 " - " ASN B 657 " " NAG B1411 " - " ASN B1074 " " 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 901 " - " ASN D 322 " " NAG E 1 " - " ASN A 331 " " NAG F 1 " - " ASN A 343 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1074 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG L 1 " - " ASN B 331 " " NAG M 1 " - " ASN B 709 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN B1098 " " NAG Q 1 " - " ASN B1134 " " NAG R 1 " - " ASN C 331 " " NAG S 1 " - " ASN C 343 " " NAG T 1 " - " ASN C 709 " " NAG U 1 " - " ASN C 717 " " NAG V 1 " - " ASN C 801 " " NAG W 1 " - " ASN C1074 " " NAG X 1 " - " ASN C1098 " " NAG Y 1 " - " ASN C1134 " " NAG Z 1 " - " ASN D 53 " " NAG a 1 " - " ASN D 90 " " NAG b 1 " - " ASN D 103 " " NAG c 1 " - " ASN D 432 " " NAG d 1 " - " ASN D 546 " Time building additional restraints: 10.93 Conformation dependent library (CDL) restraints added in 5.1 seconds 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6658 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 46 sheets defined 31.3% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.77 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.074A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.258A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.623A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.737A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.629A 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: 3.559A 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: 3.538A 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: 3.648A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.574A 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: 3.625A 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: 3.693A 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: 3.878A 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: 4.836A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.633A 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: 3.681A 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: 3.676A 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 364 through 370 removed outlier: 4.073A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.257A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.624A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.737A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 removed outlier: 3.695A 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: 3.963A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.648A 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: 3.544A 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: 3.846A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.010A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.704A 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: 4.120A 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: 3.506A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.582A 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 364 through 370 removed outlier: 4.074A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.257A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.622A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.736A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.718A 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: 4.070A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.605A pdb=" N LEU C 821 " --> pdb=" O PHE 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: 3.801A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.712A 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: 3.529A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.554A 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: 3.604A 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 'D' and resid 22 through 53 removed outlier: 3.791A pdb=" N LYS D 31 " --> pdb=" O THR D 27 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU D 37 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 81 removed outlier: 3.755A pdb=" N ASN D 64 " --> pdb=" O GLN D 60 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TRP D 69 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.641A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 130 removed outlier: 3.687A pdb=" N LYS D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.528A pdb=" N ILE D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 172 removed outlier: 3.549A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 193 removed outlier: 3.834A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 204 Processing helix chain 'D' and resid 205 through 208 removed outlier: 3.564A pdb=" N GLU D 208 " --> pdb=" O GLY D 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 205 through 208' Processing helix chain 'D' and resid 220 through 231 removed outlier: 3.907A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 252 removed outlier: 3.595A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 294 through 299 removed outlier: 3.513A pdb=" N VAL D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 removed outlier: 4.308A pdb=" N ILE D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.760A pdb=" N SER D 331 " --> pdb=" O PHE D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 383 removed outlier: 3.636A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE D 379 " --> pdb=" O GLU D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.549A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.551A pdb=" N ALA D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER D 411 " --> pdb=" O ILE D 407 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA D 412 " --> pdb=" O MET D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 removed outlier: 3.679A pdb=" N SER D 420 " --> pdb=" O LYS D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 444 removed outlier: 3.598A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE D 436 " --> pdb=" O ASN D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 465 Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.752A pdb=" N TRP D 478 " --> pdb=" O MET D 474 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG D 482 " --> pdb=" O TRP D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 502 removed outlier: 3.592A pdb=" N SER D 502 " --> pdb=" O ASP D 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 499 through 502' Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 3.878A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 548 through 559 removed outlier: 4.396A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG D 559 " --> pdb=" O PHE D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 removed outlier: 3.674A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 removed outlier: 3.579A pdb=" N TYR D 587 " --> pdb=" O PRO D 583 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 599 removed outlier: 3.576A pdb=" N TRP D 594 " --> pdb=" O PRO D 590 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP D 597 " --> pdb=" O THR D 593 " (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: 3.679A 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: 6.294A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.948A 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: 3.857A 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: 7.475A 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: 7.210A 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) removed outlier: 3.776A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.050A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (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 327 through 328 removed outlier: 5.338A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.543A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 448 through 454 removed outlier: 5.864A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) 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 654 through 655 removed outlier: 6.603A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.974A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.588A 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: 6.244A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.530A 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: 5.735A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.588A 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: 6.244A 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: 5.419A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB4, 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=AB5, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB6, 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=AB7, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.061A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.678A 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: 6.294A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.856A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC1, first strand: chain 'B' and resid 116 through 121 removed outlier: 3.731A 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: 7.659A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 309 through 319 removed outlier: 6.544A pdb=" N GLU B 309 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLY B 601 " --> pdb=" O GLU B 309 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.619A 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=AC3, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.543A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 448 through 453 removed outlier: 5.863A pdb=" N TYR B 449 " --> pdb=" O PHE B 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE B 497 " --> pdb=" O TYR B 449 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 539 through 543 removed outlier: 5.601A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.110A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.542A 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: 6.697A 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: 5.857A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.542A 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: 6.697A 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: 4.596A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, 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=AD2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD3, 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: 6.440A 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: 6.293A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.437A 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=AD4, first strand: chain 'C' and resid 49 through 55 removed outlier: 3.876A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD6, first strand: chain 'C' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 7.474A 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: 7.210A 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) removed outlier: 3.775A pdb=" N GLN C 134 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 317 removed outlier: 4.220A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.542A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 448 through 453 removed outlier: 5.864A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 539 through 543 Processing sheet with id=AE2, first strand: chain 'C' and resid 553 through 554 removed outlier: 6.444A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.452A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.837A 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=AE4, 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: 6.843A 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=AE5, 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: 6.843A 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: 3.564A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.568A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE8, first strand: chain 'D' and resid 132 through 133 Processing sheet with id=AE9, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.030A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'D' and resid 347 through 352 removed outlier: 3.582A pdb=" N LEU D 351 " --> pdb=" O ASP D 355 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) 1101 hydrogen bonds defined for protein. 3024 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: 12.79 Time building geometry restraints manager: 11.82 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: 6344 1.33 - 1.45: 7563 1.45 - 1.58: 15604 1.58 - 1.70: 0 1.70 - 1.83: 181 Bond restraints: 29692 Sorted by residual: bond pdb=" CA SER A 698 " pdb=" C SER A 698 " ideal model delta sigma weight residual 1.522 1.443 0.080 1.20e-02 6.94e+03 4.40e+01 bond pdb=" C ASP A 985 " pdb=" N PRO A 986 " ideal model delta sigma weight residual 1.329 1.391 -0.061 1.18e-02 7.18e+03 2.70e+01 bond pdb=" N PRO B 337 " pdb=" CD PRO B 337 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.87e+01 bond pdb=" N PRO A 987 " pdb=" CD PRO A 987 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.84e+01 bond pdb=" N PRO A 986 " pdb=" CD PRO A 986 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.80e+01 ... (remaining 29687 not shown) Histogram of bond angle deviations from ideal: 97.57 - 105.83: 616 105.83 - 114.08: 17453 114.08 - 122.34: 17640 122.34 - 130.60: 4561 130.60 - 138.85: 108 Bond angle restraints: 40378 Sorted by residual: angle pdb=" C ASP A 985 " pdb=" N PRO A 986 " pdb=" CA PRO A 986 " ideal model delta sigma weight residual 120.38 114.01 6.37 1.03e+00 9.43e-01 3.83e+01 angle pdb=" N THR D 362 " pdb=" CA THR D 362 " pdb=" C THR D 362 " ideal model delta sigma weight residual 109.76 119.32 -9.56 1.59e+00 3.96e-01 3.61e+01 angle pdb=" C PHE A 86 " pdb=" N ASN A 87 " pdb=" CA ASN A 87 " ideal model delta sigma weight residual 121.54 132.81 -11.27 1.91e+00 2.74e-01 3.48e+01 angle pdb=" C PHE C 86 " pdb=" N ASN C 87 " pdb=" CA ASN C 87 " ideal model delta sigma weight residual 121.54 132.79 -11.25 1.91e+00 2.74e-01 3.47e+01 angle pdb=" C PHE B 86 " pdb=" N ASN B 87 " pdb=" CA ASN B 87 " ideal model delta sigma weight residual 121.54 132.77 -11.23 1.91e+00 2.74e-01 3.46e+01 ... (remaining 40373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 16182 17.94 - 35.88: 1738 35.88 - 53.82: 575 53.82 - 71.76: 189 71.76 - 89.70: 52 Dihedral angle restraints: 18736 sinusoidal: 8408 harmonic: 10328 Sorted by residual: dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.09 71.91 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.09 71.91 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.13 71.87 1 1.00e+01 1.00e-02 6.61e+01 ... (remaining 18733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.330: 4762 0.330 - 0.659: 6 0.659 - 0.989: 6 0.989 - 1.319: 2 1.319 - 1.648: 1 Chirality restraints: 4777 Sorted by residual: chirality pdb=" C1 NAG B1407 " pdb=" O4 NAG B1406 " pdb=" C2 NAG B1407 " pdb=" O5 NAG B1407 " both_signs ideal model delta sigma weight residual False -2.40 -1.17 -1.23 2.00e-02 2.50e+03 3.81e+03 chirality pdb=" C1 NAG B1412 " pdb=" O4 NAG B1411 " pdb=" C2 NAG B1412 " pdb=" O5 NAG B1412 " both_signs ideal model delta sigma weight residual False -2.40 -3.08 0.68 2.00e-02 2.50e+03 1.16e+03 chirality pdb=" C1 NAG Y 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG Y 1 " pdb=" O5 NAG Y 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.75 -1.65 2.00e-01 2.50e+01 6.79e+01 ... (remaining 4774 not shown) Planarity restraints: 5166 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG b 2 " 0.354 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C7 NAG b 2 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG b 2 " 0.107 2.00e-02 2.50e+03 pdb=" N2 NAG b 2 " -0.544 2.00e-02 2.50e+03 pdb=" O7 NAG b 2 " 0.167 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG b 1 " 0.285 2.00e-02 2.50e+03 2.39e-01 7.16e+02 pdb=" C7 NAG b 1 " -0.075 2.00e-02 2.50e+03 pdb=" C8 NAG b 1 " 0.185 2.00e-02 2.50e+03 pdb=" N2 NAG b 1 " -0.406 2.00e-02 2.50e+03 pdb=" O7 NAG b 1 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " 0.126 2.00e-02 2.50e+03 1.85e-01 4.28e+02 pdb=" CG ASN B 331 " -0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " 0.045 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " -0.326 2.00e-02 2.50e+03 pdb=" C1 NAG L 1 " 0.210 2.00e-02 2.50e+03 ... (remaining 5163 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 140 2.43 - 3.05: 17828 3.05 - 3.66: 40356 3.66 - 4.28: 64403 4.28 - 4.90: 106749 Nonbonded interactions: 229476 Sorted by model distance: nonbonded pdb=" O ASN A 536 " pdb=" CG LYS A 537 " model vdw 1.810 3.440 nonbonded pdb=" O SER D 105 " pdb=" OG SER D 106 " model vdw 1.932 2.440 nonbonded pdb=" NH1 ARG A 346 " pdb=" O PHE A 347 " model vdw 1.982 2.520 nonbonded pdb=" NH1 ARG B 346 " pdb=" O PHE B 347 " model vdw 1.983 2.520 nonbonded pdb=" NH1 ARG C 346 " pdb=" O PHE C 347 " model vdw 1.983 2.520 ... (remaining 229471 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 455 or resid 491 through 939 or resid 944 throu \ gh 1146 or resid 1401 through 1408)) selection = (chain 'B' and (resid 27 through 1146 or resid 1401 through 1408)) selection = chain 'C' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain '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' } 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: 3.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 6.870 Check model and map are aligned: 0.430 Set scattering table: 0.250 Process input model: 77.700 Find NCS groups from input model: 2.250 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: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 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 : 0.011 0.117 29692 Z= 0.727 Angle : 1.013 13.854 40378 Z= 0.583 Chirality : 0.078 1.648 4777 Planarity : 0.009 0.306 5112 Dihedral : 17.596 89.703 11958 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 20.06 Ramachandran Plot: Outliers : 2.87 % Allowed : 9.10 % Favored : 88.03 % Rotamer: Outliers : 11.10 % Allowed : 15.90 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.36 (0.11), residues: 3484 helix: -2.95 (0.12), residues: 991 sheet: -1.98 (0.17), residues: 743 loop : -3.31 (0.12), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 104 HIS 0.009 0.001 HIS A1048 PHE 0.025 0.003 PHE A 898 TYR 0.027 0.003 TYR B1067 ARG 0.008 0.001 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 832 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 345 poor density : 487 time to evaluate : 3.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 PHE cc_start: 0.5334 (t80) cc_final: 0.5130 (t80) REVERT: A 369 TYR cc_start: 0.5212 (t80) cc_final: 0.4204 (t80) REVERT: A 599 THR cc_start: 0.8612 (OUTLIER) cc_final: 0.8389 (p) REVERT: A 692 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8114 (mm) REVERT: A 856 ASN cc_start: 0.8812 (OUTLIER) cc_final: 0.8208 (p0) REVERT: B 48 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8444 (mt) REVERT: B 118 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7251 (tp) REVERT: B 153 MET cc_start: -0.0501 (mpp) cc_final: -0.2850 (ttp) REVERT: B 158 ARG cc_start: 0.5749 (OUTLIER) cc_final: 0.4811 (mpt180) REVERT: B 164 ASN cc_start: 0.5728 (OUTLIER) cc_final: 0.5294 (t0) REVERT: B 403 ARG cc_start: 0.5451 (OUTLIER) cc_final: 0.5126 (tpt170) REVERT: B 421 TYR cc_start: 0.5721 (OUTLIER) cc_final: 0.5202 (p90) REVERT: B 535 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7153 (tttt) REVERT: B 710 ASN cc_start: 0.9518 (OUTLIER) cc_final: 0.9257 (p0) REVERT: B 748 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7174 (mp0) REVERT: B 856 ASN cc_start: 0.8677 (OUTLIER) cc_final: 0.8445 (m110) REVERT: B 1030 SER cc_start: 0.9433 (OUTLIER) cc_final: 0.9110 (m) REVERT: C 153 MET cc_start: -0.3156 (mpp) cc_final: -0.3929 (ttm) REVERT: C 535 LYS cc_start: 0.6864 (OUTLIER) cc_final: 0.6515 (ttmt) REVERT: D 82 MET cc_start: 0.5998 (mmt) cc_final: 0.3675 (tmm) REVERT: D 344 CYS cc_start: 0.4797 (OUTLIER) cc_final: 0.4481 (m) REVERT: D 379 ILE cc_start: 0.5351 (mm) cc_final: 0.4807 (tt) REVERT: D 462 MET cc_start: 0.6031 (mtp) cc_final: 0.5754 (ttt) REVERT: D 465 LYS cc_start: 0.2195 (ptpt) cc_final: 0.1941 (ttmt) REVERT: D 579 MET cc_start: 0.2163 (ptt) cc_final: 0.0836 (ttp) outliers start: 345 outliers final: 101 residues processed: 774 average time/residue: 0.4235 time to fit residues: 516.6529 Evaluate side-chains 348 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 231 time to evaluate : 3.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 164 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 310 LYS Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 344 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 298 optimal weight: 5.9990 chunk 267 optimal weight: 0.8980 chunk 148 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 276 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 168 optimal weight: 10.0000 chunk 205 optimal weight: 6.9990 chunk 320 optimal weight: 9.9990 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 81 ASN ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN A 207 HIS A 239 GLN A 271 GLN A 314 GLN A 422 ASN A 440 ASN A 498 GLN A 613 GLN A 644 GLN A 762 GLN A 901 GLN A 914 ASN A 919 ASN A 926 GLN A 955 ASN A 960 ASN A 969 ASN A 992 GLN A1002 GLN A1101 HIS B 81 ASN B 137 ASN B 188 ASN B 239 GLN B 314 GLN B 334 ASN B 422 ASN B 440 ASN B 498 GLN B 564 GLN B 613 GLN B 644 GLN B 675 GLN B 710 ASN B 762 GLN B 804 GLN B 901 GLN B 914 ASN B 919 ASN B 920 GLN B 926 GLN B 969 ASN B 992 GLN B1005 GLN B1054 GLN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN C 207 HIS C 360 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 ASN C 498 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 644 GLN C 703 ASN C 755 GLN C 784 GLN C 901 GLN C 914 ASN C 926 GLN C 969 ASN C 992 GLN C1071 GLN C1101 HIS D 42 GLN D 51 ASN D 58 ASN D 96 GLN D 134 ASN D 175 GLN D 239 HIS D 277 ASN D 330 ASN D 345 HIS D 388 GLN D 401 HIS D 472 GLN D 505 HIS D 586 ASN Total number of N/Q/H flips: 79 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 29692 Z= 0.241 Angle : 0.744 12.950 40378 Z= 0.372 Chirality : 0.050 0.548 4777 Planarity : 0.005 0.063 5112 Dihedral : 10.877 81.613 5717 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.15 % Favored : 92.51 % Rotamer: Outliers : 5.89 % Allowed : 18.96 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.60 (0.13), residues: 3484 helix: -0.55 (0.16), residues: 983 sheet: -1.27 (0.18), residues: 704 loop : -2.67 (0.12), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 477 HIS 0.005 0.001 HIS A1101 PHE 0.036 0.002 PHE D 512 TYR 0.053 0.002 TYR B 396 ARG 0.007 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 251 time to evaluate : 2.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ASP cc_start: 0.5603 (OUTLIER) cc_final: 0.5374 (t0) REVERT: A 599 THR cc_start: 0.8706 (OUTLIER) cc_final: 0.8469 (p) REVERT: A 794 ILE cc_start: 0.7878 (OUTLIER) cc_final: 0.7500 (mm) REVERT: A 856 ASN cc_start: 0.9012 (OUTLIER) cc_final: 0.8345 (p0) REVERT: B 48 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8454 (mt) REVERT: B 153 MET cc_start: -0.0572 (mpp) cc_final: -0.2820 (ttp) REVERT: B 158 ARG cc_start: 0.5854 (OUTLIER) cc_final: 0.4865 (mpt180) REVERT: B 164 ASN cc_start: 0.5752 (OUTLIER) cc_final: 0.5276 (t0) REVERT: B 217 PRO cc_start: 0.7609 (Cg_endo) cc_final: 0.7406 (Cg_exo) REVERT: B 377 PHE cc_start: 0.7670 (t80) cc_final: 0.7382 (t80) REVERT: B 403 ARG cc_start: 0.6545 (OUTLIER) cc_final: 0.5598 (tpt170) REVERT: B 535 LYS cc_start: 0.7602 (OUTLIER) cc_final: 0.7095 (tttp) REVERT: B 856 ASN cc_start: 0.8796 (OUTLIER) cc_final: 0.8567 (m110) REVERT: C 153 MET cc_start: -0.3292 (mpp) cc_final: -0.4005 (ttm) REVERT: C 298 GLU cc_start: 0.6485 (mm-30) cc_final: 0.6251 (mm-30) REVERT: C 324 GLU cc_start: 0.5596 (OUTLIER) cc_final: 0.4940 (mm-30) REVERT: C 535 LYS cc_start: 0.6922 (OUTLIER) cc_final: 0.5887 (ttmt) REVERT: C 855 PHE cc_start: 0.6107 (m-80) cc_final: 0.5870 (m-10) REVERT: C 856 ASN cc_start: 0.8889 (OUTLIER) cc_final: 0.7713 (p0) REVERT: D 82 MET cc_start: 0.5731 (mmt) cc_final: 0.3849 (ptp) REVERT: D 270 MET cc_start: 0.5356 (ttm) cc_final: 0.5000 (ttm) REVERT: D 465 LYS cc_start: 0.2616 (ptpt) cc_final: 0.2278 (tppt) outliers start: 183 outliers final: 90 residues processed: 414 average time/residue: 0.4071 time to fit residues: 272.1833 Evaluate side-chains 295 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 192 time to evaluate : 3.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR 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 530 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 551 VAL 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 813 SER Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 520 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 178 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 266 optimal weight: 0.0970 chunk 218 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 321 optimal weight: 6.9990 chunk 346 optimal weight: 20.0000 chunk 286 optimal weight: 4.9990 chunk 318 optimal weight: 0.0570 chunk 109 optimal weight: 9.9990 chunk 257 optimal weight: 1.9990 overall best weight: 2.4302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN A 540 ASN A 764 ASN B 49 HIS B 314 GLN B 450 ASN B 613 GLN B 658 ASN B 675 GLN B 804 GLN B 935 GLN B1005 GLN C 134 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN D 505 HIS D 522 GLN D 599 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 29692 Z= 0.281 Angle : 0.684 11.647 40378 Z= 0.337 Chirality : 0.049 0.459 4777 Planarity : 0.005 0.061 5112 Dihedral : 9.175 83.031 5606 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.75 % Favored : 92.05 % Rotamer: Outliers : 5.02 % Allowed : 19.31 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.83 (0.13), residues: 3484 helix: 0.38 (0.17), residues: 996 sheet: -1.01 (0.18), residues: 716 loop : -2.31 (0.13), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 461 HIS 0.006 0.001 HIS B 49 PHE 0.019 0.002 PHE C 562 TYR 0.020 0.001 TYR C1067 ARG 0.015 0.001 ARG D 482 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 213 time to evaluate : 3.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 524 VAL cc_start: 0.3808 (OUTLIER) cc_final: 0.3557 (p) REVERT: A 902 MET cc_start: 0.8535 (tpp) cc_final: 0.8319 (mmp) REVERT: B 48 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8396 (mt) REVERT: B 153 MET cc_start: -0.0485 (mpp) cc_final: -0.2702 (ttp) REVERT: B 164 ASN cc_start: 0.5823 (OUTLIER) cc_final: 0.5294 (t0) REVERT: B 377 PHE cc_start: 0.7782 (t80) cc_final: 0.7519 (t80) REVERT: C 153 MET cc_start: -0.2996 (mpp) cc_final: -0.3697 (ttm) REVERT: C 364 ASP cc_start: 0.7850 (m-30) cc_final: 0.7036 (t0) REVERT: C 535 LYS cc_start: 0.6813 (OUTLIER) cc_final: 0.5825 (ttmt) REVERT: C 1132 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8417 (pp) REVERT: D 62 MET cc_start: 0.3970 (ppp) cc_final: 0.1785 (tmm) REVERT: D 82 MET cc_start: 0.5836 (mmt) cc_final: 0.3924 (ptp) REVERT: D 270 MET cc_start: 0.5324 (ttm) cc_final: 0.4995 (ttm) REVERT: D 278 LEU cc_start: 0.2770 (tp) cc_final: 0.2148 (mt) outliers start: 156 outliers final: 95 residues processed: 353 average time/residue: 0.3692 time to fit residues: 220.3161 Evaluate side-chains 280 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 180 time to evaluate : 3.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 307 THR 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 367 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1146 ASP Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 597 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 317 optimal weight: 9.9990 chunk 241 optimal weight: 8.9990 chunk 166 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 153 optimal weight: 0.0060 chunk 215 optimal weight: 9.9990 chunk 322 optimal weight: 20.0000 chunk 341 optimal weight: 6.9990 chunk 168 optimal weight: 0.9980 chunk 305 optimal weight: 30.0000 chunk 91 optimal weight: 1.9990 overall best weight: 2.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A1002 GLN B 314 GLN B 613 GLN B 675 GLN B1005 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 ASN D 442 GLN D 505 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 29692 Z= 0.286 Angle : 0.672 12.159 40378 Z= 0.327 Chirality : 0.049 0.522 4777 Planarity : 0.004 0.068 5112 Dihedral : 8.500 87.944 5574 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.46 % Favored : 92.31 % Rotamer: Outliers : 4.80 % Allowed : 19.92 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.47 (0.14), residues: 3484 helix: 0.73 (0.17), residues: 999 sheet: -0.88 (0.19), residues: 717 loop : -2.09 (0.13), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 461 HIS 0.006 0.001 HIS B 519 PHE 0.022 0.002 PHE A 92 TYR 0.021 0.001 TYR A 369 ARG 0.005 0.000 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 190 time to evaluate : 3.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.6853 (m-80) cc_final: 0.6563 (t80) REVERT: A 856 ASN cc_start: 0.9123 (OUTLIER) cc_final: 0.8498 (p0) REVERT: B 48 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8493 (mt) REVERT: B 164 ASN cc_start: 0.5790 (OUTLIER) cc_final: 0.5271 (t0) REVERT: B 377 PHE cc_start: 0.7801 (t80) cc_final: 0.7535 (t80) REVERT: B 529 LYS cc_start: 0.6636 (OUTLIER) cc_final: 0.5977 (ptpp) REVERT: C 269 TYR cc_start: 0.6314 (m-80) cc_final: 0.6063 (m-80) REVERT: C 364 ASP cc_start: 0.7812 (m-30) cc_final: 0.7067 (t0) REVERT: C 535 LYS cc_start: 0.6888 (OUTLIER) cc_final: 0.5901 (ttmt) REVERT: C 1132 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8425 (pp) REVERT: D 62 MET cc_start: 0.4241 (ppp) cc_final: 0.1877 (tmm) REVERT: D 82 MET cc_start: 0.5953 (mmt) cc_final: 0.4223 (ptp) REVERT: D 323 MET cc_start: 0.0117 (tpt) cc_final: -0.0085 (tpp) REVERT: D 579 MET cc_start: 0.3378 (ptt) cc_final: 0.1802 (ttp) outliers start: 149 outliers final: 111 residues processed: 324 average time/residue: 0.3596 time to fit residues: 198.8356 Evaluate side-chains 291 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 174 time to evaluate : 3.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 307 THR 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 529 LYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1146 ASP Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 477 TRP Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 597 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 284 optimal weight: 0.7980 chunk 193 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 254 optimal weight: 0.7980 chunk 140 optimal weight: 9.9990 chunk 291 optimal weight: 0.0470 chunk 235 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 174 optimal weight: 0.9990 chunk 306 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN B 314 GLN B 613 GLN B 675 GLN B 804 GLN B1005 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 29692 Z= 0.153 Angle : 0.612 11.908 40378 Z= 0.297 Chirality : 0.047 0.571 4777 Planarity : 0.004 0.056 5112 Dihedral : 8.020 89.193 5572 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.54 % Favored : 93.23 % Rotamer: Outliers : 4.22 % Allowed : 20.24 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.14 (0.14), residues: 3484 helix: 1.09 (0.17), residues: 989 sheet: -0.67 (0.19), residues: 722 loop : -1.94 (0.13), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 461 HIS 0.004 0.001 HIS B 519 PHE 0.022 0.001 PHE A 92 TYR 0.019 0.001 TYR A 369 ARG 0.003 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 206 time to evaluate : 3.549 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: A 194 PHE cc_start: 0.7756 (m-80) cc_final: 0.7544 (m-10) REVERT: A 856 ASN cc_start: 0.9071 (OUTLIER) cc_final: 0.8525 (p0) REVERT: B 48 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8477 (mt) REVERT: B 141 LEU cc_start: 0.6494 (OUTLIER) cc_final: 0.6194 (pt) REVERT: B 153 MET cc_start: -0.0217 (mpp) cc_final: -0.2543 (ttp) REVERT: B 164 ASN cc_start: 0.5782 (OUTLIER) cc_final: 0.5281 (t0) REVERT: B 377 PHE cc_start: 0.7800 (t80) cc_final: 0.7526 (t80) REVERT: B 529 LYS cc_start: 0.6465 (OUTLIER) cc_final: 0.5992 (ptpp) REVERT: C 269 TYR cc_start: 0.6210 (m-80) cc_final: 0.5956 (m-80) REVERT: C 535 LYS cc_start: 0.6852 (OUTLIER) cc_final: 0.5896 (ttmt) REVERT: C 1132 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8320 (pp) REVERT: D 62 MET cc_start: 0.3957 (ppp) cc_final: 0.1965 (tmm) REVERT: D 82 MET cc_start: 0.5948 (mmt) cc_final: 0.4264 (ptp) REVERT: D 142 LEU cc_start: 0.2113 (mp) cc_final: 0.1523 (mm) REVERT: D 323 MET cc_start: -0.0014 (tpt) cc_final: -0.1409 (tpp) REVERT: D 360 MET cc_start: 0.2248 (tpt) cc_final: 0.1093 (ttt) REVERT: D 579 MET cc_start: 0.3301 (ptt) cc_final: 0.1749 (ttp) outliers start: 131 outliers final: 85 residues processed: 319 average time/residue: 0.3767 time to fit residues: 203.3777 Evaluate side-chains 275 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 183 time to evaluate : 3.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 282 ASN 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 399 SER 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 544 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 597 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 114 optimal weight: 30.0000 chunk 307 optimal weight: 20.0000 chunk 67 optimal weight: 2.9990 chunk 200 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 341 optimal weight: 7.9990 chunk 283 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 179 optimal weight: 0.0030 overall best weight: 3.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN A1011 GLN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 751 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C1002 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.4513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 29692 Z= 0.334 Angle : 0.684 12.904 40378 Z= 0.334 Chirality : 0.049 0.545 4777 Planarity : 0.004 0.063 5112 Dihedral : 8.080 83.108 5571 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.72 % Favored : 92.11 % Rotamer: Outliers : 5.02 % Allowed : 19.50 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.17 (0.14), residues: 3484 helix: 1.10 (0.17), residues: 993 sheet: -0.78 (0.18), residues: 726 loop : -1.94 (0.14), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 48 HIS 0.012 0.001 HIS C 519 PHE 0.031 0.002 PHE C 429 TYR 0.021 0.002 TYR C1067 ARG 0.004 0.001 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 190 time to evaluate : 3.222 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: A 347 PHE cc_start: 0.7070 (m-80) cc_final: 0.6620 (t80) REVERT: A 856 ASN cc_start: 0.9116 (OUTLIER) cc_final: 0.8400 (p0) REVERT: B 141 LEU cc_start: 0.6565 (OUTLIER) cc_final: 0.6088 (pt) REVERT: B 153 MET cc_start: -0.0090 (OUTLIER) cc_final: -0.1588 (mpp) REVERT: B 164 ASN cc_start: 0.5537 (OUTLIER) cc_final: 0.5243 (t0) REVERT: B 377 PHE cc_start: 0.7811 (t80) cc_final: 0.7540 (t80) REVERT: B 529 LYS cc_start: 0.6709 (OUTLIER) cc_final: 0.6238 (ptpp) REVERT: C 269 TYR cc_start: 0.6428 (m-80) cc_final: 0.6204 (m-80) REVERT: C 535 LYS cc_start: 0.6979 (OUTLIER) cc_final: 0.5987 (ttmt) REVERT: C 1132 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8480 (pp) REVERT: D 62 MET cc_start: 0.3971 (ppp) cc_final: 0.1512 (tmm) REVERT: D 82 MET cc_start: 0.6098 (mmt) cc_final: 0.4492 (ptp) REVERT: D 142 LEU cc_start: 0.2069 (mp) cc_final: 0.1764 (mm) REVERT: D 323 MET cc_start: 0.0101 (tpt) cc_final: -0.0116 (tpp) REVERT: D 383 MET cc_start: 0.5583 (mmm) cc_final: 0.5169 (mmm) REVERT: D 579 MET cc_start: 0.3445 (ptt) cc_final: 0.1913 (ttp) outliers start: 156 outliers final: 113 residues processed: 326 average time/residue: 0.3610 time to fit residues: 201.5365 Evaluate side-chains 297 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 177 time to evaluate : 3.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 307 THR 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 399 SER 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 544 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1146 ASP Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 585 LEU 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 696 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 477 TRP Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 597 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 329 optimal weight: 9.9990 chunk 38 optimal weight: 20.0000 chunk 194 optimal weight: 0.8980 chunk 249 optimal weight: 4.9990 chunk 193 optimal weight: 0.8980 chunk 287 optimal weight: 4.9990 chunk 190 optimal weight: 5.9990 chunk 340 optimal weight: 9.9990 chunk 212 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 157 optimal weight: 0.8980 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 787 GLN B 314 GLN B 519 HIS B 542 ASN B 613 GLN B 675 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 360 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C1002 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 29692 Z= 0.253 Angle : 0.634 12.699 40378 Z= 0.308 Chirality : 0.048 0.548 4777 Planarity : 0.004 0.059 5112 Dihedral : 7.730 81.889 5561 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.66 % Favored : 93.17 % Rotamer: Outliers : 4.38 % Allowed : 20.57 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.02 (0.14), residues: 3484 helix: 1.22 (0.17), residues: 985 sheet: -0.60 (0.18), residues: 716 loop : -1.87 (0.14), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 104 HIS 0.007 0.001 HIS C 519 PHE 0.055 0.001 PHE D 512 TYR 0.020 0.001 TYR C1067 ARG 0.003 0.000 ARG C 355 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 187 time to evaluate : 3.238 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 856 ASN cc_start: 0.9132 (OUTLIER) cc_final: 0.8410 (p0) REVERT: A 916 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.9014 (tp) REVERT: B 141 LEU cc_start: 0.6389 (OUTLIER) cc_final: 0.5906 (pt) REVERT: B 164 ASN cc_start: 0.5669 (OUTLIER) cc_final: 0.5266 (t0) REVERT: B 377 PHE cc_start: 0.7803 (t80) cc_final: 0.7539 (t80) REVERT: B 529 LYS cc_start: 0.6720 (OUTLIER) cc_final: 0.6343 (ptpp) REVERT: B 990 GLU cc_start: 0.6931 (tt0) cc_final: 0.6661 (tt0) REVERT: C 535 LYS cc_start: 0.7046 (OUTLIER) cc_final: 0.6067 (ttmt) REVERT: C 1132 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8478 (pp) REVERT: C 1142 GLN cc_start: 0.8270 (tm-30) cc_final: 0.8039 (pp30) REVERT: D 62 MET cc_start: 0.3882 (ppp) cc_final: 0.1500 (tmm) REVERT: D 82 MET cc_start: 0.6047 (mmt) cc_final: 0.4530 (ptp) REVERT: D 142 LEU cc_start: 0.1640 (mp) cc_final: 0.1421 (mm) REVERT: D 323 MET cc_start: 0.0027 (tpt) cc_final: -0.0328 (mmt) REVERT: D 383 MET cc_start: 0.5573 (mmm) cc_final: 0.5194 (mmm) REVERT: D 462 MET cc_start: 0.6643 (tmm) cc_final: 0.6314 (ppp) REVERT: D 579 MET cc_start: 0.3438 (ptt) cc_final: 0.1889 (ttp) outliers start: 136 outliers final: 108 residues processed: 305 average time/residue: 0.3828 time to fit residues: 196.0056 Evaluate side-chains 290 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 175 time to evaluate : 3.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 302 THR 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 399 SER 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 544 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 585 LEU 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 696 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 477 TRP Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 597 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 210 optimal weight: 0.7980 chunk 135 optimal weight: 7.9990 chunk 203 optimal weight: 2.9990 chunk 102 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 216 optimal weight: 7.9990 chunk 231 optimal weight: 8.9990 chunk 168 optimal weight: 0.0570 chunk 31 optimal weight: 20.0000 chunk 267 optimal weight: 2.9990 overall best weight: 1.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 613 GLN B 314 GLN B 519 HIS B 613 GLN B 675 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN C 360 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** D 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.4864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29692 Z= 0.182 Angle : 0.612 12.417 40378 Z= 0.296 Chirality : 0.046 0.533 4777 Planarity : 0.004 0.060 5112 Dihedral : 7.399 78.599 5560 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.86 % Favored : 92.97 % Rotamer: Outliers : 4.06 % Allowed : 20.63 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.14), residues: 3484 helix: 1.42 (0.17), residues: 982 sheet: -0.44 (0.19), residues: 711 loop : -1.81 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 477 HIS 0.019 0.001 HIS D 34 PHE 0.034 0.001 PHE D 512 TYR 0.018 0.001 TYR C1067 ARG 0.010 0.000 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 196 time to evaluate : 3.069 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: A 122 ASN cc_start: 0.4781 (OUTLIER) cc_final: 0.4321 (m-40) REVERT: A 856 ASN cc_start: 0.9128 (OUTLIER) cc_final: 0.8428 (p0) REVERT: B 141 LEU cc_start: 0.6423 (OUTLIER) cc_final: 0.5955 (pt) REVERT: B 153 MET cc_start: -0.0029 (OUTLIER) cc_final: -0.1632 (mpp) REVERT: B 377 PHE cc_start: 0.7800 (t80) cc_final: 0.7424 (t80) REVERT: C 535 LYS cc_start: 0.7116 (OUTLIER) cc_final: 0.6100 (ttmt) REVERT: C 1132 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8437 (pp) REVERT: D 62 MET cc_start: 0.4032 (ppp) cc_final: 0.1736 (tmm) REVERT: D 82 MET cc_start: 0.5841 (mmt) cc_final: 0.4397 (ptp) REVERT: D 323 MET cc_start: 0.0094 (tpt) cc_final: -0.0259 (mmt) REVERT: D 360 MET cc_start: 0.2464 (tpt) cc_final: 0.0965 (ttt) REVERT: D 383 MET cc_start: 0.5553 (mmm) cc_final: 0.5196 (mmm) REVERT: D 462 MET cc_start: 0.6580 (tmm) cc_final: 0.6140 (ppp) REVERT: D 579 MET cc_start: 0.3433 (ptt) cc_final: 0.1887 (ttp) outliers start: 126 outliers final: 97 residues processed: 299 average time/residue: 0.3630 time to fit residues: 184.5940 Evaluate side-chains 288 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 185 time to evaluate : 3.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 399 SER 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 544 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 585 LEU 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 696 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 597 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 309 optimal weight: 10.0000 chunk 325 optimal weight: 7.9990 chunk 297 optimal weight: 9.9990 chunk 317 optimal weight: 6.9990 chunk 190 optimal weight: 0.9990 chunk 138 optimal weight: 10.0000 chunk 248 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 286 optimal weight: 0.9990 chunk 299 optimal weight: 7.9990 chunk 315 optimal weight: 30.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN B 314 GLN B 613 GLN B 675 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.5057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 29692 Z= 0.348 Angle : 0.685 13.255 40378 Z= 0.334 Chirality : 0.050 0.526 4777 Planarity : 0.004 0.062 5112 Dihedral : 7.550 69.436 5550 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.72 % Favored : 92.11 % Rotamer: Outliers : 4.22 % Allowed : 20.66 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.14), residues: 3484 helix: 1.32 (0.17), residues: 977 sheet: -0.51 (0.19), residues: 715 loop : -1.88 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 477 HIS 0.012 0.001 HIS D 34 PHE 0.023 0.002 PHE D 512 TYR 0.026 0.002 TYR B 380 ARG 0.007 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 183 time to evaluate : 3.549 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: A 856 ASN cc_start: 0.9176 (OUTLIER) cc_final: 0.8426 (p0) REVERT: B 153 MET cc_start: 0.0041 (OUTLIER) cc_final: -0.1457 (mpp) REVERT: C 153 MET cc_start: 0.2594 (mmm) cc_final: -0.0415 (ptp) REVERT: C 535 LYS cc_start: 0.7167 (OUTLIER) cc_final: 0.6155 (ttmt) REVERT: C 1132 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8464 (pp) REVERT: D 62 MET cc_start: 0.4061 (ppp) cc_final: 0.1623 (tmm) REVERT: D 82 MET cc_start: 0.5957 (mmt) cc_final: 0.4571 (ptp) REVERT: D 323 MET cc_start: 0.0279 (tpt) cc_final: -0.0063 (mmt) REVERT: D 383 MET cc_start: 0.5473 (mmm) cc_final: 0.5125 (mmm) REVERT: D 462 MET cc_start: 0.6593 (tmm) cc_final: 0.6154 (ppp) REVERT: D 579 MET cc_start: 0.3484 (ptt) cc_final: 0.1957 (ttp) outliers start: 131 outliers final: 117 residues processed: 295 average time/residue: 0.3655 time to fit residues: 183.5982 Evaluate side-chains 294 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 173 time to evaluate : 3.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 585 LEU 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 696 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 464 PHE Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 477 TRP Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 597 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 208 optimal weight: 10.0000 chunk 335 optimal weight: 8.9990 chunk 204 optimal weight: 0.5980 chunk 159 optimal weight: 4.9990 chunk 233 optimal weight: 0.0270 chunk 351 optimal weight: 5.9990 chunk 323 optimal weight: 4.9990 chunk 280 optimal weight: 0.7980 chunk 29 optimal weight: 8.9990 chunk 216 optimal weight: 8.9990 chunk 171 optimal weight: 1.9990 overall best weight: 1.6842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN B 164 ASN B 613 GLN B 675 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1142 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.5147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 29692 Z= 0.210 Angle : 0.636 12.674 40378 Z= 0.308 Chirality : 0.047 0.535 4777 Planarity : 0.004 0.061 5112 Dihedral : 7.272 65.355 5550 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.83 % Favored : 93.00 % Rotamer: Outliers : 4.02 % Allowed : 21.11 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.14), residues: 3484 helix: 1.45 (0.17), residues: 974 sheet: -0.42 (0.19), residues: 713 loop : -1.80 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 477 HIS 0.015 0.001 HIS D 34 PHE 0.032 0.001 PHE C 429 TYR 0.019 0.001 TYR C1067 ARG 0.010 0.000 ARG B 567 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 183 time to evaluate : 3.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ASN cc_start: 0.4834 (OUTLIER) cc_final: 0.4347 (m-40) REVERT: A 347 PHE cc_start: 0.7727 (OUTLIER) cc_final: 0.7367 (t80) REVERT: A 856 ASN cc_start: 0.9137 (OUTLIER) cc_final: 0.8430 (p0) REVERT: B 153 MET cc_start: 0.0155 (OUTLIER) cc_final: -0.1369 (mpp) REVERT: B 524 VAL cc_start: 0.5736 (OUTLIER) cc_final: 0.5338 (p) REVERT: C 535 LYS cc_start: 0.7153 (OUTLIER) cc_final: 0.6116 (ttmt) REVERT: C 1132 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8428 (pp) REVERT: D 62 MET cc_start: 0.4174 (ppp) cc_final: 0.1625 (tmm) REVERT: D 82 MET cc_start: 0.5879 (mmt) cc_final: 0.4577 (ptp) REVERT: D 323 MET cc_start: 0.0236 (tpt) cc_final: -0.0101 (mmt) REVERT: D 360 MET cc_start: 0.2434 (tpt) cc_final: 0.1030 (ttt) REVERT: D 383 MET cc_start: 0.5496 (mmm) cc_final: 0.5157 (mmm) REVERT: D 462 MET cc_start: 0.6499 (tmm) cc_final: 0.6098 (ppp) REVERT: D 579 MET cc_start: 0.3461 (ptt) cc_final: 0.1939 (ttp) outliers start: 125 outliers final: 109 residues processed: 288 average time/residue: 0.3982 time to fit residues: 198.7431 Evaluate side-chains 293 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 177 time to evaluate : 3.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 585 LEU 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 696 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 464 PHE Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 477 TRP Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 597 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 222 optimal weight: 0.6980 chunk 298 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 258 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 280 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 288 optimal weight: 0.5980 chunk 35 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN B 314 GLN B 613 GLN B 675 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1142 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.165411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.118856 restraints weight = 53220.994| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.41 r_work: 0.3138 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.5234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29692 Z= 0.168 Angle : 0.619 12.595 40378 Z= 0.299 Chirality : 0.046 0.518 4777 Planarity : 0.004 0.062 5112 Dihedral : 6.987 62.578 5550 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.57 % Favored : 93.25 % Rotamer: Outliers : 3.51 % Allowed : 21.53 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.14), residues: 3484 helix: 1.58 (0.17), residues: 974 sheet: -0.29 (0.19), residues: 711 loop : -1.74 (0.14), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 477 HIS 0.011 0.001 HIS D 34 PHE 0.022 0.001 PHE D 512 TYR 0.018 0.001 TYR C1067 ARG 0.008 0.000 ARG B 567 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6718.73 seconds wall clock time: 131 minutes 36.43 seconds (7896.43 seconds total)