Starting phenix.real_space_refine on Fri Mar 22 18:15:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y20_33577/03_2024/7y20_33577.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y20_33577/03_2024/7y20_33577.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y20_33577/03_2024/7y20_33577.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y20_33577/03_2024/7y20_33577.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y20_33577/03_2024/7y20_33577.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y20_33577/03_2024/7y20_33577.pdb" } resolution = 3.8 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= 0.007 sd= 0.065 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 164 5.16 5 C 21851 2.51 5 N 5568 2.21 5 O 6686 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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 GLU 471": "OE1" <-> "OE2" Residue "A ARG 493": "NH1" <-> "NH2" Residue "C ARG 319": "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 GLU 471": "OE1" <-> "OE2" Residue "C ARG 493": "NH1" <-> "NH2" Residue "D GLU 22": "OE1" <-> "OE2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D GLU 140": "OE1" <-> "OE2" Residue "D GLU 145": "OE1" <-> "OE2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D GLU 224": "OE1" <-> "OE2" 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 ARG 357": "NH1" <-> "NH2" Residue "D GLU 375": "OE1" <-> "OE2" Residue "D GLU 398": "OE1" <-> "OE2" Residue "D GLU 435": "OE1" <-> "OE2" Residue "D GLU 483": "OE1" <-> "OE2" Residue "D ARG 518": "NH1" <-> "NH2" Residue "D GLU 564": "OE1" <-> "OE2" Residue "F GLU 22": "OE1" <-> "OE2" Residue "F GLU 35": "OE1" <-> "OE2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "F GLU 145": "OE1" <-> "OE2" Residue "F GLU 166": "OE1" <-> "OE2" Residue "F ARG 169": "NH1" <-> "NH2" Residue "F ARG 177": "NH1" <-> "NH2" Residue "F ARG 192": "NH1" <-> "NH2" Residue "F GLU 224": "OE1" <-> "OE2" Residue "F GLU 227": "OE1" <-> "OE2" Residue "F ARG 245": "NH1" <-> "NH2" Residue "F ARG 273": "NH1" <-> "NH2" Residue "F ARG 306": "NH1" <-> "NH2" Residue "F ARG 357": "NH1" <-> "NH2" Residue "F GLU 375": "OE1" <-> "OE2" Residue "F GLU 398": "OE1" <-> "OE2" Residue "F GLU 435": "OE1" <-> "OE2" Residue "F GLU 483": "OE1" <-> "OE2" Residue "F ARG 518": "NH1" <-> "NH2" Residue "F GLU 564": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 34269 Number of models: 1 Model: "" Number of chains: 43 Chain: "A" Number of atoms: 7837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7837 Classifications: {'peptide': 998} Link IDs: {'PTRANS': 54, 'TRANS': 943} Chain breaks: 9 Chain: "B" Number of atoms: 7553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 963, 7553 Classifications: {'peptide': 963} Link IDs: {'PTRANS': 52, 'TRANS': 910} Chain breaks: 10 Chain: "C" Number of atoms: 7837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7837 Classifications: {'peptide': 998} Link IDs: {'PTRANS': 54, 'TRANS': 943} Chain breaks: 9 Chain: "D" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Chain: "F" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} 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: "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: "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: "A" 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: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "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 Chain: "F" 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: 16.89, per 1000 atoms: 0.49 Number of scatterers: 34269 At special positions: 0 Unit cell: (134.788, 194.573, 250.01, 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 164 16.00 O 6686 8.00 N 5568 7.00 C 21851 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.09 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=1.97 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=1.85 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=1.84 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=1.80 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.06 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.05 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.08 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.20 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.09 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=1.83 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.39 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.06 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.05 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.12 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.18 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.07 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.14 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.09 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=1.86 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.05 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.06 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.05 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.26 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=1.97 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.17 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.10 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.04 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.02 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 141 " distance=2.04 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 530 " - pdb=" SG CYS F 542 " distance=2.02 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 E 1 " - " NAG E 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 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-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 B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 282 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 616 " " NAG B1408 " - " ASN B 657 " " NAG B1409 " - " ASN B 709 " " 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 701 " - " ASN D 322 " " NAG E 1 " - " ASN A 331 " " NAG F 701 " - " ASN F 322 " " NAG G 1 " - " ASN A 343 " " NAG H 1 " - " ASN A 709 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1074 " " NAG L 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN B 331 " " NAG O 1 " - " ASN B 343 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN B1074 " " NAG S 1 " - " ASN B1098 " " NAG T 1 " - " ASN B1134 " " NAG U 1 " - " ASN C 331 " " NAG V 1 " - " ASN C 343 " " NAG W 1 " - " ASN C 709 " " NAG X 1 " - " ASN C 717 " " NAG Y 1 " - " ASN C 801 " " NAG Z 1 " - " ASN C1074 " " NAG a 1 " - " ASN C1098 " " NAG b 1 " - " ASN C1134 " " NAG c 1 " - " ASN D 53 " " NAG d 1 " - " ASN D 90 " " NAG e 1 " - " ASN D 103 " " NAG f 1 " - " ASN D 432 " " NAG g 1 " - " ASN D 546 " " NAG h 1 " - " ASN F 53 " " NAG i 1 " - " ASN F 90 " " NAG j 1 " - " ASN F 103 " " NAG k 1 " - " ASN F 432 " " NAG l 1 " - " ASN F 546 " Time building additional restraints: 13.41 Conformation dependent library (CDL) restraints added in 5.7 seconds 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7818 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 47 sheets defined 36.4% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.81 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.679A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.693A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ARG A 408 " --> pdb=" O ASN A 405 " (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 753 Processing helix chain 'A' and resid 754 through 756 No H-bonds generated for 'chain 'A' and resid 754 through 756' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.612A pdb=" N ILE A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.655A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 933 Processing helix chain 'A' and resid 933 through 939 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.322A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 981 removed outlier: 3.810A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.931A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 364 through 368 Processing helix chain 'B' and resid 386 through 390 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.491A pdb=" N ARG B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.542A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.529A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (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: 3.791A pdb=" N LYS B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 815 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.701A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.252A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 932 Processing helix chain 'B' and resid 933 through 940 Processing helix chain 'B' and resid 945 through 964 removed outlier: 3.761A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 968 removed outlier: 3.703A pdb=" N SER B 968 " --> pdb=" O GLN B 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 965 through 968' Processing helix chain 'B' and resid 976 through 981 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.758A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.982A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.502A pdb=" N THR C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.679A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 385 through 389 removed outlier: 4.018A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 385 through 389' Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.693A pdb=" N GLU C 406 " --> pdb=" O ARG C 403 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ARG C 408 " --> pdb=" O ASN C 405 " (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 747 through 754 removed outlier: 4.087A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.872A 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: 3.985A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 removed outlier: 3.590A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.515A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.576A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.650A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.591A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 4.077A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.757A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 983 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.323A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 Processing helix chain 'D' and resid 22 through 53 removed outlier: 4.096A pdb=" N LYS D 31 " --> pdb=" O THR D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 81 removed outlier: 4.155A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN D 64 " --> pdb=" O GLN D 60 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 192 removed outlier: 3.909A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU D 176 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG D 177 " --> pdb=" O GLY D 173 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 4.190A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 220 through 252 removed outlier: 3.731A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS D 234 " --> pdb=" O PHE D 230 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 4.083A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 281 removed outlier: 4.179A pdb=" N SER D 280 " --> pdb=" O ASN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 299 removed outlier: 3.785A pdb=" N VAL D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 removed outlier: 3.729A pdb=" N ILE D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.652A pdb=" N ASN D 330 " --> pdb=" O GLY D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.692A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.563A pdb=" N ILE D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 420 Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'D' and resid 448 through 466 removed outlier: 4.608A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 531 removed outlier: 4.535A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 548 through 559 removed outlier: 3.973A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG D 559 " --> pdb=" O PHE D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 removed outlier: 3.743A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 598 Proline residue: D 590 - end of helix removed outlier: 3.599A pdb=" N ASP D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 53 removed outlier: 4.097A pdb=" N LYS F 31 " --> pdb=" O THR F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 81 removed outlier: 4.155A pdb=" N GLN F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN F 64 " --> pdb=" O GLN F 60 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA F 65 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN F 81 " --> pdb=" O SER F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 101 Processing helix chain 'F' and resid 109 through 129 Processing helix chain 'F' and resid 147 through 155 Processing helix chain 'F' and resid 157 through 192 removed outlier: 3.909A pdb=" N TRP F 168 " --> pdb=" O ALA F 164 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG F 169 " --> pdb=" O TRP F 165 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LYS F 174 " --> pdb=" O SER F 170 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN F 175 " --> pdb=" O GLU F 171 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU F 176 " --> pdb=" O VAL F 172 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG F 177 " --> pdb=" O GLY F 173 " (cutoff:3.500A) Proline residue: F 178 - end of helix removed outlier: 4.189A pdb=" N GLU F 182 " --> pdb=" O PRO F 178 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 205 Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'F' and resid 220 through 252 removed outlier: 3.732A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU F 231 " --> pdb=" O GLU F 227 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLU F 232 " --> pdb=" O HIS F 228 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE F 233 " --> pdb=" O THR F 229 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS F 234 " --> pdb=" O PHE F 230 " (cutoff:3.500A) Proline residue: F 235 - end of helix removed outlier: 4.084A pdb=" N HIS F 239 " --> pdb=" O PRO F 235 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASN F 250 " --> pdb=" O ALA F 246 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA F 251 " --> pdb=" O LYS F 247 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR F 252 " --> pdb=" O LEU F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 267 No H-bonds generated for 'chain 'F' and resid 265 through 267' Processing helix chain 'F' and resid 275 through 281 removed outlier: 4.178A pdb=" N SER F 280 " --> pdb=" O ASN F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 299 removed outlier: 3.784A pdb=" N VAL F 298 " --> pdb=" O THR F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 319 removed outlier: 3.728A pdb=" N ILE F 307 " --> pdb=" O ASP F 303 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE F 308 " --> pdb=" O ALA F 304 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL F 318 " --> pdb=" O PHE F 314 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY F 319 " --> pdb=" O PHE F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 331 removed outlier: 3.652A pdb=" N ASN F 330 " --> pdb=" O GLY F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 385 removed outlier: 3.691A pdb=" N HIS F 373 " --> pdb=" O PHE F 369 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N HIS F 378 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 393 Processing helix chain 'F' and resid 399 through 413 removed outlier: 3.564A pdb=" N ILE F 407 " --> pdb=" O ALA F 403 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 420 Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 448 through 466 removed outlier: 4.607A pdb=" N PHE F 452 " --> pdb=" O GLY F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 484 Processing helix chain 'F' and resid 499 through 502 Processing helix chain 'F' and resid 503 through 508 Processing helix chain 'F' and resid 513 through 531 removed outlier: 4.534A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE F 523 " --> pdb=" O THR F 519 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 Processing helix chain 'F' and resid 548 through 559 removed outlier: 3.973A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG F 559 " --> pdb=" O PHE F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 572 removed outlier: 3.743A pdb=" N GLU F 571 " --> pdb=" O THR F 567 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 598 Proline residue: F 590 - end of helix removed outlier: 3.599A pdb=" N ASP F 597 " --> pdb=" O THR F 593 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.686A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 7.499A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.924A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLU A 132 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 92 removed outlier: 3.740A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.735A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 323 through 328 removed outlier: 3.953A pdb=" N ASN A 540 " --> pdb=" O THR A 323 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SER A 325 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ASN A 542 " --> pdb=" O SER A 325 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL A 327 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 357 removed outlier: 3.797A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.811A pdb=" N ARG A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.082A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.892A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.721A 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: 6.892A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.302A 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 removed outlier: 5.638A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.686A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 49 through 55 removed outlier: 7.498A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.924A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLU B 132 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.739A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.602A pdb=" N GLY B 311 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 323 through 328 removed outlier: 5.716A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.777A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.173A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.411A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.753A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.663A 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: 6.753A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.628A 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: 4.485A 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 1125 removed outlier: 4.851A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.686A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 49 through 55 removed outlier: 6.904A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.924A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU C 117 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLU C 132 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 90 through 92 removed outlier: 3.739A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.951A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 323 through 328 Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 357 removed outlier: 3.797A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.812A pdb=" N ARG C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 553 through 554 removed outlier: 3.524A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 656 removed outlier: 5.541A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE C 693 " --> pdb=" O SER C 673 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER C 673 " --> pdb=" O ILE C 693 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR C 695 " --> pdb=" O CYS C 671 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS C 671 " --> pdb=" O TYR C 695 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.151A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.740A 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: 7.151A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.449A 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: 4.498A 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 1125 removed outlier: 4.944A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.805A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'D' and resid 347 through 350 Processing sheet with id=AF1, first strand: chain 'F' and resid 262 through 263 removed outlier: 5.806A pdb=" N LEU F 262 " --> pdb=" O VAL F 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'F' and resid 347 through 350 1341 hydrogen bonds defined for protein. 3732 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: 13.18 Time building geometry restraints manager: 14.51 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: 7327 1.33 - 1.45: 9441 1.45 - 1.58: 18082 1.58 - 1.71: 0 1.71 - 1.83: 233 Bond restraints: 35083 Sorted by residual: bond pdb=" C TYR C 655 " pdb=" N VAL C 656 " ideal model delta sigma weight residual 1.329 1.434 -0.105 1.07e-02 8.73e+03 9.69e+01 bond pdb=" CA SER B 698 " pdb=" C SER B 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 THR B 208 " pdb=" N PRO B 209 " ideal model delta sigma weight residual 1.329 1.387 -0.058 1.20e-02 6.94e+03 2.33e+01 bond pdb=" C THR C 208 " pdb=" N PRO C 209 " ideal model delta sigma weight residual 1.329 1.387 -0.058 1.20e-02 6.94e+03 2.32e+01 bond pdb=" C THR A 208 " pdb=" N PRO A 209 " ideal model delta sigma weight residual 1.329 1.386 -0.057 1.20e-02 6.94e+03 2.29e+01 ... (remaining 35078 not shown) Histogram of bond angle deviations from ideal: 99.75 - 107.51: 1495 107.51 - 115.26: 21010 115.26 - 123.01: 22579 123.01 - 130.76: 2467 130.76 - 138.51: 146 Bond angle restraints: 47697 Sorted by residual: angle pdb=" N PHE D 28 " pdb=" CA PHE D 28 " pdb=" C PHE D 28 " ideal model delta sigma weight residual 111.24 101.83 9.41 1.29e+00 6.01e-01 5.32e+01 angle pdb=" N PHE F 28 " pdb=" CA PHE F 28 " pdb=" C PHE F 28 " ideal model delta sigma weight residual 111.24 101.87 9.37 1.29e+00 6.01e-01 5.28e+01 angle pdb=" N SER A 591 " pdb=" CA SER A 591 " pdb=" C SER A 591 " ideal model delta sigma weight residual 110.24 120.40 -10.16 1.47e+00 4.63e-01 4.78e+01 angle pdb=" N LEU D 45 " pdb=" CA LEU D 45 " pdb=" C LEU D 45 " ideal model delta sigma weight residual 111.07 103.93 7.14 1.07e+00 8.73e-01 4.45e+01 angle pdb=" N LEU F 45 " pdb=" CA LEU F 45 " pdb=" C LEU F 45 " ideal model delta sigma weight residual 111.07 103.96 7.11 1.07e+00 8.73e-01 4.41e+01 ... (remaining 47692 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 20465 17.68 - 35.36: 1164 35.36 - 53.04: 313 53.04 - 70.72: 72 70.72 - 88.41: 56 Dihedral angle restraints: 22070 sinusoidal: 9940 harmonic: 12130 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -16.69 -69.31 1 1.00e+01 1.00e-02 6.21e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -18.16 -67.84 1 1.00e+01 1.00e-02 5.98e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -23.72 -62.28 1 1.00e+01 1.00e-02 5.13e+01 ... (remaining 22067 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.334: 5540 0.334 - 0.669: 3 0.669 - 1.003: 2 1.003 - 1.338: 1 1.338 - 1.672: 3 Chirality restraints: 5549 Sorted by residual: chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.28 -1.12 2.00e-02 2.50e+03 3.16e+03 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.73 -1.67 2.00e-01 2.50e+01 6.99e+01 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN A1134 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.75 -1.65 2.00e-01 2.50e+01 6.80e+01 ... (remaining 5546 not shown) Planarity restraints: 6096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " -0.193 2.00e-02 2.50e+03 2.92e-01 1.06e+03 pdb=" CG ASN B 331 " 0.091 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " -0.057 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " 0.506 2.00e-02 2.50e+03 pdb=" C1 NAG N 1 " -0.348 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 343 " -0.197 2.00e-02 2.50e+03 2.43e-01 7.41e+02 pdb=" CG ASN B 343 " 0.077 2.00e-02 2.50e+03 pdb=" OD1 ASN B 343 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN B 343 " 0.415 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " -0.281 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " 0.129 2.00e-02 2.50e+03 2.04e-01 5.21e+02 pdb=" CG ASN A 331 " -0.060 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.062 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.362 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " 0.231 2.00e-02 2.50e+03 ... (remaining 6093 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 327 2.61 - 3.18: 29767 3.18 - 3.75: 48149 3.75 - 4.33: 69884 4.33 - 4.90: 113197 Nonbonded interactions: 261324 Sorted by model distance: nonbonded pdb=" O VAL A 445 " pdb=" OG SER A 446 " model vdw 2.034 2.440 nonbonded pdb=" O VAL C 445 " pdb=" OG SER C 446 " model vdw 2.034 2.440 nonbonded pdb=" O PRO C 39 " pdb=" CG ASP C 40 " model vdw 2.114 3.270 nonbonded pdb=" O CYS B 590 " pdb=" O SER B 591 " model vdw 2.165 3.040 nonbonded pdb=" OG1 THR C 333 " pdb=" N ASN C 334 " model vdw 2.207 2.520 ... (remaining 261319 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 454 or resid 491 through 1146 or resid 1401 thr \ ough 1408)) selection = (chain 'B' and (resid 27 through 939 or resid 944 through 1146 or resid 1401 thr \ ough 1408)) selection = (chain 'C' and (resid 27 through 454 or resid 491 through 1146 or resid 1401 thr \ ough 1408)) } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'E' 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' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 7.200 Check model and map are aligned: 0.490 Set scattering table: 0.340 Process input model: 85.090 Find NCS groups from input model: 2.250 Set up NCS constraints: 0.610 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5511 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.105 35083 Z= 0.501 Angle : 0.910 13.512 47697 Z= 0.551 Chirality : 0.073 1.672 5549 Planarity : 0.005 0.104 6036 Dihedral : 12.640 88.406 14120 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 1.66 % Allowed : 6.53 % Favored : 91.80 % Rotamer: Outliers : 1.31 % Allowed : 3.99 % Favored : 94.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.11), residues: 4087 helix: -1.56 (0.12), residues: 1308 sheet: -0.92 (0.19), residues: 655 loop : -2.67 (0.12), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 594 HIS 0.005 0.001 HIS B 505 PHE 0.038 0.001 PHE B 377 TYR 0.026 0.001 TYR B 453 ARG 0.004 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 3655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 636 time to evaluate : 3.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 SER cc_start: 0.5581 (t) cc_final: 0.5330 (p) REVERT: A 525 CYS cc_start: 0.4024 (OUTLIER) cc_final: 0.3755 (m) REVERT: B 390 LEU cc_start: 0.7942 (tp) cc_final: 0.7706 (tp) REVERT: B 1037 SER cc_start: 0.8677 (t) cc_final: 0.8461 (t) REVERT: D 37 GLU cc_start: 0.0176 (OUTLIER) cc_final: -0.0299 (tt0) REVERT: D 322 ASN cc_start: 0.2241 (m-40) cc_final: 0.1743 (m110) REVERT: D 323 MET cc_start: 0.2118 (mmp) cc_final: 0.1713 (mmp) REVERT: D 474 MET cc_start: -0.0046 (mmp) cc_final: -0.1840 (mmt) REVERT: F 28 PHE cc_start: 0.0549 (t80) cc_final: -0.0272 (t80) REVERT: F 37 GLU cc_start: -0.0595 (OUTLIER) cc_final: -0.1818 (mt-10) REVERT: F 327 PHE cc_start: 0.5146 (t80) cc_final: 0.4765 (t80) REVERT: F 510 TYR cc_start: 0.3405 (m-80) cc_final: 0.2822 (t80) outliers start: 48 outliers final: 13 residues processed: 680 average time/residue: 0.4491 time to fit residues: 493.7493 Evaluate side-chains 273 residues out of total 3655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 257 time to evaluate : 3.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 493 ARG Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 37 GLU Chi-restraints excluded: chain F residue 351 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 347 optimal weight: 50.0000 chunk 312 optimal weight: 50.0000 chunk 173 optimal weight: 0.9990 chunk 106 optimal weight: 9.9990 chunk 210 optimal weight: 10.0000 chunk 166 optimal weight: 0.8980 chunk 322 optimal weight: 40.0000 chunk 124 optimal weight: 5.9990 chunk 196 optimal weight: 2.9990 chunk 240 optimal weight: 8.9990 chunk 374 optimal weight: 20.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 370 ASN A 417 ASN A 477 ASN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 207 HIS B 314 GLN B1011 GLN B1088 HIS C 49 HIS C 81 ASN C 207 HIS C 370 ASN C 417 ASN C 556 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN D 101 GLN D 137 ASN D 277 ASN D 394 ASN D 417 HIS D 442 GLN D 472 GLN D 580 ASN D 599 ASN F 24 GLN F 101 GLN F 137 ASN F 277 ASN F 417 HIS F 442 GLN F 472 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5942 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 35083 Z= 0.365 Angle : 0.782 11.910 47697 Z= 0.391 Chirality : 0.050 0.650 5549 Planarity : 0.005 0.074 6036 Dihedral : 7.064 75.611 6445 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.07 % Favored : 93.56 % Rotamer: Outliers : 2.82 % Allowed : 11.19 % Favored : 85.99 % 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: -2.04 (0.12), residues: 4087 helix: -0.09 (0.14), residues: 1333 sheet: -1.11 (0.19), residues: 585 loop : -2.31 (0.12), residues: 2169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 64 HIS 0.009 0.001 HIS B1064 PHE 0.035 0.002 PHE F 512 TYR 0.027 0.002 TYR A 873 ARG 0.012 0.001 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 261 time to evaluate : 3.536 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: A 153 MET cc_start: 0.2216 (ppp) cc_final: 0.1925 (ppp) REVERT: A 697 MET cc_start: 0.8004 (pmm) cc_final: 0.7736 (pmm) REVERT: A 775 ASP cc_start: 0.6383 (OUTLIER) cc_final: 0.6090 (t0) REVERT: B 315 THR cc_start: 0.7967 (p) cc_final: 0.7758 (p) REVERT: B 357 ARG cc_start: 0.6040 (mtp85) cc_final: 0.5676 (mtp85) REVERT: B 1050 MET cc_start: 0.7125 (ptp) cc_final: 0.6885 (ptp) REVERT: C 153 MET cc_start: 0.4158 (tmm) cc_final: 0.3667 (tmm) REVERT: D 62 MET cc_start: -0.1897 (ttp) cc_final: -0.2380 (ttp) REVERT: D 249 MET cc_start: -0.0256 (mtt) cc_final: -0.1171 (ptt) REVERT: D 332 MET cc_start: -0.1124 (mmm) cc_final: -0.3363 (ttm) REVERT: D 367 ASP cc_start: 0.5240 (m-30) cc_final: 0.4731 (t0) REVERT: D 474 MET cc_start: 0.0221 (mmp) cc_final: -0.0524 (tmm) REVERT: D 508 ASN cc_start: 0.5702 (m110) cc_final: 0.4929 (t0) REVERT: F 28 PHE cc_start: 0.0367 (t80) cc_final: -0.0327 (t80) REVERT: F 297 MET cc_start: 0.0225 (mpp) cc_final: -0.1275 (mpp) REVERT: F 383 MET cc_start: -0.0084 (mtp) cc_final: -0.1984 (tmm) REVERT: F 474 MET cc_start: 0.3116 (mpp) cc_final: 0.2732 (ptp) outliers start: 103 outliers final: 47 residues processed: 342 average time/residue: 0.4252 time to fit residues: 242.2333 Evaluate side-chains 233 residues out of total 3655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 185 time to evaluate : 3.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain F residue 574 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 207 optimal weight: 10.0000 chunk 116 optimal weight: 0.6980 chunk 311 optimal weight: 0.0030 chunk 254 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 chunk 374 optimal weight: 50.0000 chunk 404 optimal weight: 0.2980 chunk 333 optimal weight: 10.0000 chunk 371 optimal weight: 40.0000 chunk 127 optimal weight: 0.5980 chunk 300 optimal weight: 30.0000 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN A 992 GLN A1002 GLN A1005 GLN C 207 HIS C 450 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN C 955 ASN D 58 ASN F 373 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5866 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 35083 Z= 0.158 Angle : 0.626 16.149 47697 Z= 0.308 Chirality : 0.046 0.685 5549 Planarity : 0.004 0.045 6036 Dihedral : 6.068 59.757 6408 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.02 % Favored : 94.69 % Rotamer: Outliers : 2.24 % Allowed : 11.98 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.38 (0.12), residues: 4087 helix: 0.49 (0.14), residues: 1332 sheet: -0.56 (0.19), residues: 637 loop : -2.03 (0.12), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 104 HIS 0.003 0.001 HIS C 954 PHE 0.028 0.001 PHE B 970 TYR 0.018 0.001 TYR A1138 ARG 0.007 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 232 time to evaluate : 3.470 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 697 MET cc_start: 0.7986 (pmm) cc_final: 0.7683 (pmm) REVERT: B 270 LEU cc_start: 0.6765 (OUTLIER) cc_final: 0.6186 (mp) REVERT: C 153 MET cc_start: 0.4718 (tmm) cc_final: 0.3279 (ttp) REVERT: D 62 MET cc_start: -0.1838 (ttp) cc_final: -0.2304 (ttp) REVERT: D 332 MET cc_start: -0.1233 (mmm) cc_final: -0.3370 (ttt) REVERT: D 474 MET cc_start: -0.0189 (mmp) cc_final: -0.0648 (tmm) REVERT: D 508 ASN cc_start: 0.5885 (m110) cc_final: 0.5125 (t0) REVERT: F 28 PHE cc_start: 0.0617 (t80) cc_final: 0.0063 (t80) REVERT: F 383 MET cc_start: 0.0211 (mtp) cc_final: -0.1846 (tmm) outliers start: 82 outliers final: 34 residues processed: 305 average time/residue: 0.3923 time to fit residues: 204.5254 Evaluate side-chains 223 residues out of total 3655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 188 time to evaluate : 3.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 574 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 370 optimal weight: 0.9980 chunk 281 optimal weight: 0.7980 chunk 194 optimal weight: 7.9990 chunk 41 optimal weight: 30.0000 chunk 178 optimal weight: 4.9990 chunk 251 optimal weight: 7.9990 chunk 376 optimal weight: 10.0000 chunk 398 optimal weight: 20.0000 chunk 196 optimal weight: 0.0060 chunk 356 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 overall best weight: 2.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN B 644 GLN B 703 ASN C 49 HIS C 125 ASN C 207 HIS C 271 GLN C 532 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN D 51 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6015 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 35083 Z= 0.274 Angle : 0.664 12.074 47697 Z= 0.329 Chirality : 0.047 0.745 5549 Planarity : 0.004 0.041 6036 Dihedral : 5.894 59.934 6406 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.26 % Favored : 94.42 % Rotamer: Outliers : 2.71 % Allowed : 12.80 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.26 (0.13), residues: 4087 helix: 0.73 (0.15), residues: 1326 sheet: -0.77 (0.20), residues: 575 loop : -1.93 (0.12), residues: 2186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 69 HIS 0.010 0.001 HIS B1064 PHE 0.019 0.002 PHE C 86 TYR 0.021 0.001 TYR A1067 ARG 0.007 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 225 time to evaluate : 4.019 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: A 270 LEU cc_start: 0.6884 (OUTLIER) cc_final: 0.6564 (mp) REVERT: A 317 ASN cc_start: 0.8043 (OUTLIER) cc_final: 0.7556 (m-40) REVERT: A 697 MET cc_start: 0.7983 (pmm) cc_final: 0.7759 (ptp) REVERT: B 1050 MET cc_start: 0.7312 (ptp) cc_final: 0.7082 (ptp) REVERT: C 153 MET cc_start: 0.4697 (tmm) cc_final: 0.3723 (ttp) REVERT: D 62 MET cc_start: -0.1700 (ttp) cc_final: -0.2185 (ttp) REVERT: D 82 MET cc_start: 0.1746 (OUTLIER) cc_final: 0.1465 (mmt) REVERT: D 332 MET cc_start: -0.1516 (mmm) cc_final: -0.3355 (ttt) REVERT: D 455 MET cc_start: -0.0094 (ttm) cc_final: -0.0535 (ttm) REVERT: D 474 MET cc_start: -0.0305 (mmp) cc_final: -0.0614 (tmm) REVERT: D 508 ASN cc_start: 0.5869 (m110) cc_final: 0.5232 (t0) REVERT: F 28 PHE cc_start: 0.0717 (t80) cc_final: 0.0112 (t80) REVERT: F 37 GLU cc_start: -0.1636 (tm-30) cc_final: -0.2001 (mp0) REVERT: F 190 MET cc_start: 0.1218 (mtp) cc_final: 0.0979 (mtt) REVERT: F 351 LEU cc_start: 0.3812 (OUTLIER) cc_final: 0.3412 (mp) REVERT: F 383 MET cc_start: 0.0281 (mtp) cc_final: -0.2357 (tmm) REVERT: F 510 TYR cc_start: 0.3217 (m-80) cc_final: 0.2498 (t80) outliers start: 99 outliers final: 56 residues processed: 306 average time/residue: 0.4108 time to fit residues: 216.5862 Evaluate side-chains 263 residues out of total 3655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 203 time to evaluate : 3.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 480 MET Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain F residue 574 VAL Chi-restraints excluded: chain F residue 604 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 331 optimal weight: 40.0000 chunk 226 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 296 optimal weight: 40.0000 chunk 164 optimal weight: 7.9990 chunk 339 optimal weight: 50.0000 chunk 275 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 203 optimal weight: 7.9990 chunk 357 optimal weight: 40.0000 chunk 100 optimal weight: 5.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN C 81 ASN C 207 HIS C 370 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 GLN D 373 HIS F 505 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6206 moved from start: 0.5434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 35083 Z= 0.452 Angle : 0.796 11.450 47697 Z= 0.399 Chirality : 0.050 0.619 5549 Planarity : 0.005 0.044 6036 Dihedral : 6.691 59.837 6406 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.51 % Favored : 93.20 % Rotamer: Outliers : 3.34 % Allowed : 12.67 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.12), residues: 4087 helix: 0.42 (0.14), residues: 1348 sheet: -1.07 (0.19), residues: 591 loop : -2.08 (0.12), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 104 HIS 0.015 0.002 HIS B1064 PHE 0.027 0.003 PHE B1095 TYR 0.029 0.002 TYR B 508 ARG 0.006 0.001 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 205 time to evaluate : 4.095 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 238 PHE cc_start: 0.6622 (p90) cc_final: 0.6330 (p90) REVERT: A 282 ASN cc_start: 0.7694 (OUTLIER) cc_final: 0.7365 (m110) REVERT: A 317 ASN cc_start: 0.8165 (OUTLIER) cc_final: 0.7699 (m-40) REVERT: A 740 MET cc_start: 0.7958 (mmm) cc_final: 0.7653 (tpp) REVERT: B 869 MET cc_start: 0.7332 (mpp) cc_final: 0.7022 (mtp) REVERT: C 153 MET cc_start: 0.5009 (tmm) cc_final: 0.4558 (tmm) REVERT: D 62 MET cc_start: -0.1737 (ttp) cc_final: -0.2378 (ttp) REVERT: D 82 MET cc_start: 0.2636 (tmm) cc_final: 0.1410 (mmt) REVERT: D 332 MET cc_start: -0.1380 (mmm) cc_final: -0.3292 (ttt) REVERT: D 455 MET cc_start: 0.0583 (ttm) cc_final: -0.0026 (ttm) REVERT: D 508 ASN cc_start: 0.5944 (m110) cc_final: 0.5232 (t0) REVERT: D 571 GLU cc_start: 0.2181 (OUTLIER) cc_final: 0.1643 (pt0) REVERT: F 37 GLU cc_start: -0.1091 (tm-30) cc_final: -0.1870 (mp0) REVERT: F 249 MET cc_start: 0.0733 (ptt) cc_final: 0.0180 (tpp) REVERT: F 297 MET cc_start: -0.0585 (mpp) cc_final: -0.3166 (ttt) REVERT: F 351 LEU cc_start: 0.3970 (OUTLIER) cc_final: 0.3585 (mp) REVERT: F 383 MET cc_start: 0.0552 (mtp) cc_final: -0.1669 (tmm) REVERT: F 455 MET cc_start: 0.1907 (mmm) cc_final: 0.1558 (mmm) REVERT: F 510 TYR cc_start: 0.3349 (m-80) cc_final: 0.2535 (t80) outliers start: 122 outliers final: 78 residues processed: 313 average time/residue: 0.4085 time to fit residues: 219.9880 Evaluate side-chains 262 residues out of total 3655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 180 time to evaluate : 3.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 917 TYR Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 571 GLU Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain F residue 574 VAL Chi-restraints excluded: chain F residue 604 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 133 optimal weight: 20.0000 chunk 358 optimal weight: 50.0000 chunk 78 optimal weight: 1.9990 chunk 233 optimal weight: 0.0000 chunk 98 optimal weight: 0.6980 chunk 398 optimal weight: 5.9990 chunk 330 optimal weight: 50.0000 chunk 184 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 131 optimal weight: 0.3980 chunk 209 optimal weight: 5.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN B 644 GLN C 81 ASN C 207 HIS ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C1011 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6072 moved from start: 0.5475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 35083 Z= 0.154 Angle : 0.614 10.996 47697 Z= 0.301 Chirality : 0.046 0.699 5549 Planarity : 0.004 0.050 6036 Dihedral : 5.976 59.905 6406 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.89 % Favored : 94.86 % Rotamer: Outliers : 2.11 % Allowed : 14.47 % Favored : 83.42 % 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: -1.09 (0.13), residues: 4087 helix: 1.01 (0.15), residues: 1336 sheet: -0.76 (0.19), residues: 652 loop : -1.93 (0.13), residues: 2099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 104 HIS 0.004 0.001 HIS F 373 PHE 0.025 0.001 PHE B 855 TYR 0.043 0.001 TYR F 183 ARG 0.008 0.000 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 209 time to evaluate : 3.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 ASN cc_start: 0.8154 (OUTLIER) cc_final: 0.7797 (m-40) REVERT: B 1050 MET cc_start: 0.7085 (ptp) cc_final: 0.6882 (ptp) REVERT: C 153 MET cc_start: 0.4947 (tmm) cc_final: 0.4508 (tmm) REVERT: D 62 MET cc_start: -0.1730 (ttp) cc_final: -0.2375 (ttp) REVERT: D 332 MET cc_start: -0.1538 (mmm) cc_final: -0.3327 (ttt) REVERT: D 455 MET cc_start: 0.0544 (ttm) cc_final: -0.0049 (ttm) REVERT: D 480 MET cc_start: 0.0944 (OUTLIER) cc_final: -0.1319 (mmt) REVERT: D 508 ASN cc_start: 0.6006 (m110) cc_final: 0.5260 (t0) REVERT: D 557 MET cc_start: 0.1684 (tmm) cc_final: 0.1073 (tmm) REVERT: F 37 GLU cc_start: -0.1265 (tm-30) cc_final: -0.1845 (mp0) REVERT: F 249 MET cc_start: 0.1180 (ptt) cc_final: -0.0109 (tpp) REVERT: F 297 MET cc_start: -0.0683 (mpp) cc_final: -0.3228 (ttt) REVERT: F 351 LEU cc_start: 0.3650 (OUTLIER) cc_final: 0.3338 (mp) REVERT: F 383 MET cc_start: 0.0419 (mtp) cc_final: -0.1836 (tmm) REVERT: F 510 TYR cc_start: 0.3124 (m-80) cc_final: 0.2438 (t80) outliers start: 77 outliers final: 51 residues processed: 275 average time/residue: 0.4105 time to fit residues: 196.0971 Evaluate side-chains 236 residues out of total 3655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 182 time to evaluate : 3.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 917 TYR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 480 MET Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 574 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 384 optimal weight: 50.0000 chunk 44 optimal weight: 0.4980 chunk 227 optimal weight: 8.9990 chunk 291 optimal weight: 1.9990 chunk 225 optimal weight: 0.8980 chunk 335 optimal weight: 9.9990 chunk 222 optimal weight: 20.0000 chunk 397 optimal weight: 50.0000 chunk 248 optimal weight: 2.9990 chunk 242 optimal weight: 1.9990 chunk 183 optimal weight: 7.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN A1005 GLN B 81 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN C 207 HIS ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6094 moved from start: 0.5632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 35083 Z= 0.183 Angle : 0.609 12.139 47697 Z= 0.297 Chirality : 0.045 0.579 5549 Planarity : 0.004 0.068 6036 Dihedral : 5.691 59.816 6406 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.21 % Favored : 94.52 % Rotamer: Outliers : 2.13 % Allowed : 14.97 % Favored : 82.90 % 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: -0.99 (0.13), residues: 4087 helix: 1.09 (0.15), residues: 1354 sheet: -0.79 (0.19), residues: 636 loop : -1.86 (0.13), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 104 HIS 0.005 0.001 HIS B1064 PHE 0.033 0.001 PHE A 238 TYR 0.032 0.001 TYR F 183 ARG 0.009 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 198 time to evaluate : 3.643 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 317 ASN cc_start: 0.8191 (OUTLIER) cc_final: 0.7807 (m-40) REVERT: C 153 MET cc_start: 0.4921 (tmm) cc_final: 0.3979 (ttp) REVERT: D 62 MET cc_start: -0.1791 (ttp) cc_final: -0.2406 (ttp) REVERT: D 82 MET cc_start: 0.2157 (tmm) cc_final: 0.0180 (mmt) REVERT: D 332 MET cc_start: -0.1544 (mmm) cc_final: -0.3301 (ttt) REVERT: D 455 MET cc_start: 0.0559 (ttm) cc_final: -0.0034 (ttm) REVERT: D 480 MET cc_start: 0.1293 (OUTLIER) cc_final: -0.1005 (mmt) REVERT: D 508 ASN cc_start: 0.6020 (m110) cc_final: 0.5287 (t0) REVERT: F 37 GLU cc_start: -0.1287 (tm-30) cc_final: -0.1868 (mp0) REVERT: F 249 MET cc_start: 0.1325 (ptt) cc_final: 0.0002 (tpp) REVERT: F 297 MET cc_start: -0.0705 (mpp) cc_final: -0.3004 (ttp) REVERT: F 383 MET cc_start: 0.0564 (mtp) cc_final: -0.1740 (tmm) REVERT: F 455 MET cc_start: 0.1628 (mmm) cc_final: 0.1230 (mmm) REVERT: F 510 TYR cc_start: 0.3166 (m-80) cc_final: 0.2528 (t80) outliers start: 78 outliers final: 60 residues processed: 261 average time/residue: 0.3926 time to fit residues: 177.7239 Evaluate side-chains 244 residues out of total 3655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 182 time to evaluate : 3.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 95 ILE 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 223 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 917 TYR Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 480 MET Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 574 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 245 optimal weight: 9.9990 chunk 158 optimal weight: 0.5980 chunk 237 optimal weight: 50.0000 chunk 119 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 76 optimal weight: 0.0980 chunk 252 optimal weight: 1.9990 chunk 270 optimal weight: 0.7980 chunk 196 optimal weight: 6.9990 chunk 37 optimal weight: 0.4980 chunk 312 optimal weight: 50.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 675 GLN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 207 HIS B 314 GLN B 613 GLN B 644 GLN C 207 HIS ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6053 moved from start: 0.5739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 35083 Z= 0.144 Angle : 0.589 10.837 47697 Z= 0.287 Chirality : 0.045 0.552 5549 Planarity : 0.004 0.059 6036 Dihedral : 5.300 59.926 6406 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.80 % Favored : 94.96 % Rotamer: Outliers : 2.08 % Allowed : 15.35 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.13), residues: 4087 helix: 1.30 (0.15), residues: 1348 sheet: -0.56 (0.19), residues: 672 loop : -1.78 (0.13), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 104 HIS 0.003 0.001 HIS C 207 PHE 0.029 0.001 PHE A 238 TYR 0.031 0.001 TYR F 183 ARG 0.009 0.000 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 197 time to evaluate : 3.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.2665 (ppp) cc_final: 0.2446 (ppp) REVERT: A 317 ASN cc_start: 0.8160 (OUTLIER) cc_final: 0.7812 (m-40) REVERT: A 753 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8119 (tp) REVERT: B 517 LEU cc_start: 0.1287 (OUTLIER) cc_final: 0.0838 (mt) REVERT: B 1050 MET cc_start: 0.7006 (ptp) cc_final: 0.6776 (ptp) REVERT: C 153 MET cc_start: 0.4957 (tmm) cc_final: 0.4213 (ttp) REVERT: D 62 MET cc_start: -0.1794 (ttp) cc_final: -0.2736 (ttp) REVERT: D 94 LYS cc_start: -0.1263 (pttt) cc_final: -0.2608 (mttt) REVERT: D 187 LYS cc_start: 0.1672 (mmmt) cc_final: 0.1401 (mmmt) REVERT: D 332 MET cc_start: -0.1253 (mmm) cc_final: -0.3096 (ttm) REVERT: D 360 MET cc_start: -0.2170 (mmt) cc_final: -0.2636 (mmt) REVERT: D 455 MET cc_start: 0.0556 (ttm) cc_final: -0.0052 (ttm) REVERT: D 480 MET cc_start: 0.1241 (OUTLIER) cc_final: -0.1087 (mmt) REVERT: D 508 ASN cc_start: 0.6008 (m110) cc_final: 0.5316 (t0) REVERT: D 557 MET cc_start: 0.1966 (tmm) cc_final: 0.1103 (tmm) REVERT: F 249 MET cc_start: 0.1636 (ptt) cc_final: 0.0214 (tpp) REVERT: F 297 MET cc_start: -0.0249 (mpp) cc_final: -0.2062 (ttt) REVERT: F 376 MET cc_start: -0.0396 (mtt) cc_final: -0.0687 (mtt) REVERT: F 383 MET cc_start: 0.0672 (mtp) cc_final: -0.1558 (tmm) REVERT: F 480 MET cc_start: 0.1129 (mpp) cc_final: -0.0220 (ptp) REVERT: F 510 TYR cc_start: 0.2868 (m-80) cc_final: 0.2433 (t80) outliers start: 76 outliers final: 54 residues processed: 262 average time/residue: 0.4046 time to fit residues: 183.5731 Evaluate side-chains 239 residues out of total 3655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 181 time to evaluate : 3.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 917 TYR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 480 MET Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 574 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 361 optimal weight: 0.9990 chunk 380 optimal weight: 30.0000 chunk 347 optimal weight: 50.0000 chunk 370 optimal weight: 40.0000 chunk 222 optimal weight: 3.9990 chunk 161 optimal weight: 7.9990 chunk 290 optimal weight: 0.0970 chunk 113 optimal weight: 3.9990 chunk 334 optimal weight: 0.0470 chunk 349 optimal weight: 4.9990 chunk 368 optimal weight: 0.1980 overall best weight: 1.0680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 613 GLN B 644 GLN C 207 HIS ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6058 moved from start: 0.5851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 35083 Z= 0.152 Angle : 0.589 10.733 47697 Z= 0.285 Chirality : 0.045 0.538 5549 Planarity : 0.004 0.055 6036 Dihedral : 5.092 59.860 6406 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.94 % Favored : 94.81 % Rotamer: Outliers : 1.70 % Allowed : 16.06 % Favored : 82.24 % 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: -0.69 (0.13), residues: 4087 helix: 1.35 (0.15), residues: 1349 sheet: -0.51 (0.19), residues: 675 loop : -1.73 (0.13), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 104 HIS 0.003 0.000 HIS B1064 PHE 0.027 0.001 PHE A 238 TYR 0.028 0.001 TYR F 183 ARG 0.010 0.000 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 188 time to evaluate : 3.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.2640 (ppp) cc_final: 0.2404 (ppp) REVERT: A 317 ASN cc_start: 0.8160 (OUTLIER) cc_final: 0.7830 (m-40) REVERT: A 753 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8081 (tp) REVERT: C 153 MET cc_start: 0.4993 (tmm) cc_final: 0.4309 (ttp) REVERT: D 62 MET cc_start: -0.1752 (ttp) cc_final: -0.2686 (ttp) REVERT: D 82 MET cc_start: 0.2326 (tmm) cc_final: 0.0256 (mmt) REVERT: D 86 GLN cc_start: 0.2965 (mp-120) cc_final: 0.2063 (pt0) REVERT: D 332 MET cc_start: -0.1242 (mmm) cc_final: -0.2963 (ttm) REVERT: D 360 MET cc_start: -0.1996 (mmt) cc_final: -0.2569 (mmt) REVERT: D 455 MET cc_start: 0.0557 (ttm) cc_final: -0.0049 (ttm) REVERT: D 480 MET cc_start: 0.1118 (OUTLIER) cc_final: -0.1243 (mmt) REVERT: D 508 ASN cc_start: 0.5968 (m110) cc_final: 0.5293 (t0) REVERT: D 557 MET cc_start: 0.1910 (tmm) cc_final: 0.1129 (tmm) REVERT: F 123 MET cc_start: -0.1602 (ptm) cc_final: -0.1927 (ttp) REVERT: F 249 MET cc_start: 0.1545 (ptt) cc_final: 0.0131 (tpp) REVERT: F 297 MET cc_start: -0.0272 (mpp) cc_final: -0.2076 (ttt) REVERT: F 383 MET cc_start: 0.0541 (mtp) cc_final: -0.1655 (tmm) REVERT: F 480 MET cc_start: 0.1237 (mpp) cc_final: -0.0221 (ptp) REVERT: F 510 TYR cc_start: 0.2583 (m-80) cc_final: 0.2217 (t80) outliers start: 62 outliers final: 53 residues processed: 244 average time/residue: 0.4093 time to fit residues: 174.0083 Evaluate side-chains 235 residues out of total 3655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 179 time to evaluate : 3.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 480 MET Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 574 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 242 optimal weight: 0.9990 chunk 391 optimal weight: 50.0000 chunk 238 optimal weight: 8.9990 chunk 185 optimal weight: 5.9990 chunk 272 optimal weight: 0.4980 chunk 410 optimal weight: 20.0000 chunk 377 optimal weight: 20.0000 chunk 326 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 252 optimal weight: 0.3980 chunk 200 optimal weight: 10.0000 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 GLN A1088 HIS B 644 GLN C 207 HIS ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 505 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6134 moved from start: 0.6091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 35083 Z= 0.256 Angle : 0.629 10.654 47697 Z= 0.307 Chirality : 0.045 0.540 5549 Planarity : 0.004 0.053 6036 Dihedral : 5.243 59.687 6406 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.51 % Favored : 94.25 % Rotamer: Outliers : 1.86 % Allowed : 16.09 % Favored : 82.05 % 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: -0.77 (0.13), residues: 4087 helix: 1.28 (0.15), residues: 1361 sheet: -0.62 (0.19), residues: 625 loop : -1.76 (0.13), residues: 2101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 104 HIS 0.009 0.001 HIS B1064 PHE 0.031 0.001 PHE A 238 TYR 0.027 0.001 TYR F 183 ARG 0.010 0.000 ARG B1019 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 184 time to evaluate : 3.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 ASN cc_start: 0.8170 (OUTLIER) cc_final: 0.7811 (m-40) REVERT: B 1050 MET cc_start: 0.7231 (ptp) cc_final: 0.7002 (ptp) REVERT: C 153 MET cc_start: 0.5392 (tmm) cc_final: 0.4743 (ttp) REVERT: D 62 MET cc_start: -0.1671 (ttp) cc_final: -0.2643 (ttp) REVERT: D 86 GLN cc_start: 0.3087 (mp-120) cc_final: 0.2095 (pt0) REVERT: D 332 MET cc_start: -0.1213 (mmm) cc_final: -0.2926 (ttm) REVERT: D 360 MET cc_start: -0.2131 (mmt) cc_final: -0.2565 (mmt) REVERT: D 455 MET cc_start: 0.0571 (ttm) cc_final: -0.0108 (ttm) REVERT: D 480 MET cc_start: 0.1098 (OUTLIER) cc_final: -0.1214 (mmt) REVERT: D 508 ASN cc_start: 0.6016 (m110) cc_final: 0.5363 (t0) REVERT: D 557 MET cc_start: 0.1914 (tmm) cc_final: 0.1162 (tmm) REVERT: F 249 MET cc_start: 0.1546 (ptt) cc_final: 0.0132 (tpp) REVERT: F 297 MET cc_start: -0.0426 (mpp) cc_final: -0.2246 (ttt) REVERT: F 332 MET cc_start: 0.4435 (tpt) cc_final: 0.4173 (tpt) REVERT: F 383 MET cc_start: 0.0279 (mtp) cc_final: -0.1648 (ppp) REVERT: F 510 TYR cc_start: 0.2730 (m-80) cc_final: 0.2086 (t80) outliers start: 68 outliers final: 59 residues processed: 245 average time/residue: 0.4181 time to fit residues: 178.5059 Evaluate side-chains 238 residues out of total 3655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 177 time to evaluate : 3.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 480 MET Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 574 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 259 optimal weight: 0.5980 chunk 348 optimal weight: 0.4980 chunk 100 optimal weight: 9.9990 chunk 301 optimal weight: 0.8980 chunk 48 optimal weight: 0.3980 chunk 90 optimal weight: 1.9990 chunk 327 optimal weight: 20.0000 chunk 137 optimal weight: 30.0000 chunk 336 optimal weight: 50.0000 chunk 41 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 GLN B 314 GLN B 644 GLN C 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.191534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.120507 restraints weight = 92056.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.107654 restraints weight = 78437.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.107235 restraints weight = 80731.736| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.6155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 35083 Z= 0.146 Angle : 0.596 14.285 47697 Z= 0.286 Chirality : 0.044 0.522 5549 Planarity : 0.004 0.053 6036 Dihedral : 5.002 59.782 6406 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.92 % Favored : 94.81 % Rotamer: Outliers : 1.67 % Allowed : 16.36 % Favored : 81.97 % 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: -0.59 (0.13), residues: 4087 helix: 1.45 (0.15), residues: 1339 sheet: -0.43 (0.19), residues: 668 loop : -1.69 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 566 HIS 0.003 0.001 HIS F 373 PHE 0.029 0.001 PHE A 238 TYR 0.025 0.001 TYR F 183 ARG 0.011 0.000 ARG B1019 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6492.27 seconds wall clock time: 118 minutes 39.44 seconds (7119.44 seconds total)