Starting phenix.real_space_refine on Wed Feb 21 15:18:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czq_30513/02_2024/7czq_30513.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czq_30513/02_2024/7czq_30513.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czq_30513/02_2024/7czq_30513.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czq_30513/02_2024/7czq_30513.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czq_30513/02_2024/7czq_30513.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czq_30513/02_2024/7czq_30513.pdb" } resolution = 2.8 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 133 5.16 5 C 19667 2.51 5 N 5064 2.21 5 O 6152 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A GLU 725": "OE1" <-> "OE2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A ARG 1107": "NH1" <-> "NH2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 246": "NH1" <-> "NH2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B ARG 408": "NH1" <-> "NH2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B ARG 509": "NH1" <-> "NH2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B GLU 918": "OE1" <-> "OE2" Residue "B GLU 1072": "OE1" <-> "OE2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C GLU 132": "OE1" <-> "OE2" Residue "C GLU 154": "OE1" <-> "OE2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C ARG 246": "NH1" <-> "NH2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C GLU 725": "OE1" <-> "OE2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C GLU 1031": "OE1" <-> "OE2" Residue "C GLU 1072": "OE1" <-> "OE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 1": "OE1" <-> "OE2" Residue "H ARG 19": "NH1" <-> "NH2" Residue "H ARG 86": "NH1" <-> "NH2" Residue "H ARG 97": "NH1" <-> "NH2" Residue "K GLU 55": "OE1" <-> "OE2" Residue "K ARG 61": "NH1" <-> "NH2" Residue "K GLU 81": "OE1" <-> "OE2" Residue "K GLU 106": "OE1" <-> "OE2" Residue "K GLU 166": "OE1" <-> "OE2" Residue "K PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 1": "OE1" <-> "OE2" Residue "J ARG 19": "NH1" <-> "NH2" Residue "J ARG 86": "NH1" <-> "NH2" Residue "J ARG 97": "NH1" <-> "NH2" Residue "N GLU 55": "OE1" <-> "OE2" Residue "N ARG 61": "NH1" <-> "NH2" Residue "N GLU 81": "OE1" <-> "OE2" Residue "N GLU 106": "OE1" <-> "OE2" Residue "N GLU 166": "OE1" <-> "OE2" Residue "N PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 31016 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 7863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7863 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 50, 'TRANS': 955} Chain breaks: 8 Chain: "B" Number of atoms: 7696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7696 Classifications: {'peptide': 982} Link IDs: {'PTRANS': 47, 'TRANS': 934} Chain breaks: 11 Chain: "C" Number of atoms: 7853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1004, 7853 Classifications: {'peptide': 1004} Link IDs: {'PTRANS': 49, 'TRANS': 954} Chain breaks: 8 Chain: "H" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1647 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 12, 'TRANS': 210} Chain: "K" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1665 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 11, 'TRANS': 203} Chain: "J" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1647 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 12, 'TRANS': 210} Chain: "N" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1665 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 11, 'TRANS': 203} 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: "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: "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: "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: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 16.53, per 1000 atoms: 0.53 Number of scatterers: 31016 At special positions: 0 Unit cell: (135.875, 173.92, 235.879, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 133 16.00 O 6152 8.00 N 5064 7.00 C 19667 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=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.08 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.05 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.05 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.08 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=2.17 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=1.98 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 204 " distance=2.03 Simple disulfide: pdb=" SG CYS K 135 " - pdb=" SG CYS K 195 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 95 " distance=2.03 Simple disulfide: pdb=" SG CYS J 148 " - pdb=" SG CYS J 204 " distance=2.03 Simple disulfide: pdb=" SG CYS N 135 " - pdb=" SG CYS N 195 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B1410 " - " NAG B1411 " " 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 I 1 " - " NAG I 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 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-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 603 " " NAG A1407 " - " ASN A 616 " " NAG A1408 " - " ASN A 657 " " NAG A1409 " - " ASN A 709 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 282 " " NAG B1406 " - " ASN B 343 " " NAG B1407 " - " ASN B 603 " " NAG B1408 " - " ASN B 616 " " NAG B1409 " - " ASN B 657 " " NAG B1410 " - " ASN B1074 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 282 " " NAG C1406 " - " ASN C 603 " " NAG C1407 " - " ASN C 616 " " NAG C1408 " - " ASN C 657 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A 343 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1074 " " NAG L 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 331 " " NAG P 1 " - " ASN B 709 " " NAG Q 1 " - " ASN B 717 " " NAG R 1 " - " ASN B 801 " " 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 " Time building additional restraints: 12.49 Conformation dependent library (CDL) restraints added in 5.6 seconds 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7228 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 64 sheets defined 19.2% alpha, 32.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.89 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.074A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.257A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.624A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.738A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.631A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.771A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.634A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 815' Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.647A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.575A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.994A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.625A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.878A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.631A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.646A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.640A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.964A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.544A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.603A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.011A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.372A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.074A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.257A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.624A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.739A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.582A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.718A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.560A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.604A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.590A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.356A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.220A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'H' and resid 195 through 197 No H-bonds generated for 'chain 'H' and resid 195 through 197' Processing helix chain 'K' and resid 122 through 129 Processing helix chain 'K' and resid 184 through 188 Processing helix chain 'J' and resid 195 through 197 No H-bonds generated for 'chain 'J' and resid 195 through 197' Processing helix chain 'N' and resid 122 through 129 Processing helix chain 'N' and resid 184 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.569A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.731A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 309 through 319 removed outlier: 6.679A pdb=" N GLU A 309 " --> pdb=" O GLY A 601 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLY A 601 " --> pdb=" O GLU A 309 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.543A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 448 through 454 removed outlier: 5.864A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 539 through 543 removed outlier: 5.338A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.256A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.505A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.713A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.538A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.441A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 10.074A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.650A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.779A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.572A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.673A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC7, first strand: chain 'B' and resid 539 through 543 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.220A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.579A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 8.151A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 10.527A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.757A pdb=" N THR C 274 " --> pdb=" O CYS C 291 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N CYS C 291 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 128 through 131 removed outlier: 4.248A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.667A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.543A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 448 through 454 removed outlier: 5.864A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE3, first strand: chain 'C' and resid 538 through 543 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.231A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.591A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.591A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.568A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE9, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.573A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.036A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET H 34 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TYR H 33 " --> pdb=" O GLU H 98 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N CYS H 95 " --> pdb=" O TRP H 111 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N TRP H 111 " --> pdb=" O CYS H 95 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ARG H 97 " --> pdb=" O ASP H 109 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.036A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET H 34 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TYR H 33 " --> pdb=" O GLU H 98 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 128 through 132 removed outlier: 5.008A pdb=" N ALA H 145 " --> pdb=" O VAL H 192 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL H 192 " --> pdb=" O ALA H 145 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY H 147 " --> pdb=" O VAL H 190 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL H 190 " --> pdb=" O GLY H 147 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU H 149 " --> pdb=" O SER H 188 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER H 188 " --> pdb=" O LEU H 149 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS H 151 " --> pdb=" O LEU H 186 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU H 186 " --> pdb=" O LYS H 151 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 128 through 132 removed outlier: 5.008A pdb=" N ALA H 145 " --> pdb=" O VAL H 192 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL H 192 " --> pdb=" O ALA H 145 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY H 147 " --> pdb=" O VAL H 190 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL H 190 " --> pdb=" O GLY H 147 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU H 149 " --> pdb=" O SER H 188 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER H 188 " --> pdb=" O LEU H 149 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS H 151 " --> pdb=" O LEU H 186 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU H 186 " --> pdb=" O LYS H 151 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 158 through 162 Processing sheet with id=AF6, first strand: chain 'K' and resid 5 through 6 removed outlier: 3.631A pdb=" N VAL K 19 " --> pdb=" O ILE K 75 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 44 through 46 Processing sheet with id=AF8, first strand: chain 'K' and resid 115 through 119 Processing sheet with id=AF9, first strand: chain 'K' and resid 154 through 155 Processing sheet with id=AG1, first strand: chain 'J' and resid 5 through 7 removed outlier: 3.573A pdb=" N THR J 77 " --> pdb=" O ASP J 72 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 57 through 59 removed outlier: 5.036A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET J 34 " --> pdb=" O ILE J 51 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TYR J 33 " --> pdb=" O GLU J 98 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N CYS J 95 " --> pdb=" O TRP J 111 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N TRP J 111 " --> pdb=" O CYS J 95 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ARG J 97 " --> pdb=" O ASP J 109 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 57 through 59 removed outlier: 5.036A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET J 34 " --> pdb=" O ILE J 51 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TYR J 33 " --> pdb=" O GLU J 98 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 128 through 132 removed outlier: 5.008A pdb=" N ALA J 145 " --> pdb=" O VAL J 192 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL J 192 " --> pdb=" O ALA J 145 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY J 147 " --> pdb=" O VAL J 190 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL J 190 " --> pdb=" O GLY J 147 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU J 149 " --> pdb=" O SER J 188 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER J 188 " --> pdb=" O LEU J 149 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS J 151 " --> pdb=" O LEU J 186 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU J 186 " --> pdb=" O LYS J 151 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 128 through 132 removed outlier: 5.008A pdb=" N ALA J 145 " --> pdb=" O VAL J 192 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL J 192 " --> pdb=" O ALA J 145 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY J 147 " --> pdb=" O VAL J 190 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL J 190 " --> pdb=" O GLY J 147 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU J 149 " --> pdb=" O SER J 188 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER J 188 " --> pdb=" O LEU J 149 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS J 151 " --> pdb=" O LEU J 186 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU J 186 " --> pdb=" O LYS J 151 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 158 through 162 Processing sheet with id=AG7, first strand: chain 'N' and resid 5 through 6 removed outlier: 3.632A pdb=" N VAL N 19 " --> pdb=" O ILE N 75 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'N' and resid 44 through 46 Processing sheet with id=AG9, first strand: chain 'N' and resid 115 through 119 Processing sheet with id=AH1, first strand: chain 'N' and resid 154 through 155 1173 hydrogen bonds defined for protein. 3189 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: 15.34 Time building geometry restraints manager: 13.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9676 1.34 - 1.46: 8205 1.46 - 1.59: 13632 1.59 - 1.72: 0 1.72 - 1.85: 168 Bond restraints: 31681 Sorted by residual: bond pdb=" C LEU K 94 " pdb=" N PRO K 95 " ideal model delta sigma weight residual 1.331 1.389 -0.058 1.27e-02 6.20e+03 2.09e+01 bond pdb=" C LEU N 94 " pdb=" N PRO N 95 " ideal model delta sigma weight residual 1.331 1.389 -0.058 1.27e-02 6.20e+03 2.07e+01 bond pdb=" C THR C 588 " pdb=" N PRO C 589 " ideal model delta sigma weight residual 1.332 1.390 -0.058 1.34e-02 5.57e+03 1.87e+01 bond pdb=" N PRO K 142 " pdb=" CD PRO K 142 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.85e+01 bond pdb=" N PRO N 142 " pdb=" CD PRO N 142 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.83e+01 ... (remaining 31676 not shown) Histogram of bond angle deviations from ideal: 97.52 - 105.78: 665 105.78 - 114.03: 18493 114.03 - 122.29: 18375 122.29 - 130.54: 5457 130.54 - 138.80: 92 Bond angle restraints: 43082 Sorted by residual: angle pdb=" C PHE A 86 " pdb=" N ASN A 87 " pdb=" CA ASN A 87 " ideal model delta sigma weight residual 121.54 132.86 -11.32 1.91e+00 2.74e-01 3.51e+01 angle pdb=" N GLU C 156 " pdb=" CA GLU C 156 " pdb=" C GLU C 156 " ideal model delta sigma weight residual 108.45 115.81 -7.36 1.26e+00 6.30e-01 3.41e+01 angle pdb=" C LEU N 94 " pdb=" N PRO N 95 " pdb=" CA PRO N 95 " ideal model delta sigma weight residual 119.90 114.11 5.79 1.02e+00 9.61e-01 3.22e+01 angle pdb=" C LEU K 94 " pdb=" N PRO K 95 " pdb=" CA PRO K 95 " ideal model delta sigma weight residual 119.90 114.13 5.77 1.02e+00 9.61e-01 3.21e+01 angle pdb=" C THR C 588 " pdb=" N PRO C 589 " pdb=" CA PRO C 589 " ideal model delta sigma weight residual 119.78 114.00 5.78 1.03e+00 9.43e-01 3.14e+01 ... (remaining 43077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 17108 17.92 - 35.83: 1899 35.83 - 53.75: 557 53.75 - 71.67: 195 71.67 - 89.59: 57 Dihedral angle restraints: 19816 sinusoidal: 8581 harmonic: 11235 Sorted by residual: dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual 93.00 12.13 80.87 1 1.00e+01 1.00e-02 8.08e+01 dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 19.58 73.42 1 1.00e+01 1.00e-02 6.86e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.07 71.93 1 1.00e+01 1.00e-02 6.62e+01 ... (remaining 19813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.328: 5096 0.328 - 0.656: 4 0.656 - 0.985: 2 0.985 - 1.313: 0 1.313 - 1.641: 1 Chirality restraints: 5103 Sorted by residual: chirality pdb=" C1 NAG B1411 " pdb=" O4 NAG B1410 " pdb=" C2 NAG B1411 " pdb=" O5 NAG B1411 " both_signs ideal model delta sigma weight residual False -2.40 -3.08 0.68 2.00e-02 2.50e+03 1.15e+03 chirality pdb=" C1 NAG b 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG b 1 " pdb=" O5 NAG b 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.76 -1.64 2.00e-01 2.50e+01 6.73e+01 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A1074 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.64 -0.76 2.00e-01 2.50e+01 1.43e+01 ... (remaining 5100 not shown) Planarity restraints: 5518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " 0.171 2.00e-02 2.50e+03 1.76e-01 3.87e+02 pdb=" CG ASN A 331 " -0.063 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.065 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.263 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " 0.220 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " -0.074 2.00e-02 2.50e+03 1.04e-01 1.35e+02 pdb=" CG ASN C 331 " 0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " -0.025 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " 0.184 2.00e-02 2.50e+03 pdb=" C1 NAG U 1 " -0.115 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C1134 " -0.022 2.00e-02 2.50e+03 3.15e-02 1.24e+01 pdb=" CG ASN C1134 " 0.010 2.00e-02 2.50e+03 pdb=" OD1 ASN C1134 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN C1134 " 0.056 2.00e-02 2.50e+03 pdb=" C1 NAG b 1 " -0.034 2.00e-02 2.50e+03 ... (remaining 5515 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 128 2.40 - 3.02: 18150 3.02 - 3.65: 43122 3.65 - 4.27: 68983 4.27 - 4.90: 115782 Nonbonded interactions: 246165 Sorted by model distance: nonbonded pdb=" ND2 ASN C 334 " pdb=" CA CYS C 361 " model vdw 1.770 3.550 nonbonded pdb=" N GLU K 81 " pdb=" OE1 GLU K 81 " model vdw 1.877 2.520 nonbonded pdb=" N GLU N 81 " pdb=" OE1 GLU N 81 " model vdw 1.877 2.520 nonbonded pdb=" N GLN H 3 " pdb=" OE1 GLN H 3 " model vdw 1.878 2.520 nonbonded pdb=" N GLN J 3 " pdb=" OE1 GLN J 3 " model vdw 1.878 2.520 ... (remaining 246160 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 441 or resid 451 through 475 or resid 487 throu \ gh 497 or resid 503 through 620 or resid 641 through 939 or resid 944 through 11 \ 46 or resid 1401 through 1408)) selection = (chain 'B' and (resid 27 through 620 or resid 641 through 826 or resid 855 throu \ gh 1146 or resid 1401 through 1408)) selection = (chain 'C' and (resid 27 through 441 or resid 451 through 475 or resid 487 throu \ gh 497 or resid 503 through 826 or resid 855 through 1146 or resid 1401 through \ 1408)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'L' selection = chain 'M' 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' } ncs_group { reference = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 7.070 Check model and map are aligned: 0.510 Set scattering table: 0.330 Process input model: 85.400 Find NCS groups from input model: 2.400 Set up NCS constraints: 0.420 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.118 31681 Z= 0.697 Angle : 1.036 13.797 43082 Z= 0.593 Chirality : 0.069 1.641 5103 Planarity : 0.006 0.078 5470 Dihedral : 17.514 89.587 12456 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 20.76 Ramachandran Plot: Outliers : 1.68 % Allowed : 9.74 % Favored : 88.58 % Rotamer: Outliers : 11.76 % Allowed : 18.01 % Favored : 70.23 % 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: -3.58 (0.11), residues: 3800 helix: -2.14 (0.16), residues: 661 sheet: -1.50 (0.15), residues: 1059 loop : -3.02 (0.11), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP K 35 HIS 0.009 0.002 HIS A1048 PHE 0.025 0.003 PHE A 898 TYR 0.027 0.003 TYR B1067 ARG 0.009 0.001 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 397 poor density : 410 time to evaluate : 3.595 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: A 81 ASN cc_start: 0.6614 (OUTLIER) cc_final: 0.6186 (t0) REVERT: A 153 MET cc_start: 0.2219 (mpp) cc_final: -0.1865 (ttp) REVERT: A 203 ILE cc_start: 0.7778 (mt) cc_final: 0.7411 (mp) REVERT: A 438 SER cc_start: 0.4587 (OUTLIER) cc_final: 0.4202 (t) REVERT: A 556 ASN cc_start: 0.7055 (OUTLIER) cc_final: 0.6605 (p0) REVERT: A 878 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8951 (mt) REVERT: A 1039 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.8572 (mtp180) REVERT: B 45 SER cc_start: 0.7917 (OUTLIER) cc_final: 0.7704 (p) REVERT: B 60 SER cc_start: 0.8041 (OUTLIER) cc_final: 0.7766 (m) REVERT: B 472 ILE cc_start: 0.3381 (OUTLIER) cc_final: 0.3089 (tt) REVERT: B 473 TYR cc_start: 0.2237 (OUTLIER) cc_final: 0.2004 (m-10) REVERT: B 569 ILE cc_start: 0.4333 (OUTLIER) cc_final: 0.4051 (mm) REVERT: B 676 THR cc_start: 0.5577 (OUTLIER) cc_final: 0.5140 (m) REVERT: C 99 ASN cc_start: 0.7173 (t0) cc_final: 0.6624 (m-40) REVERT: C 133 PHE cc_start: 0.4450 (m-80) cc_final: 0.4141 (m-80) REVERT: C 215 ASP cc_start: 0.3371 (OUTLIER) cc_final: 0.2503 (p0) REVERT: C 216 LEU cc_start: 0.6307 (OUTLIER) cc_final: 0.6063 (tp) REVERT: C 234 ASN cc_start: 0.5650 (OUTLIER) cc_final: 0.4890 (m-40) REVERT: C 574 ASP cc_start: 0.8097 (p0) cc_final: 0.7869 (p0) REVERT: C 1136 THR cc_start: 0.9087 (OUTLIER) cc_final: 0.8887 (t) REVERT: H 34 MET cc_start: 0.2832 (mmm) cc_final: 0.2032 (mpp) REVERT: H 82 MET cc_start: 0.1192 (tmm) cc_final: 0.0882 (ttp) REVERT: H 178 LEU cc_start: 0.2915 (tm) cc_final: 0.2663 (mp) REVERT: H 211 SER cc_start: -0.1638 (OUTLIER) cc_final: -0.1860 (p) REVERT: J 151 LYS cc_start: 0.3913 (ptmm) cc_final: 0.3706 (pptt) REVERT: J 164 SER cc_start: 0.2472 (OUTLIER) cc_final: 0.1962 (p) REVERT: J 209 LYS cc_start: 0.2452 (mmpt) cc_final: 0.1835 (mtmt) REVERT: J 214 LYS cc_start: 0.4108 (tppt) cc_final: 0.3660 (mtmt) REVERT: J 222 LYS cc_start: 0.1103 (mttp) cc_final: -0.0769 (ttpt) REVERT: N 49 TYR cc_start: 0.3758 (p90) cc_final: 0.3224 (p90) REVERT: N 53 ASN cc_start: 0.4002 (OUTLIER) cc_final: 0.3338 (t0) outliers start: 397 outliers final: 85 residues processed: 748 average time/residue: 1.0368 time to fit residues: 960.4606 Evaluate side-chains 319 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 216 time to evaluate : 3.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 116 SER 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 325 SER Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 211 SER Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain J residue 12 ILE Chi-restraints excluded: chain J residue 164 SER Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 53 ASN Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain N residue 94 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 9.9990 chunk 291 optimal weight: 0.9980 chunk 161 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 196 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 300 optimal weight: 40.0000 chunk 116 optimal weight: 0.8980 chunk 183 optimal weight: 0.8980 chunk 224 optimal weight: 6.9990 chunk 348 optimal weight: 5.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 137 ASN A 188 ASN A 239 GLN A 422 ASN A 440 ASN A 498 GLN A 540 ASN A 556 ASN A 644 GLN A 690 GLN A 703 ASN A 779 GLN A 804 GLN A 856 ASN A 901 GLN A 914 ASN A 919 ASN A 926 GLN A 935 GLN A 955 ASN A 969 ASN A 992 GLN B 115 GLN B 134 GLN B 354 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 563 GLN B 703 ASN B 755 GLN B 901 GLN B 914 ASN B 919 ASN B 920 GLN B 926 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1054 GLN C 66 HIS C 81 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN C 188 ASN C 321 GLN C 334 ASN C 360 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 ASN C 493 GLN C 498 GLN C 556 ASN C 606 ASN C 641 ASN C 690 GLN C 703 ASN C 784 GLN C 804 GLN C 901 GLN C 907 ASN C 914 ASN C 926 GLN C 935 GLN C 969 ASN C 992 GLN C1002 GLN C1010 GLN C1071 GLN C1101 HIS K 6 GLN K 38 GLN ** K 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 200 GLN J 3 GLN ** J 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 113 GLN N 6 GLN N 38 GLN ** N 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 73 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31681 Z= 0.222 Angle : 0.760 13.732 43082 Z= 0.379 Chirality : 0.050 0.490 5103 Planarity : 0.005 0.059 5470 Dihedral : 9.550 67.635 5751 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.29 % Favored : 92.42 % Rotamer: Outliers : 6.10 % Allowed : 22.42 % Favored : 71.48 % 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: -2.29 (0.12), residues: 3800 helix: -0.10 (0.19), residues: 679 sheet: -0.73 (0.15), residues: 1077 loop : -2.57 (0.12), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 436 HIS 0.004 0.001 HIS C1101 PHE 0.025 0.002 PHE B 168 TYR 0.021 0.001 TYR K 49 ARG 0.006 0.001 ARG K 109 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 258 time to evaluate : 4.481 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 90 VAL cc_start: 0.8228 (OUTLIER) cc_final: 0.8012 (t) REVERT: A 153 MET cc_start: 0.2204 (mpp) cc_final: -0.1896 (ttp) REVERT: A 335 LEU cc_start: 0.5210 (OUTLIER) cc_final: 0.4828 (pp) REVERT: A 588 THR cc_start: 0.8962 (OUTLIER) cc_final: 0.8597 (m) REVERT: A 787 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.7970 (mt0) REVERT: B 214 ARG cc_start: 0.3601 (OUTLIER) cc_final: 0.3107 (mpt90) REVERT: B 473 TYR cc_start: 0.2183 (OUTLIER) cc_final: 0.1891 (m-10) REVERT: B 569 ILE cc_start: 0.4251 (OUTLIER) cc_final: 0.3946 (mm) REVERT: B 676 THR cc_start: 0.6111 (OUTLIER) cc_final: 0.5671 (m) REVERT: B 878 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8890 (mt) REVERT: B 983 ARG cc_start: 0.7544 (ttp-110) cc_final: 0.7262 (ttm110) REVERT: C 472 ILE cc_start: -0.0735 (OUTLIER) cc_final: -0.1615 (pp) REVERT: C 529 LYS cc_start: 0.6704 (OUTLIER) cc_final: 0.6281 (mmtm) REVERT: C 740 MET cc_start: 0.7649 (tpp) cc_final: 0.7435 (tpt) REVERT: H 34 MET cc_start: 0.3227 (mmm) cc_final: 0.2512 (mpp) REVERT: H 82 MET cc_start: 0.1302 (tmm) cc_final: 0.0850 (ttp) REVERT: H 123 SER cc_start: -0.1904 (OUTLIER) cc_final: -0.2114 (p) REVERT: H 186 LEU cc_start: 0.1665 (OUTLIER) cc_final: 0.1393 (tp) REVERT: J 4 LEU cc_start: 0.1761 (OUTLIER) cc_final: 0.1551 (tt) REVERT: J 125 LYS cc_start: 0.3434 (tppt) cc_final: 0.2896 (mttp) REVERT: J 209 LYS cc_start: 0.2164 (mmpt) cc_final: 0.1660 (mtmt) REVERT: J 214 LYS cc_start: 0.4051 (tppt) cc_final: 0.3496 (mtpt) REVERT: J 222 LYS cc_start: 0.2172 (mttp) cc_final: 0.0504 (mptm) REVERT: N 104 LYS cc_start: 0.2688 (mtpp) cc_final: 0.1517 (mptt) outliers start: 206 outliers final: 74 residues processed: 440 average time/residue: 0.9518 time to fit residues: 532.4057 Evaluate side-chains 281 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 193 time to evaluate : 3.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 205 ASN Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 146 LYS Chi-restraints excluded: chain K residue 177 SER Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain N residue 17 ASP Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 117 PHE Chi-restraints excluded: chain N residue 150 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 290 optimal weight: 4.9990 chunk 237 optimal weight: 20.0000 chunk 96 optimal weight: 4.9990 chunk 349 optimal weight: 20.0000 chunk 377 optimal weight: 50.0000 chunk 311 optimal weight: 50.0000 chunk 346 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 280 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 207 HIS A 450 ASN A 935 GLN A1101 HIS A1142 GLN B 30 ASN B 414 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN B 540 ASN B 690 GLN B 755 GLN B 992 GLN C 49 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C1005 GLN K 6 GLN ** K 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 113 GLN J 212 ASN N 6 GLN N 53 ASN ** N 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 31681 Z= 0.433 Angle : 0.830 15.857 43082 Z= 0.412 Chirality : 0.055 0.796 5103 Planarity : 0.006 0.073 5470 Dihedral : 8.858 59.935 5658 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.53 % Favored : 91.21 % Rotamer: Outliers : 7.08 % Allowed : 21.74 % Favored : 71.18 % 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: -1.90 (0.13), residues: 3800 helix: 0.29 (0.20), residues: 682 sheet: -0.53 (0.15), residues: 1064 loop : -2.30 (0.12), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 104 HIS 0.008 0.002 HIS C1058 PHE 0.022 0.003 PHE B 43 TYR 0.026 0.002 TYR C1067 ARG 0.006 0.001 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 202 time to evaluate : 3.810 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.2655 (mpp) cc_final: -0.1471 (ttt) REVERT: A 239 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.6954 (tm-30) REVERT: A 459 SER cc_start: 0.3543 (OUTLIER) cc_final: 0.3069 (t) REVERT: A 553 THR cc_start: 0.8528 (OUTLIER) cc_final: 0.8239 (p) REVERT: A 588 THR cc_start: 0.8971 (OUTLIER) cc_final: 0.8642 (m) REVERT: A 692 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8658 (mm) REVERT: A 856 ASN cc_start: 0.8686 (OUTLIER) cc_final: 0.8411 (p0) REVERT: A 1050 MET cc_start: 0.8693 (ptm) cc_final: 0.8476 (ptm) REVERT: B 214 ARG cc_start: 0.3649 (OUTLIER) cc_final: 0.3080 (mtt180) REVERT: B 453 TYR cc_start: 0.5484 (OUTLIER) cc_final: 0.5119 (p90) REVERT: B 473 TYR cc_start: 0.1937 (OUTLIER) cc_final: 0.1577 (m-80) REVERT: B 569 ILE cc_start: 0.4798 (OUTLIER) cc_final: 0.4535 (mm) REVERT: B 676 THR cc_start: 0.6144 (OUTLIER) cc_final: 0.5653 (m) REVERT: B 740 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7472 (ttp) REVERT: C 133 PHE cc_start: 0.4452 (m-80) cc_final: 0.4241 (m-80) REVERT: C 529 LYS cc_start: 0.6793 (OUTLIER) cc_final: 0.6359 (mmtm) REVERT: C 740 MET cc_start: 0.7742 (tpp) cc_final: 0.7531 (tpt) REVERT: H 34 MET cc_start: 0.3294 (mmm) cc_final: 0.2595 (mpp) REVERT: J 4 LEU cc_start: 0.1780 (OUTLIER) cc_final: 0.1212 (pp) REVERT: J 101 LYS cc_start: 0.2635 (ptpt) cc_final: 0.1781 (tppt) REVERT: J 125 LYS cc_start: 0.3654 (tppt) cc_final: 0.3111 (mttp) REVERT: J 197 LEU cc_start: 0.0174 (OUTLIER) cc_final: -0.0270 (mt) REVERT: J 209 LYS cc_start: 0.1962 (mmpt) cc_final: 0.1545 (mtmt) REVERT: J 214 LYS cc_start: 0.3788 (tppt) cc_final: 0.3334 (mtmt) REVERT: J 220 GLU cc_start: 0.2111 (OUTLIER) cc_final: 0.1197 (tp30) REVERT: J 222 LYS cc_start: 0.2236 (mttp) cc_final: 0.0683 (mptm) REVERT: N 49 TYR cc_start: 0.3591 (OUTLIER) cc_final: 0.3295 (p90) outliers start: 239 outliers final: 113 residues processed: 420 average time/residue: 0.9999 time to fit residues: 527.6624 Evaluate side-chains 307 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 177 time to evaluate : 3.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain H residue 168 THR Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 205 ASN Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 146 LYS Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 177 SER Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 220 GLU Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 150 LYS Chi-restraints excluded: chain N residue 204 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 30.0000 chunk 262 optimal weight: 5.9990 chunk 181 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 166 optimal weight: 0.9990 chunk 234 optimal weight: 9.9990 chunk 350 optimal weight: 20.0000 chunk 371 optimal weight: 20.0000 chunk 183 optimal weight: 1.9990 chunk 332 optimal weight: 20.0000 chunk 100 optimal weight: 10.0000 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 207 HIS A 779 GLN A 935 GLN A1142 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 613 GLN B 755 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 138 ASN N 6 GLN ** N 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 138 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 31681 Z= 0.274 Angle : 0.712 15.004 43082 Z= 0.350 Chirality : 0.051 0.970 5103 Planarity : 0.005 0.051 5470 Dihedral : 8.267 59.918 5648 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.82 % Favored : 92.97 % Rotamer: Outliers : 5.89 % Allowed : 22.87 % Favored : 71.24 % 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: -1.48 (0.13), residues: 3800 helix: 0.71 (0.20), residues: 688 sheet: -0.27 (0.15), residues: 1083 loop : -2.08 (0.12), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.003 0.001 HIS A 519 PHE 0.025 0.002 PHE C 342 TYR 0.020 0.001 TYR C1067 ARG 0.006 0.000 ARG C 646 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 184 time to evaluate : 4.144 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: 0.2863 (mpp) cc_final: -0.1282 (ttt) REVERT: A 195 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7909 (ptmt) REVERT: A 239 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7121 (tm-30) REVERT: A 433 VAL cc_start: 0.8432 (OUTLIER) cc_final: 0.8008 (m) REVERT: A 459 SER cc_start: 0.3507 (OUTLIER) cc_final: 0.3145 (t) REVERT: A 553 THR cc_start: 0.8512 (OUTLIER) cc_final: 0.8312 (p) REVERT: A 588 THR cc_start: 0.8994 (OUTLIER) cc_final: 0.8640 (m) REVERT: A 787 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8068 (mt0) REVERT: A 856 ASN cc_start: 0.8663 (OUTLIER) cc_final: 0.8420 (p0) REVERT: A 1050 MET cc_start: 0.8579 (ptm) cc_final: 0.8340 (ptm) REVERT: B 97 LYS cc_start: 0.6603 (OUTLIER) cc_final: 0.6091 (mtmm) REVERT: B 214 ARG cc_start: 0.3019 (OUTLIER) cc_final: 0.2349 (mpt-90) REVERT: B 453 TYR cc_start: 0.5148 (OUTLIER) cc_final: 0.4808 (p90) REVERT: B 473 TYR cc_start: 0.1522 (OUTLIER) cc_final: 0.1244 (m-80) REVERT: B 569 ILE cc_start: 0.4719 (OUTLIER) cc_final: 0.4458 (mm) REVERT: B 676 THR cc_start: 0.6376 (OUTLIER) cc_final: 0.5889 (m) REVERT: B 854 LYS cc_start: 0.5874 (OUTLIER) cc_final: 0.5460 (mmmm) REVERT: B 900 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8234 (mtp) REVERT: C 133 PHE cc_start: 0.4711 (m-80) cc_final: 0.4217 (m-80) REVERT: C 569 ILE cc_start: 0.8418 (mp) cc_final: 0.8158 (mp) REVERT: C 740 MET cc_start: 0.7710 (tpp) cc_final: 0.7460 (tpt) REVERT: C 778 THR cc_start: 0.9496 (OUTLIER) cc_final: 0.9009 (m) REVERT: C 787 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7831 (mm-40) REVERT: H 186 LEU cc_start: 0.1904 (OUTLIER) cc_final: 0.1415 (tp) REVERT: J 4 LEU cc_start: 0.1687 (OUTLIER) cc_final: 0.1081 (pp) REVERT: J 125 LYS cc_start: 0.3656 (tppt) cc_final: 0.3107 (mttm) REVERT: J 209 LYS cc_start: 0.1855 (mmpt) cc_final: 0.1449 (mtmt) REVERT: J 214 LYS cc_start: 0.3833 (tppt) cc_final: 0.3395 (mtmt) REVERT: J 222 LYS cc_start: 0.2296 (mttp) cc_final: 0.0616 (mptm) REVERT: N 49 TYR cc_start: 0.3789 (OUTLIER) cc_final: 0.3470 (p90) outliers start: 199 outliers final: 94 residues processed: 359 average time/residue: 1.0129 time to fit residues: 459.8296 Evaluate side-chains 283 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 168 time to evaluate : 3.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 205 ASN Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 177 SER Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 150 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 4.9990 chunk 210 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 276 optimal weight: 0.9990 chunk 153 optimal weight: 0.7980 chunk 316 optimal weight: 50.0000 chunk 256 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 189 optimal weight: 1.9990 chunk 333 optimal weight: 40.0000 chunk 93 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 188 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A1125 ASN A1142 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 658 ASN B 978 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 31681 Z= 0.235 Angle : 0.685 15.552 43082 Z= 0.336 Chirality : 0.049 0.847 5103 Planarity : 0.004 0.066 5470 Dihedral : 7.743 59.515 5639 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.21 % Favored : 92.58 % Rotamer: Outliers : 5.78 % Allowed : 22.96 % Favored : 71.27 % 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: -1.23 (0.13), residues: 3800 helix: 0.96 (0.20), residues: 690 sheet: -0.08 (0.15), residues: 1079 loop : -1.95 (0.13), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 104 HIS 0.003 0.001 HIS A 519 PHE 0.024 0.002 PHE B 168 TYR 0.020 0.001 TYR C1067 ARG 0.007 0.000 ARG C 646 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 181 time to evaluate : 3.599 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 116 SER cc_start: 0.7862 (OUTLIER) cc_final: 0.7541 (t) REVERT: A 153 MET cc_start: 0.3008 (mpp) cc_final: -0.1073 (ttm) REVERT: A 433 VAL cc_start: 0.8426 (OUTLIER) cc_final: 0.8018 (m) REVERT: A 459 SER cc_start: 0.3517 (OUTLIER) cc_final: 0.3178 (t) REVERT: A 588 THR cc_start: 0.8941 (OUTLIER) cc_final: 0.8589 (m) REVERT: A 787 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8049 (mt0) REVERT: A 856 ASN cc_start: 0.8700 (OUTLIER) cc_final: 0.8457 (p0) REVERT: A 1050 MET cc_start: 0.8552 (ptm) cc_final: 0.8318 (ptm) REVERT: B 214 ARG cc_start: 0.2720 (OUTLIER) cc_final: 0.2022 (mpt90) REVERT: B 335 LEU cc_start: 0.6712 (mp) cc_final: 0.6511 (mp) REVERT: B 453 TYR cc_start: 0.5233 (OUTLIER) cc_final: 0.4986 (p90) REVERT: B 458 LYS cc_start: 0.6008 (OUTLIER) cc_final: 0.5744 (ttpp) REVERT: B 473 TYR cc_start: 0.1290 (OUTLIER) cc_final: 0.0963 (m-80) REVERT: B 569 ILE cc_start: 0.4737 (OUTLIER) cc_final: 0.4488 (mm) REVERT: B 740 MET cc_start: 0.7696 (OUTLIER) cc_final: 0.7388 (ttp) REVERT: C 314 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8001 (tp40) REVERT: C 343 ASN cc_start: 0.2633 (OUTLIER) cc_final: 0.1634 (t0) REVERT: C 368 LEU cc_start: 0.6022 (OUTLIER) cc_final: 0.5819 (mt) REVERT: C 529 LYS cc_start: 0.6763 (OUTLIER) cc_final: 0.6343 (mmtm) REVERT: C 569 ILE cc_start: 0.8446 (mp) cc_final: 0.8195 (mp) REVERT: C 740 MET cc_start: 0.7786 (tpp) cc_final: 0.7531 (tpt) REVERT: C 778 THR cc_start: 0.9496 (OUTLIER) cc_final: 0.9001 (m) REVERT: C 787 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.7896 (mm-40) REVERT: H 34 MET cc_start: 0.3771 (mmt) cc_final: 0.3503 (mmt) REVERT: K 90 GLN cc_start: 0.4623 (OUTLIER) cc_final: 0.4013 (tt0) REVERT: J 101 LYS cc_start: 0.2804 (ptpt) cc_final: 0.1764 (tppt) REVERT: J 125 LYS cc_start: 0.3651 (tppt) cc_final: 0.3114 (mttm) REVERT: J 209 LYS cc_start: 0.1959 (mmpt) cc_final: 0.1550 (mtmt) REVERT: J 214 LYS cc_start: 0.3896 (tppt) cc_final: 0.3471 (mtmt) REVERT: J 222 LYS cc_start: 0.2174 (mttp) cc_final: 0.0606 (mptm) REVERT: N 49 TYR cc_start: 0.3792 (OUTLIER) cc_final: 0.3408 (p90) outliers start: 195 outliers final: 105 residues processed: 358 average time/residue: 0.9686 time to fit residues: 436.8745 Evaluate side-chains 293 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 168 time to evaluate : 3.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain H residue 205 ASN Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 177 SER Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 150 LYS Chi-restraints excluded: chain N residue 204 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 5.9990 chunk 334 optimal weight: 20.0000 chunk 73 optimal weight: 2.9990 chunk 217 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 371 optimal weight: 9.9990 chunk 308 optimal weight: 5.9990 chunk 172 optimal weight: 0.0370 chunk 30 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 overall best weight: 1.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN B 81 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 804 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN ** N 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31681 Z= 0.194 Angle : 0.651 15.846 43082 Z= 0.318 Chirality : 0.048 0.799 5103 Planarity : 0.004 0.068 5470 Dihedral : 7.326 59.772 5636 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.68 % Favored : 93.16 % Rotamer: Outliers : 5.07 % Allowed : 23.82 % Favored : 71.12 % 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: -1.02 (0.13), residues: 3800 helix: 1.23 (0.20), residues: 687 sheet: 0.06 (0.15), residues: 1080 loop : -1.85 (0.13), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 36 HIS 0.002 0.001 HIS A 519 PHE 0.019 0.001 PHE C 168 TYR 0.018 0.001 TYR A1067 ARG 0.008 0.000 ARG C 646 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 187 time to evaluate : 3.430 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 116 SER cc_start: 0.7938 (OUTLIER) cc_final: 0.7647 (t) REVERT: A 126 VAL cc_start: 0.8441 (t) cc_final: 0.8226 (t) REVERT: A 153 MET cc_start: 0.3098 (mpp) cc_final: -0.1082 (ttm) REVERT: A 195 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.7878 (ptmt) REVERT: A 433 VAL cc_start: 0.8266 (OUTLIER) cc_final: 0.7940 (m) REVERT: A 459 SER cc_start: 0.3726 (OUTLIER) cc_final: 0.3435 (t) REVERT: A 588 THR cc_start: 0.8953 (OUTLIER) cc_final: 0.8604 (m) REVERT: A 787 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8051 (mt0) REVERT: A 1050 MET cc_start: 0.8507 (ptm) cc_final: 0.8263 (ptm) REVERT: B 214 ARG cc_start: 0.2033 (OUTLIER) cc_final: 0.1135 (mpt90) REVERT: B 473 TYR cc_start: 0.1367 (OUTLIER) cc_final: 0.0997 (m-80) REVERT: B 569 ILE cc_start: 0.5037 (OUTLIER) cc_final: 0.4812 (mm) REVERT: C 314 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7967 (tp40) REVERT: C 514 SER cc_start: 0.5918 (OUTLIER) cc_final: 0.5319 (t) REVERT: C 529 LYS cc_start: 0.6762 (OUTLIER) cc_final: 0.6344 (mmtm) REVERT: C 569 ILE cc_start: 0.8479 (mp) cc_final: 0.8228 (mp) REVERT: C 582 LEU cc_start: 0.8151 (mt) cc_final: 0.7905 (mp) REVERT: C 787 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7929 (mm-40) REVERT: C 854 LYS cc_start: 0.6206 (OUTLIER) cc_final: 0.5900 (pmtt) REVERT: H 34 MET cc_start: 0.3782 (mmt) cc_final: 0.3520 (mmt) REVERT: H 200 GLN cc_start: 0.2963 (OUTLIER) cc_final: 0.2377 (pp30) REVERT: K 4 MET cc_start: 0.0903 (mpp) cc_final: -0.0268 (ptp) REVERT: K 90 GLN cc_start: 0.4668 (OUTLIER) cc_final: 0.4173 (tt0) REVERT: J 101 LYS cc_start: 0.2750 (ptpt) cc_final: 0.1714 (tppt) REVERT: J 125 LYS cc_start: 0.3653 (tppt) cc_final: 0.3118 (mttm) REVERT: J 209 LYS cc_start: 0.1963 (mmpt) cc_final: 0.1560 (mtmt) REVERT: J 214 LYS cc_start: 0.3739 (tppt) cc_final: 0.3428 (mtmt) REVERT: J 220 GLU cc_start: 0.2043 (OUTLIER) cc_final: 0.1076 (tp30) REVERT: J 222 LYS cc_start: 0.2592 (mttp) cc_final: 0.0810 (mptm) REVERT: N 49 TYR cc_start: 0.4141 (OUTLIER) cc_final: 0.3618 (p90) outliers start: 171 outliers final: 93 residues processed: 343 average time/residue: 1.0462 time to fit residues: 451.6691 Evaluate side-chains 279 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 168 time to evaluate : 3.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 200 GLN Chi-restraints excluded: chain H residue 205 ASN Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 177 SER Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain J residue 220 GLU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 111 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 211 optimal weight: 9.9990 chunk 271 optimal weight: 2.9990 chunk 210 optimal weight: 9.9990 chunk 312 optimal weight: 7.9990 chunk 207 optimal weight: 1.9990 chunk 370 optimal weight: 20.0000 chunk 231 optimal weight: 9.9990 chunk 225 optimal weight: 9.9990 chunk 170 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 188 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN A1142 GLN B 81 ASN B 207 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 703 ASN B 755 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN K 24 GLN ** K 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 167 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.114 31681 Z= 0.490 Angle : 0.812 16.266 43082 Z= 0.399 Chirality : 0.057 1.045 5103 Planarity : 0.005 0.069 5470 Dihedral : 8.037 59.932 5634 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.97 % Favored : 91.87 % Rotamer: Outliers : 5.98 % Allowed : 22.75 % Favored : 71.27 % 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: -1.31 (0.13), residues: 3800 helix: 0.69 (0.20), residues: 692 sheet: -0.10 (0.15), residues: 1096 loop : -1.95 (0.13), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 104 HIS 0.006 0.002 HIS A1064 PHE 0.023 0.003 PHE B 43 TYR 0.027 0.002 TYR C1067 ARG 0.006 0.001 ARG C 646 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 180 time to evaluate : 3.651 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 117 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7236 (tt) REVERT: A 153 MET cc_start: 0.3672 (mpp) cc_final: 0.0381 (ttm) REVERT: A 239 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7241 (tm-30) REVERT: A 433 VAL cc_start: 0.8506 (OUTLIER) cc_final: 0.8073 (m) REVERT: A 459 SER cc_start: 0.3922 (OUTLIER) cc_final: 0.3413 (t) REVERT: A 517 LEU cc_start: 0.5878 (OUTLIER) cc_final: 0.5644 (mm) REVERT: A 726 ILE cc_start: 0.9437 (OUTLIER) cc_final: 0.9197 (mt) REVERT: A 787 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8151 (mt0) REVERT: A 856 ASN cc_start: 0.8780 (OUTLIER) cc_final: 0.8521 (p0) REVERT: B 214 ARG cc_start: 0.2212 (OUTLIER) cc_final: 0.0946 (mpt180) REVERT: B 389 ASP cc_start: 0.7378 (m-30) cc_final: 0.7142 (m-30) REVERT: B 569 ILE cc_start: 0.5134 (OUTLIER) cc_final: 0.4927 (mm) REVERT: C 34 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.7175 (mmp-170) REVERT: C 133 PHE cc_start: 0.4478 (m-80) cc_final: 0.4039 (t80) REVERT: C 314 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8046 (tp40) REVERT: C 529 LYS cc_start: 0.6814 (OUTLIER) cc_final: 0.6372 (mmtm) REVERT: C 569 ILE cc_start: 0.8538 (mp) cc_final: 0.8300 (mp) REVERT: C 856 ASN cc_start: 0.7693 (OUTLIER) cc_final: 0.7432 (p0) REVERT: H 1 GLU cc_start: 0.2249 (OUTLIER) cc_final: 0.1779 (pm20) REVERT: H 34 MET cc_start: 0.3561 (mmt) cc_final: 0.3219 (mmt) REVERT: H 200 GLN cc_start: 0.3032 (OUTLIER) cc_final: 0.2479 (pp30) REVERT: K 4 MET cc_start: 0.0768 (mpp) cc_final: 0.0201 (ptp) REVERT: K 90 GLN cc_start: 0.4899 (OUTLIER) cc_final: 0.4090 (tt0) REVERT: J 101 LYS cc_start: 0.2762 (ptpt) cc_final: 0.1614 (tppt) REVERT: J 125 LYS cc_start: 0.3635 (tppt) cc_final: 0.3117 (mttm) REVERT: J 197 LEU cc_start: 0.0320 (OUTLIER) cc_final: -0.0004 (mt) REVERT: J 209 LYS cc_start: 0.1902 (mmpt) cc_final: 0.1602 (mtmt) REVERT: J 214 LYS cc_start: 0.3961 (tppt) cc_final: 0.3647 (mtmt) REVERT: J 222 LYS cc_start: 0.2376 (mttp) cc_final: 0.0720 (mptm) REVERT: N 49 TYR cc_start: 0.4238 (OUTLIER) cc_final: 0.3736 (p90) outliers start: 202 outliers final: 113 residues processed: 360 average time/residue: 0.9480 time to fit residues: 435.9755 Evaluate side-chains 286 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 154 time to evaluate : 3.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 1 GLU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain H residue 168 THR Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 200 GLN Chi-restraints excluded: chain H residue 205 ASN Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 177 SER Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 140 SER Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 204 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 8.9990 chunk 147 optimal weight: 0.9990 chunk 221 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 72 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 chunk 235 optimal weight: 5.9990 chunk 252 optimal weight: 3.9990 chunk 182 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 290 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 196 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1125 ASN A1142 GLN B 81 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN N 6 GLN ** N 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31681 Z= 0.171 Angle : 0.650 12.654 43082 Z= 0.317 Chirality : 0.048 0.807 5103 Planarity : 0.004 0.070 5470 Dihedral : 7.342 59.746 5634 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.11 % Favored : 93.74 % Rotamer: Outliers : 3.61 % Allowed : 25.59 % Favored : 70.79 % 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: -0.96 (0.13), residues: 3800 helix: 1.30 (0.20), residues: 682 sheet: 0.11 (0.15), residues: 1086 loop : -1.83 (0.13), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.014 0.001 HIS N 199 PHE 0.015 0.001 PHE C 168 TYR 0.017 0.001 TYR K 49 ARG 0.009 0.000 ARG C 646 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 177 time to evaluate : 3.465 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 117 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7316 (tt) REVERT: A 126 VAL cc_start: 0.8323 (t) cc_final: 0.8098 (t) REVERT: A 153 MET cc_start: 0.3540 (mpp) cc_final: 0.0284 (ttm) REVERT: A 433 VAL cc_start: 0.8423 (OUTLIER) cc_final: 0.8051 (m) REVERT: A 459 SER cc_start: 0.4035 (OUTLIER) cc_final: 0.3665 (t) REVERT: A 588 THR cc_start: 0.8954 (OUTLIER) cc_final: 0.8614 (m) REVERT: A 787 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8097 (mt0) REVERT: A 856 ASN cc_start: 0.8647 (OUTLIER) cc_final: 0.8375 (p0) REVERT: B 214 ARG cc_start: 0.1660 (OUTLIER) cc_final: 0.0611 (mpt90) REVERT: B 335 LEU cc_start: 0.6546 (mp) cc_final: 0.6289 (mt) REVERT: B 389 ASP cc_start: 0.7277 (m-30) cc_final: 0.7071 (m-30) REVERT: B 396 TYR cc_start: 0.6888 (m-10) cc_final: 0.6665 (m-10) REVERT: C 133 PHE cc_start: 0.4603 (m-80) cc_final: 0.4088 (t80) REVERT: C 514 SER cc_start: 0.5903 (OUTLIER) cc_final: 0.5394 (t) REVERT: C 529 LYS cc_start: 0.6766 (OUTLIER) cc_final: 0.6174 (mmtm) REVERT: C 569 ILE cc_start: 0.8449 (mp) cc_final: 0.8197 (mp) REVERT: H 34 MET cc_start: 0.3453 (mmt) cc_final: 0.3133 (mmt) REVERT: H 200 GLN cc_start: 0.2912 (OUTLIER) cc_final: 0.2413 (pp30) REVERT: K 4 MET cc_start: 0.0937 (mpp) cc_final: 0.0198 (ptp) REVERT: K 90 GLN cc_start: 0.4579 (OUTLIER) cc_final: 0.4187 (tt0) REVERT: J 6 GLU cc_start: 0.2764 (OUTLIER) cc_final: 0.2249 (pm20) REVERT: J 197 LEU cc_start: 0.0170 (OUTLIER) cc_final: -0.0173 (mt) REVERT: J 209 LYS cc_start: 0.1852 (mmpt) cc_final: 0.1518 (mtmt) REVERT: J 214 LYS cc_start: 0.3787 (tppt) cc_final: 0.3555 (mtmt) REVERT: N 27 GLN cc_start: 0.3444 (pp30) cc_final: 0.2205 (pm20) REVERT: N 49 TYR cc_start: 0.4187 (OUTLIER) cc_final: 0.3768 (p90) outliers start: 122 outliers final: 73 residues processed: 286 average time/residue: 0.9568 time to fit residues: 350.0586 Evaluate side-chains 244 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 157 time to evaluate : 3.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 168 THR Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 200 GLN Chi-restraints excluded: chain H residue 205 ASN Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain J residue 6 GLU Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 204 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 0.9980 chunk 354 optimal weight: 50.0000 chunk 323 optimal weight: 20.0000 chunk 344 optimal weight: 30.0000 chunk 207 optimal weight: 8.9990 chunk 150 optimal weight: 5.9990 chunk 270 optimal weight: 0.9980 chunk 105 optimal weight: 10.0000 chunk 311 optimal weight: 0.0070 chunk 326 optimal weight: 40.0000 chunk 343 optimal weight: 0.5980 overall best weight: 1.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 388 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN B 81 ASN B 87 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN C 81 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 GLN J 179 GLN N 6 GLN ** N 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.4767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31681 Z= 0.217 Angle : 0.660 12.665 43082 Z= 0.323 Chirality : 0.048 0.677 5103 Planarity : 0.004 0.064 5470 Dihedral : 7.171 59.857 5630 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.08 % Favored : 92.76 % Rotamer: Outliers : 3.29 % Allowed : 25.95 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.13), residues: 3800 helix: 1.38 (0.20), residues: 684 sheet: 0.09 (0.15), residues: 1104 loop : -1.78 (0.13), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.005 0.001 HIS N 199 PHE 0.018 0.001 PHE C 400 TYR 0.021 0.001 TYR C1067 ARG 0.009 0.000 ARG C 646 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 160 time to evaluate : 3.685 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 126 VAL cc_start: 0.8342 (t) cc_final: 0.8123 (t) REVERT: A 153 MET cc_start: 0.3647 (mpp) cc_final: 0.0390 (ttm) REVERT: A 433 VAL cc_start: 0.8433 (OUTLIER) cc_final: 0.8051 (m) REVERT: A 459 SER cc_start: 0.4109 (OUTLIER) cc_final: 0.3710 (t) REVERT: A 588 THR cc_start: 0.9004 (OUTLIER) cc_final: 0.8656 (m) REVERT: A 787 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.8075 (mt0) REVERT: A 856 ASN cc_start: 0.8675 (OUTLIER) cc_final: 0.8424 (p0) REVERT: B 214 ARG cc_start: 0.1630 (OUTLIER) cc_final: 0.0432 (mpt90) REVERT: B 335 LEU cc_start: 0.6487 (mp) cc_final: 0.6229 (mt) REVERT: B 389 ASP cc_start: 0.7324 (m-30) cc_final: 0.7110 (m-30) REVERT: B 396 TYR cc_start: 0.6874 (m-10) cc_final: 0.6574 (m-10) REVERT: C 133 PHE cc_start: 0.4526 (m-80) cc_final: 0.4181 (m-80) REVERT: C 514 SER cc_start: 0.5845 (OUTLIER) cc_final: 0.5253 (t) REVERT: C 529 LYS cc_start: 0.6766 (OUTLIER) cc_final: 0.6338 (mmtm) REVERT: C 569 ILE cc_start: 0.8466 (mp) cc_final: 0.8211 (mp) REVERT: C 787 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7770 (mm-40) REVERT: H 34 MET cc_start: 0.3354 (mmt) cc_final: 0.3070 (mmt) REVERT: H 200 GLN cc_start: 0.2904 (OUTLIER) cc_final: 0.2387 (pp30) REVERT: K 4 MET cc_start: 0.0924 (mpp) cc_final: 0.0352 (ptp) REVERT: K 90 GLN cc_start: 0.4615 (OUTLIER) cc_final: 0.4276 (tt0) REVERT: J 6 GLU cc_start: 0.2922 (OUTLIER) cc_final: 0.2471 (pm20) REVERT: J 197 LEU cc_start: 0.0206 (OUTLIER) cc_final: -0.0133 (mt) REVERT: J 209 LYS cc_start: 0.1805 (mmpt) cc_final: 0.1538 (mtmt) REVERT: N 27 GLN cc_start: 0.3377 (pp30) cc_final: 0.2105 (pm20) REVERT: N 49 TYR cc_start: 0.3908 (OUTLIER) cc_final: 0.3507 (p90) outliers start: 111 outliers final: 80 residues processed: 263 average time/residue: 0.9446 time to fit residues: 320.1277 Evaluate side-chains 250 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 156 time to evaluate : 3.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 168 THR Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 200 GLN Chi-restraints excluded: chain H residue 205 ASN Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain J residue 6 GLU Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 204 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 5.9990 chunk 364 optimal weight: 0.9990 chunk 222 optimal weight: 10.0000 chunk 173 optimal weight: 0.6980 chunk 253 optimal weight: 0.7980 chunk 382 optimal weight: 9.9990 chunk 352 optimal weight: 1.9990 chunk 304 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 235 optimal weight: 1.9990 chunk 186 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 196 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1125 ASN A1142 GLN B 81 ASN B 87 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN C 81 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN K 24 GLN J 179 GLN ** N 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31681 Z= 0.186 Angle : 0.644 11.992 43082 Z= 0.313 Chirality : 0.048 0.751 5103 Planarity : 0.004 0.064 5470 Dihedral : 6.966 59.632 5630 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.66 % Favored : 93.18 % Rotamer: Outliers : 3.17 % Allowed : 26.04 % Favored : 70.79 % 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: 3800 helix: 1.50 (0.20), residues: 685 sheet: 0.20 (0.15), residues: 1088 loop : -1.71 (0.13), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.004 0.001 HIS N 199 PHE 0.021 0.001 PHE A 140 TYR 0.018 0.001 TYR A1067 ARG 0.011 0.000 ARG C 646 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 161 time to evaluate : 3.791 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 153 MET cc_start: 0.3427 (mpp) cc_final: -0.0043 (ttm) REVERT: A 433 VAL cc_start: 0.8397 (OUTLIER) cc_final: 0.8032 (m) REVERT: A 459 SER cc_start: 0.3978 (OUTLIER) cc_final: 0.3591 (t) REVERT: A 588 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8664 (m) REVERT: A 787 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8063 (mt0) REVERT: A 856 ASN cc_start: 0.8668 (OUTLIER) cc_final: 0.8402 (p0) REVERT: B 214 ARG cc_start: 0.1480 (OUTLIER) cc_final: 0.0329 (mpt90) REVERT: B 335 LEU cc_start: 0.6268 (mp) cc_final: 0.6047 (mt) REVERT: B 355 ARG cc_start: 0.6848 (ptm-80) cc_final: 0.6580 (ptp-110) REVERT: B 389 ASP cc_start: 0.7261 (m-30) cc_final: 0.7060 (m-30) REVERT: B 396 TYR cc_start: 0.6877 (m-10) cc_final: 0.6534 (m-10) REVERT: C 133 PHE cc_start: 0.4521 (m-80) cc_final: 0.4174 (m-80) REVERT: C 514 SER cc_start: 0.5838 (OUTLIER) cc_final: 0.5315 (t) REVERT: C 529 LYS cc_start: 0.6753 (OUTLIER) cc_final: 0.6328 (mmtm) REVERT: C 569 ILE cc_start: 0.8468 (mp) cc_final: 0.8213 (mp) REVERT: C 787 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.7860 (mm-40) REVERT: H 34 MET cc_start: 0.3363 (mmt) cc_final: 0.3070 (mmt) REVERT: H 200 GLN cc_start: 0.2739 (OUTLIER) cc_final: 0.2245 (pp30) REVERT: H 205 ASN cc_start: 0.2618 (OUTLIER) cc_final: 0.0951 (t0) REVERT: K 4 MET cc_start: 0.0671 (mpp) cc_final: -0.0054 (ptp) REVERT: K 90 GLN cc_start: 0.4572 (OUTLIER) cc_final: 0.4260 (tt0) REVERT: J 6 GLU cc_start: 0.2961 (OUTLIER) cc_final: 0.2508 (pm20) REVERT: J 197 LEU cc_start: 0.0175 (OUTLIER) cc_final: -0.0169 (mt) REVERT: J 209 LYS cc_start: 0.1920 (mmpt) cc_final: 0.1661 (mtmt) REVERT: N 27 GLN cc_start: 0.3345 (pp30) cc_final: 0.2089 (pm20) REVERT: N 49 TYR cc_start: 0.3774 (OUTLIER) cc_final: 0.3387 (p90) outliers start: 107 outliers final: 75 residues processed: 260 average time/residue: 0.9566 time to fit residues: 321.6104 Evaluate side-chains 244 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 154 time to evaluate : 3.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 168 THR Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 200 GLN Chi-restraints excluded: chain H residue 205 ASN Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain J residue 6 GLU Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 204 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 9.9990 chunk 324 optimal weight: 20.0000 chunk 93 optimal weight: 0.9990 chunk 280 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 84 optimal weight: 0.0970 chunk 305 optimal weight: 20.0000 chunk 127 optimal weight: 5.9990 chunk 313 optimal weight: 8.9990 chunk 38 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 207 HIS ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN B 81 ASN B 87 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 GLN J 113 GLN J 179 GLN ** N 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.192862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.141667 restraints weight = 47059.621| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.68 r_work: 0.3201 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.391 31681 Z= 0.270 Angle : 0.746 59.195 43082 Z= 0.392 Chirality : 0.049 0.804 5103 Planarity : 0.004 0.069 5470 Dihedral : 6.939 59.616 5627 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.79 % Favored : 93.08 % Rotamer: Outliers : 3.32 % Allowed : 25.80 % Favored : 70.88 % Cbeta Deviations : 0.03 % 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: 3800 helix: 1.50 (0.20), residues: 685 sheet: 0.20 (0.15), residues: 1088 loop : -1.71 (0.13), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.004 0.001 HIS N 199 PHE 0.021 0.001 PHE A 140 TYR 0.018 0.001 TYR A1067 ARG 0.010 0.000 ARG C 646 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8970.92 seconds wall clock time: 161 minutes 53.03 seconds (9713.03 seconds total)