Starting phenix.real_space_refine on Wed Feb 21 14:07:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czr_30514/02_2024/7czr_30514.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czr_30514/02_2024/7czr_30514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czr_30514/02_2024/7czr_30514.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czr_30514/02_2024/7czr_30514.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czr_30514/02_2024/7czr_30514.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czr_30514/02_2024/7czr_30514.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 129 5.16 5 C 19603 2.51 5 N 5046 2.21 5 O 6108 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 ARG 19": "NH1" <-> "NH2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H ARG 97": "NH1" <-> "NH2" Residue "H GLU 98": "OE1" <-> "OE2" Residue "K GLU 81": "OE1" <-> "OE2" Residue "K GLU 165": "OE1" <-> "OE2" Residue "K PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 19": "NH1" <-> "NH2" Residue "J GLU 46": "OE1" <-> "OE2" Residue "J ARG 97": "NH1" <-> "NH2" Residue "J GLU 98": "OE1" <-> "OE2" Residue "N GLU 81": "OE1" <-> "OE2" Residue "N GLU 165": "OE1" <-> "OE2" Residue "N PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 30886 Number of models: 1 Model: "" Number of chains: 30 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: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1614 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain: "K" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1633 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 12, 'TRANS': 201} Chain: "J" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1614 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain: "N" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1633 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 12, 'TRANS': 201} 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: "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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 16.18, per 1000 atoms: 0.52 Number of scatterers: 30886 At special positions: 0 Unit cell: (134.788, 171.746, 236.966, 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 129 16.00 O 6108 8.00 N 5046 7.00 C 19603 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, 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=2.10 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=2.29 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=2.04 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=2.04 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=2.06 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=2.29 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=2.04 Simple disulfide: pdb=" SG CYS H 142 " - pdb=" SG CYS H 198 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 134 " - pdb=" SG CYS K 194 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 95 " distance=2.04 Simple disulfide: pdb=" SG CYS J 142 " - pdb=" SG CYS J 198 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 134 " - pdb=" SG CYS N 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B1410 " - " NAG B1411 " " NAG C1406 " - " NAG C1407 " " 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-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 331 " " NAG C1408 " - " ASN C 603 " " NAG C1409 " - " ASN C 616 " " NAG C1410 " - " 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 343 " " NAG V 1 " - " ASN C 709 " " NAG W 1 " - " ASN C 717 " " NAG X 1 " - " ASN C 801 " " NAG Y 1 " - " ASN C1074 " " NAG Z 1 " - " ASN C1098 " " NAG a 1 " - " ASN C1134 " Time building additional restraints: 11.72 Conformation dependent library (CDL) restraints added in 5.3 seconds 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7200 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 62 sheets defined 19.7% alpha, 30.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.58 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.073A 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: 3.686A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.623A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.738A 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: 3.651A 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: 3.646A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.574A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.994A 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: 3.694A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.878A 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: 4.632A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.647A 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: 3.647A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.641A 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: 3.965A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.543A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.602A 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: 3.605A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.371A 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: 3.674A 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: 4.073A 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: 3.686A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.623A 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: 3.717A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.561A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.604A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.635A 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: 3.591A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.713A 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: 3.553A 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: 3.603A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.535A 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 28 through 32 removed outlier: 4.238A pdb=" N ASN H 32 " --> pdb=" O VAL H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 189 through 191 No H-bonds generated for 'chain 'H' and resid 189 through 191' Processing helix chain 'K' and resid 121 through 128 Processing helix chain 'K' and resid 183 through 187 Processing helix chain 'J' and resid 28 through 32 removed outlier: 4.237A pdb=" N ASN J 32 " --> pdb=" O VAL J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 189 through 191 No H-bonds generated for 'chain 'J' and resid 189 through 191' Processing helix chain 'N' and resid 121 through 128 Processing helix chain 'N' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.438A 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: 3.857A 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: 7.475A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.046A 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: 6.678A pdb=" N GLU A 309 " --> pdb=" O GLY A 601 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N GLY A 601 " --> pdb=" O GLU A 309 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 7.013A 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: 5.863A 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: 6.445A 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: 6.257A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.418A 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: 6.607A 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: 3.529A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.969A 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: 6.607A 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: 3.978A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.728A 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: 8.539A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.887A 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: 3.649A 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: 6.715A 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: 3.537A 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: 5.776A 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: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.525A 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: 6.167A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.525A 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: 3.799A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.578A 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: 3.578A 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: 7.063A 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: 4.247A 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: 5.666A 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: 3.708A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.497A 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: 5.863A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.783A 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: 6.230A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.534A 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: 6.592A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.690A 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: 6.146A 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: 5.891A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.592A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.690A 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: 6.146A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.569A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE9, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AF1, first strand: chain 'H' and resid 45 through 51 removed outlier: 6.529A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR H 33 " --> pdb=" O GLU H 98 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 123 through 126 removed outlier: 5.010A pdb=" N ALA H 139 " --> pdb=" O VAL H 186 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL H 186 " --> pdb=" O ALA H 139 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY H 141 " --> pdb=" O VAL H 184 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL H 184 " --> pdb=" O GLY H 141 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU H 143 " --> pdb=" O SER H 182 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER H 182 " --> pdb=" O LEU H 143 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS H 145 " --> pdb=" O LEU H 180 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU H 180 " --> pdb=" O LYS H 145 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 123 through 126 removed outlier: 5.010A pdb=" N ALA H 139 " --> pdb=" O VAL H 186 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL H 186 " --> pdb=" O ALA H 139 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY H 141 " --> pdb=" O VAL H 184 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL H 184 " --> pdb=" O GLY H 141 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU H 143 " --> pdb=" O SER H 182 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER H 182 " --> pdb=" O LEU H 143 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS H 145 " --> pdb=" O LEU H 180 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU H 180 " --> pdb=" O LYS H 145 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 152 through 156 Processing sheet with id=AF5, first strand: chain 'K' and resid 11 through 13 removed outlier: 6.527A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR K 87 " --> pdb=" O TYR K 36 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 18 through 23 Processing sheet with id=AF7, first strand: chain 'K' and resid 114 through 118 Processing sheet with id=AF8, first strand: chain 'K' and resid 153 through 154 Processing sheet with id=AF9, first strand: chain 'J' and resid 5 through 7 Processing sheet with id=AG1, first strand: chain 'J' and resid 45 through 51 removed outlier: 6.531A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N MET J 34 " --> pdb=" O VAL J 50 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR J 33 " --> pdb=" O GLU J 98 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 123 through 126 removed outlier: 5.010A pdb=" N ALA J 139 " --> pdb=" O VAL J 186 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL J 186 " --> pdb=" O ALA J 139 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY J 141 " --> pdb=" O VAL J 184 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL J 184 " --> pdb=" O GLY J 141 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU J 143 " --> pdb=" O SER J 182 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER J 182 " --> pdb=" O LEU J 143 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS J 145 " --> pdb=" O LEU J 180 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU J 180 " --> pdb=" O LYS J 145 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 123 through 126 removed outlier: 5.010A pdb=" N ALA J 139 " --> pdb=" O VAL J 186 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL J 186 " --> pdb=" O ALA J 139 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY J 141 " --> pdb=" O VAL J 184 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL J 184 " --> pdb=" O GLY J 141 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU J 143 " --> pdb=" O SER J 182 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER J 182 " --> pdb=" O LEU J 143 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS J 145 " --> pdb=" O LEU J 180 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU J 180 " --> pdb=" O LYS J 145 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 152 through 156 Processing sheet with id=AG5, first strand: chain 'N' and resid 11 through 13 removed outlier: 6.526A pdb=" N LEU N 11 " --> pdb=" O GLU N 105 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR N 87 " --> pdb=" O TYR N 36 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 18 through 23 Processing sheet with id=AG7, first strand: chain 'N' and resid 114 through 118 Processing sheet with id=AG8, first strand: chain 'N' and resid 153 through 154 1125 hydrogen bonds defined for protein. 3045 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.80 Time building geometry restraints manager: 12.74 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: 9628 1.34 - 1.46: 8206 1.46 - 1.59: 13559 1.59 - 1.72: 0 1.72 - 1.85: 160 Bond restraints: 31553 Sorted by residual: bond pdb=" N PRO C 479 " pdb=" CD PRO C 479 " ideal model delta sigma weight residual 1.473 1.534 -0.061 1.40e-02 5.10e+03 1.91e+01 bond pdb=" N PRO K 141 " pdb=" CD PRO K 141 " ideal model delta sigma weight residual 1.473 1.534 -0.061 1.40e-02 5.10e+03 1.88e+01 bond pdb=" N PRO H 14 " pdb=" CD PRO H 14 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.86e+01 bond pdb=" N PRO C 330 " pdb=" CD PRO C 330 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.86e+01 bond pdb=" N PRO A 479 " pdb=" CD PRO A 479 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.83e+01 ... (remaining 31548 not shown) Histogram of bond angle deviations from ideal: 97.53 - 105.72: 656 105.72 - 113.91: 18337 113.91 - 122.10: 17909 122.10 - 130.29: 5905 130.29 - 138.49: 105 Bond angle restraints: 42912 Sorted by residual: angle pdb=" N THR J 28 " pdb=" CA THR J 28 " pdb=" C THR J 28 " ideal model delta sigma weight residual 111.24 121.58 -10.34 1.38e+00 5.25e-01 5.62e+01 angle pdb=" N THR H 28 " pdb=" CA THR H 28 " pdb=" C THR H 28 " ideal model delta sigma weight residual 111.24 121.58 -10.34 1.38e+00 5.25e-01 5.61e+01 angle pdb=" C PHE A 86 " pdb=" N ASN A 87 " pdb=" CA ASN A 87 " ideal model delta sigma weight residual 121.54 132.78 -11.24 1.91e+00 2.74e-01 3.46e+01 angle pdb=" N GLU C 156 " pdb=" CA GLU C 156 " pdb=" C GLU C 156 " ideal model delta sigma weight residual 108.45 115.83 -7.38 1.26e+00 6.30e-01 3.43e+01 angle pdb=" C THR C 588 " pdb=" N PRO C 589 " pdb=" CA PRO C 589 " ideal model delta sigma weight residual 119.78 114.03 5.75 1.03e+00 9.43e-01 3.11e+01 ... (remaining 42907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 16996 17.91 - 35.82: 1938 35.82 - 53.73: 553 53.73 - 71.63: 194 71.63 - 89.54: 57 Dihedral angle restraints: 19738 sinusoidal: 8547 harmonic: 11191 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 12.16 80.84 1 1.00e+01 1.00e-02 8.07e+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 19.60 73.40 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 21.14 71.86 1 1.00e+01 1.00e-02 6.61e+01 ... (remaining 19735 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.328: 5077 0.328 - 0.657: 5 0.657 - 0.985: 4 0.985 - 1.313: 0 1.313 - 1.641: 1 Chirality restraints: 5087 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 1.14e+03 chirality pdb=" C1 NAG a 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.76 -1.64 2.00e-01 2.50e+01 6.74e+01 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.63 -0.77 2.00e-01 2.50e+01 1.48e+01 ... (remaining 5084 not shown) Planarity restraints: 5492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1407 " -0.239 2.00e-02 2.50e+03 1.99e-01 4.93e+02 pdb=" C7 NAG C1407 " 0.064 2.00e-02 2.50e+03 pdb=" C8 NAG C1407 " -0.167 2.00e-02 2.50e+03 pdb=" N2 NAG C1407 " 0.329 2.00e-02 2.50e+03 pdb=" O7 NAG C1407 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1406 " 0.230 2.00e-02 2.50e+03 1.91e-01 4.58e+02 pdb=" C7 NAG C1406 " -0.062 2.00e-02 2.50e+03 pdb=" C8 NAG C1406 " 0.162 2.00e-02 2.50e+03 pdb=" N2 NAG C1406 " -0.316 2.00e-02 2.50e+03 pdb=" O7 NAG C1406 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " -0.014 2.00e-02 2.50e+03 7.03e-02 6.18e+01 pdb=" CG ASN C 331 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " -0.054 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " 0.125 2.00e-02 2.50e+03 pdb=" C1 NAG C1406 " -0.075 2.00e-02 2.50e+03 ... (remaining 5489 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 384 2.56 - 3.15: 24487 3.15 - 3.73: 44951 3.73 - 4.32: 65942 4.32 - 4.90: 109321 Nonbonded interactions: 245085 Sorted by model distance: nonbonded pdb=" NH1 ARG A 346 " pdb=" O PHE A 347 " model vdw 1.981 2.520 nonbonded pdb=" NH1 ARG C 346 " pdb=" O PHE C 347 " model vdw 1.982 2.520 nonbonded pdb=" O ALA C 522 " pdb=" OG1 THR C 523 " model vdw 1.986 2.440 nonbonded pdb=" O ASN K 137 " pdb=" O ASN K 138 " model vdw 2.039 3.040 nonbonded pdb=" O ASN N 137 " pdb=" O ASN N 138 " model vdw 2.039 3.040 ... (remaining 245080 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 1409)) selection = (chain 'B' and (resid 27 through 620 or resid 641 through 826 or resid 855 throu \ gh 1146 or resid 1401 through 1409)) 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 \ 1409)) } 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' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.020 Check model and map are aligned: 0.440 Set scattering table: 0.280 Process input model: 79.800 Find NCS groups from input model: 2.470 Set up NCS constraints: 0.410 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 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 0.119 31553 Z= 0.712 Angle : 1.039 13.485 42912 Z= 0.592 Chirality : 0.070 1.641 5087 Planarity : 0.007 0.199 5444 Dihedral : 17.536 89.542 12400 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 21.59 Ramachandran Plot: Outliers : 1.77 % Allowed : 10.38 % Favored : 87.85 % Rotamer: Outliers : 11.95 % Allowed : 18.21 % Favored : 69.85 % 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: -3.83 (0.11), residues: 3786 helix: -2.15 (0.16), residues: 661 sheet: -1.72 (0.14), residues: 1057 loop : -3.24 (0.11), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 104 HIS 0.009 0.002 HIS A1048 PHE 0.025 0.003 PHE A 898 TYR 0.026 0.003 TYR B1067 ARG 0.011 0.001 ARG J 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 921 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 401 poor density : 520 time to evaluate : 3.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.3712 (OUTLIER) cc_final: 0.3408 (mtm-85) REVERT: A 231 ILE cc_start: 0.6831 (OUTLIER) cc_final: 0.6626 (mt) REVERT: A 529 LYS cc_start: 0.6263 (OUTLIER) cc_final: 0.5862 (mmtm) REVERT: A 902 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.8033 (mmt) REVERT: A 1004 LEU cc_start: 0.9051 (tp) cc_final: 0.8818 (tp) REVERT: A 1039 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8700 (mtp180) REVERT: A 1100 THR cc_start: 0.8014 (OUTLIER) cc_final: 0.7681 (m) REVERT: B 417 LYS cc_start: 0.4144 (OUTLIER) cc_final: 0.3131 (mptt) REVERT: B 473 TYR cc_start: 0.3257 (OUTLIER) cc_final: 0.2375 (m-80) REVERT: B 569 ILE cc_start: 0.3698 (OUTLIER) cc_final: 0.3366 (mm) REVERT: C 280 ASN cc_start: 0.6588 (t0) cc_final: 0.6376 (t0) REVERT: C 555 SER cc_start: 0.7022 (OUTLIER) cc_final: 0.6036 (t) REVERT: C 955 ASN cc_start: 0.7496 (m-40) cc_final: 0.7274 (m-40) REVERT: C 979 ASP cc_start: 0.7401 (m-30) cc_final: 0.7158 (m-30) REVERT: K 35 TRP cc_start: 0.3626 (m100) cc_final: 0.3182 (m100) REVERT: J 143 LEU cc_start: 0.3574 (tt) cc_final: 0.3314 (mt) REVERT: J 144 VAL cc_start: -0.2418 (OUTLIER) cc_final: -0.2747 (p) REVERT: J 197 ILE cc_start: -0.0734 (OUTLIER) cc_final: -0.1055 (pt) REVERT: N 45 LYS cc_start: 0.2077 (ptmt) cc_final: 0.1728 (mmtt) REVERT: N 63 SER cc_start: 0.1619 (OUTLIER) cc_final: 0.1289 (t) REVERT: N 103 LYS cc_start: 0.1898 (tmtt) cc_final: 0.1000 (mttp) REVERT: N 107 LYS cc_start: 0.2283 (OUTLIER) cc_final: 0.1419 (pttt) outliers start: 401 outliers final: 90 residues processed: 856 average time/residue: 0.4090 time to fit residues: 559.8197 Evaluate side-chains 334 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 230 time to evaluate : 3.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 494 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 640 SER Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 772 VAL 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 976 VAL Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 50 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 234 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 197 ILE Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 62 PHE Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 107 LYS Chi-restraints excluded: chain K residue 108 ARG Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 105 TRP Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 197 ILE Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain N residue 142 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 322 optimal weight: 8.9990 chunk 289 optimal weight: 9.9990 chunk 160 optimal weight: 3.9990 chunk 98 optimal weight: 0.1980 chunk 195 optimal weight: 4.9990 chunk 154 optimal weight: 0.6980 chunk 299 optimal weight: 20.0000 chunk 115 optimal weight: 6.9990 chunk 182 optimal weight: 3.9990 chunk 222 optimal weight: 30.0000 chunk 346 optimal weight: 7.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN A 422 ASN A 450 ASN A 487 ASN A 493 GLN A 498 GLN A 644 GLN A 658 ASN A 690 GLN A 703 ASN A 762 GLN A 787 GLN A 856 ASN A 901 GLN A 914 ASN A 919 ASN A 926 GLN A 992 GLN A1002 GLN A1010 GLN A1125 ASN B 115 GLN B 134 GLN B 188 ASN B 207 HIS ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN B 540 ASN B 563 GLN B 613 GLN B 762 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 914 ASN B 919 ASN B 920 GLN B 926 GLN B 992 GLN C 49 HIS C 87 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 134 GLN C 188 ASN ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN C 440 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN C 498 GLN C 606 ASN C 641 ASN C 690 GLN C 703 ASN C 751 ASN C 784 GLN C 901 GLN C 914 ASN C 926 GLN C 969 ASN C 992 GLN C1002 GLN C1005 GLN C1010 GLN C1071 GLN C1101 HIS C1106 GLN K 37 GLN K 55 GLN ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 173 GLN ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 31553 Z= 0.289 Angle : 0.793 11.134 42912 Z= 0.397 Chirality : 0.052 0.590 5087 Planarity : 0.005 0.065 5444 Dihedral : 9.800 59.855 5766 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.61 % Favored : 92.08 % Rotamer: Outliers : 6.64 % Allowed : 19.90 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.12), residues: 3786 helix: -0.19 (0.19), residues: 680 sheet: -0.96 (0.15), residues: 1048 loop : -2.69 (0.12), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP H 105 HIS 0.004 0.001 HIS B1058 PHE 0.029 0.002 PHE C 377 TYR 0.032 0.002 TYR A 200 ARG 0.005 0.001 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 247 time to evaluate : 3.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 TYR cc_start: 0.6502 (m-80) cc_final: 0.6261 (m-10) REVERT: A 436 TRP cc_start: 0.5696 (p-90) cc_final: 0.5402 (p-90) REVERT: A 529 LYS cc_start: 0.6154 (OUTLIER) cc_final: 0.5854 (mmtm) REVERT: A 608 VAL cc_start: 0.8851 (OUTLIER) cc_final: 0.8624 (m) REVERT: A 756 TYR cc_start: 0.8574 (m-80) cc_final: 0.8336 (m-80) REVERT: A 856 ASN cc_start: 0.8642 (OUTLIER) cc_final: 0.8404 (p0) REVERT: B 47 VAL cc_start: 0.8710 (OUTLIER) cc_final: 0.8445 (t) REVERT: B 214 ARG cc_start: 0.2514 (OUTLIER) cc_final: 0.2307 (mtp-110) REVERT: B 287 ASP cc_start: 0.7027 (OUTLIER) cc_final: 0.6774 (m-30) REVERT: B 359 SER cc_start: 0.4712 (OUTLIER) cc_final: 0.4361 (m) REVERT: B 569 ILE cc_start: 0.3792 (OUTLIER) cc_final: 0.3455 (mm) REVERT: B 750 SER cc_start: 0.8673 (t) cc_final: 0.8306 (p) REVERT: B 784 GLN cc_start: 0.8311 (mt0) cc_final: 0.8071 (mt0) REVERT: B 960 ASN cc_start: 0.8151 (t0) cc_final: 0.7941 (t0) REVERT: B 983 ARG cc_start: 0.6838 (mtm110) cc_final: 0.6539 (mtm180) REVERT: C 205 SER cc_start: 0.8508 (OUTLIER) cc_final: 0.8109 (t) REVERT: C 740 MET cc_start: 0.8143 (tpp) cc_final: 0.7901 (tpt) REVERT: C 955 ASN cc_start: 0.7635 (m-40) cc_final: 0.7339 (m110) REVERT: C 979 ASP cc_start: 0.7371 (m-30) cc_final: 0.7133 (m-30) REVERT: K 35 TRP cc_start: 0.3739 (m100) cc_final: 0.3382 (m100) REVERT: K 145 LYS cc_start: 0.1439 (mtpt) cc_final: -0.0087 (tttp) REVERT: K 190 LYS cc_start: 0.3576 (ttmt) cc_final: 0.3211 (tmtt) REVERT: N 5 THR cc_start: 0.0578 (OUTLIER) cc_final: 0.0349 (m) REVERT: N 107 LYS cc_start: 0.1516 (OUTLIER) cc_final: 0.0879 (pttp) outliers start: 223 outliers final: 108 residues processed: 446 average time/residue: 0.3645 time to fit residues: 271.8337 Evaluate side-chains 312 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 193 time to evaluate : 3.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 602 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 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 607 GLN Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 ASP 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 C residue 1145 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain K residue 39 LYS Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 107 LYS Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 116 PHE Chi-restraints excluded: chain J residue 27 PHE Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 181 SER Chi-restraints excluded: chain J residue 205 SER Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 107 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 192 optimal weight: 0.5980 chunk 107 optimal weight: 20.0000 chunk 288 optimal weight: 0.0040 chunk 236 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 347 optimal weight: 30.0000 chunk 375 optimal weight: 20.0000 chunk 309 optimal weight: 20.0000 chunk 344 optimal weight: 30.0000 chunk 118 optimal weight: 4.9990 chunk 278 optimal weight: 8.9990 overall best weight: 3.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 ASN A 493 GLN A 969 ASN A1011 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN C 87 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 321 GLN C 493 GLN C 542 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN H 3 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN K 92 ASN J 81 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 31553 Z= 0.304 Angle : 0.729 10.795 42912 Z= 0.362 Chirality : 0.050 0.700 5087 Planarity : 0.005 0.070 5444 Dihedral : 8.622 59.592 5652 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.03 % Favored : 91.79 % Rotamer: Outliers : 6.20 % Allowed : 20.83 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.13), residues: 3786 helix: 0.53 (0.20), residues: 673 sheet: -0.61 (0.15), residues: 1049 loop : -2.47 (0.12), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 105 HIS 0.005 0.001 HIS A 655 PHE 0.020 0.002 PHE B 86 TYR 0.023 0.002 TYR C 495 ARG 0.009 0.001 ARG K 108 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 191 time to evaluate : 3.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 856 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.8329 (p0) REVERT: A 1130 ILE cc_start: 0.8544 (pt) cc_final: 0.8318 (mt) REVERT: B 88 ASP cc_start: 0.6379 (t0) cc_final: 0.6061 (t0) REVERT: B 153 MET cc_start: 0.2576 (OUTLIER) cc_final: 0.0946 (mmm) REVERT: B 214 ARG cc_start: 0.2666 (OUTLIER) cc_final: 0.2399 (mtp-110) REVERT: B 287 ASP cc_start: 0.7279 (OUTLIER) cc_final: 0.7047 (m-30) REVERT: B 473 TYR cc_start: 0.3674 (OUTLIER) cc_final: 0.2651 (m-80) REVERT: B 569 ILE cc_start: 0.3748 (OUTLIER) cc_final: 0.3403 (mm) REVERT: B 746 SER cc_start: 0.7457 (OUTLIER) cc_final: 0.7250 (t) REVERT: B 750 SER cc_start: 0.8685 (t) cc_final: 0.8341 (p) REVERT: B 960 ASN cc_start: 0.8232 (t0) cc_final: 0.7866 (t0) REVERT: C 86 PHE cc_start: 0.4117 (OUTLIER) cc_final: 0.3367 (m-80) REVERT: C 281 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7199 (pm20) REVERT: C 740 MET cc_start: 0.8156 (tpp) cc_final: 0.7907 (tpt) REVERT: H 92 VAL cc_start: 0.3284 (OUTLIER) cc_final: 0.2995 (p) REVERT: H 102 PHE cc_start: -0.3223 (OUTLIER) cc_final: -0.3733 (m-80) REVERT: K 27 GLN cc_start: 0.4254 (tm-30) cc_final: 0.3940 (tt0) REVERT: K 35 TRP cc_start: 0.3832 (m100) cc_final: 0.3459 (m100) REVERT: K 190 LYS cc_start: 0.3615 (ttmt) cc_final: 0.3194 (tmtt) REVERT: N 5 THR cc_start: 0.0687 (OUTLIER) cc_final: 0.0454 (m) outliers start: 208 outliers final: 133 residues processed: 380 average time/residue: 0.4098 time to fit residues: 264.8554 Evaluate side-chains 313 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 168 time to evaluate : 3.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 302 THR 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 364 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 607 GLN Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 102 PHE Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain K residue 39 LYS Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 56 SER Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 27 PHE Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain J residue 102 PHE Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 181 SER Chi-restraints excluded: chain J residue 194 GLN Chi-restraints excluded: chain J residue 205 SER Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 91 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 343 optimal weight: 9.9990 chunk 261 optimal weight: 0.0170 chunk 180 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 chunk 165 optimal weight: 0.8980 chunk 233 optimal weight: 4.9990 chunk 348 optimal weight: 30.0000 chunk 369 optimal weight: 0.8980 chunk 182 optimal weight: 5.9990 chunk 330 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 overall best weight: 2.5622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 134 GLN A 188 ASN A 856 ASN A1106 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B 960 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN K 160 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 31553 Z= 0.245 Angle : 0.675 11.066 42912 Z= 0.333 Chirality : 0.050 0.794 5087 Planarity : 0.004 0.058 5444 Dihedral : 8.028 59.677 5634 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.08 % Favored : 92.74 % Rotamer: Outliers : 5.81 % Allowed : 21.63 % Favored : 72.56 % 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: -1.70 (0.13), residues: 3786 helix: 0.81 (0.21), residues: 680 sheet: -0.47 (0.15), residues: 1060 loop : -2.26 (0.12), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP J 105 HIS 0.004 0.001 HIS H 202 PHE 0.020 0.001 PHE H 27 TYR 0.019 0.001 TYR B1067 ARG 0.004 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 181 time to evaluate : 3.624 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: 0.0252 (mmt) cc_final: -0.0046 (mmt) REVERT: A 856 ASN cc_start: 0.8470 (OUTLIER) cc_final: 0.8140 (p0) REVERT: B 47 VAL cc_start: 0.8717 (OUTLIER) cc_final: 0.8402 (t) REVERT: B 88 ASP cc_start: 0.6249 (t0) cc_final: 0.5961 (t0) REVERT: B 97 LYS cc_start: 0.4731 (OUTLIER) cc_final: 0.4515 (ptmt) REVERT: B 153 MET cc_start: 0.3077 (OUTLIER) cc_final: 0.1311 (mmm) REVERT: B 359 SER cc_start: 0.4894 (OUTLIER) cc_final: 0.4632 (m) REVERT: B 459 SER cc_start: 0.1889 (OUTLIER) cc_final: 0.0875 (t) REVERT: B 473 TYR cc_start: 0.3666 (OUTLIER) cc_final: 0.2646 (m-80) REVERT: B 569 ILE cc_start: 0.3561 (OUTLIER) cc_final: 0.3234 (mm) REVERT: B 750 SER cc_start: 0.8685 (t) cc_final: 0.8363 (p) REVERT: B 960 ASN cc_start: 0.8164 (t0) cc_final: 0.7780 (t0) REVERT: B 1029 MET cc_start: 0.8921 (tpp) cc_final: 0.8443 (ttm) REVERT: C 303 LEU cc_start: 0.8862 (mt) cc_final: 0.8653 (mt) REVERT: H 102 PHE cc_start: -0.3254 (OUTLIER) cc_final: -0.3918 (m-80) REVERT: K 27 GLN cc_start: 0.4323 (tm-30) cc_final: 0.3891 (tt0) REVERT: K 35 TRP cc_start: 0.3776 (m100) cc_final: 0.3520 (m100) REVERT: K 145 LYS cc_start: 0.1879 (mtpt) cc_final: -0.0040 (tttp) REVERT: K 190 LYS cc_start: 0.3419 (ttmt) cc_final: 0.2960 (tmtt) REVERT: J 25 SER cc_start: 0.0384 (OUTLIER) cc_final: -0.0235 (t) outliers start: 195 outliers final: 129 residues processed: 359 average time/residue: 0.3676 time to fit residues: 225.6015 Evaluate side-chains 298 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 159 time to evaluate : 3.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 296 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 364 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 607 GLN Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 102 PHE Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 197 ILE Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain K residue 39 LYS Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain J residue 102 PHE Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 181 SER Chi-restraints excluded: chain J residue 194 GLN Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 207 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 307 optimal weight: 20.0000 chunk 209 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 274 optimal weight: 3.9990 chunk 152 optimal weight: 7.9990 chunk 315 optimal weight: 30.0000 chunk 255 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 188 optimal weight: 0.0770 chunk 331 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 overall best weight: 4.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 856 ASN ** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 173 GLN K 37 GLN N 166 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 31553 Z= 0.382 Angle : 0.734 12.268 42912 Z= 0.363 Chirality : 0.052 0.855 5087 Planarity : 0.005 0.057 5444 Dihedral : 8.172 59.854 5626 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.32 % Favored : 91.47 % Rotamer: Outliers : 6.41 % Allowed : 21.63 % Favored : 71.96 % 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: -1.70 (0.13), residues: 3786 helix: 0.72 (0.20), residues: 682 sheet: -0.41 (0.15), residues: 1091 loop : -2.30 (0.12), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 105 HIS 0.005 0.001 HIS B1048 PHE 0.020 0.002 PHE J 67 TYR 0.019 0.002 TYR C1067 ARG 0.004 0.001 ARG J 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 171 time to evaluate : 3.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 ASN cc_start: 0.4330 (m-40) cc_final: 0.3114 (p0) REVERT: A 613 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.8006 (mm-40) REVERT: B 47 VAL cc_start: 0.8710 (OUTLIER) cc_final: 0.8405 (t) REVERT: B 88 ASP cc_start: 0.6347 (t0) cc_final: 0.6054 (t0) REVERT: B 97 LYS cc_start: 0.5255 (OUTLIER) cc_final: 0.4982 (tmtt) REVERT: B 153 MET cc_start: 0.3615 (OUTLIER) cc_final: 0.1311 (mmm) REVERT: B 214 ARG cc_start: 0.2973 (OUTLIER) cc_final: 0.2661 (mpt180) REVERT: B 287 ASP cc_start: 0.7467 (OUTLIER) cc_final: 0.7237 (m-30) REVERT: B 456 PHE cc_start: 0.5129 (OUTLIER) cc_final: 0.3615 (t80) REVERT: B 473 TYR cc_start: 0.3783 (OUTLIER) cc_final: 0.2765 (m-80) REVERT: B 560 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7626 (mp) REVERT: B 569 ILE cc_start: 0.3452 (OUTLIER) cc_final: 0.3142 (mm) REVERT: B 854 LYS cc_start: 0.7407 (OUTLIER) cc_final: 0.7117 (mtpp) REVERT: B 960 ASN cc_start: 0.8407 (t0) cc_final: 0.7959 (t0) REVERT: B 1029 MET cc_start: 0.8962 (tpp) cc_final: 0.8543 (ttm) REVERT: C 137 ASN cc_start: 0.0071 (OUTLIER) cc_final: -0.0817 (m-40) REVERT: C 153 MET cc_start: 0.2690 (mtt) cc_final: 0.0588 (tpt) REVERT: C 424 LYS cc_start: 0.5018 (tttm) cc_final: 0.3421 (ttmt) REVERT: H 27 PHE cc_start: 0.4468 (OUTLIER) cc_final: 0.3749 (p90) REVERT: H 28 THR cc_start: 0.0480 (t) cc_final: -0.0455 (p) REVERT: H 102 PHE cc_start: -0.3758 (OUTLIER) cc_final: -0.4168 (m-80) REVERT: H 194 GLN cc_start: 0.2150 (OUTLIER) cc_final: 0.1474 (mt0) REVERT: K 27 GLN cc_start: 0.4715 (tm-30) cc_final: 0.4491 (tt0) REVERT: K 90 GLN cc_start: 0.3560 (OUTLIER) cc_final: 0.1773 (mm110) REVERT: K 145 LYS cc_start: 0.1979 (mtpt) cc_final: -0.0117 (tttp) REVERT: K 207 LYS cc_start: 0.0659 (mmtt) cc_final: 0.0187 (mmmt) REVERT: J 25 SER cc_start: 0.0932 (OUTLIER) cc_final: 0.0336 (t) REVERT: N 90 GLN cc_start: 0.1791 (OUTLIER) cc_final: 0.1465 (pp30) outliers start: 215 outliers final: 154 residues processed: 374 average time/residue: 0.3706 time to fit residues: 234.2875 Evaluate side-chains 320 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 148 time to evaluate : 3.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 607 GLN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 102 PHE Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 197 ILE Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain K residue 39 LYS Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 56 SER Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 27 PHE Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain J residue 102 PHE Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 181 SER Chi-restraints excluded: chain J residue 194 GLN Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 90 GLN Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 207 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 124 optimal weight: 6.9990 chunk 332 optimal weight: 50.0000 chunk 72 optimal weight: 0.9990 chunk 216 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 369 optimal weight: 6.9990 chunk 306 optimal weight: 1.9990 chunk 171 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 194 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 360 ASN A 955 ASN B 134 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN C 30 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN J 81 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.4840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31553 Z= 0.167 Angle : 0.633 10.427 42912 Z= 0.310 Chirality : 0.048 0.846 5087 Planarity : 0.004 0.060 5444 Dihedral : 7.764 59.867 5626 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.52 % Favored : 93.26 % Rotamer: Outliers : 4.20 % Allowed : 23.96 % Favored : 71.84 % 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: -1.36 (0.13), residues: 3786 helix: 1.14 (0.21), residues: 684 sheet: -0.17 (0.15), residues: 1059 loop : -2.13 (0.12), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 105 HIS 0.003 0.000 HIS H 202 PHE 0.017 0.001 PHE A 86 TYR 0.019 0.001 TYR B1067 ARG 0.005 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 176 time to evaluate : 3.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 LEU cc_start: 0.5450 (OUTLIER) cc_final: 0.5182 (pp) REVERT: A 571 ASP cc_start: 0.6804 (t70) cc_final: 0.6588 (t0) REVERT: B 88 ASP cc_start: 0.6142 (t0) cc_final: 0.5885 (t0) REVERT: B 97 LYS cc_start: 0.5291 (OUTLIER) cc_final: 0.4509 (tmtt) REVERT: B 153 MET cc_start: 0.3595 (OUTLIER) cc_final: 0.1410 (mmm) REVERT: B 456 PHE cc_start: 0.4877 (OUTLIER) cc_final: 0.3425 (t80) REVERT: B 473 TYR cc_start: 0.3627 (OUTLIER) cc_final: 0.2713 (m-80) REVERT: B 560 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7459 (mp) REVERT: B 569 ILE cc_start: 0.3222 (OUTLIER) cc_final: 0.2916 (mm) REVERT: B 960 ASN cc_start: 0.8354 (t0) cc_final: 0.7883 (t0) REVERT: B 1029 MET cc_start: 0.8875 (tpp) cc_final: 0.8478 (ttm) REVERT: C 153 MET cc_start: 0.2756 (mtt) cc_final: 0.0773 (tpt) REVERT: C 424 LYS cc_start: 0.5050 (tttm) cc_final: 0.3445 (ttmt) REVERT: H 45 LEU cc_start: 0.1132 (mm) cc_final: 0.0770 (mt) REVERT: H 102 PHE cc_start: -0.3342 (OUTLIER) cc_final: -0.4047 (m-80) REVERT: K 27 GLN cc_start: 0.4839 (tm-30) cc_final: 0.4498 (tt0) REVERT: K 145 LYS cc_start: 0.1780 (mtpt) cc_final: -0.0260 (tttp) REVERT: K 207 LYS cc_start: 0.0658 (mmtt) cc_final: 0.0263 (mmmt) REVERT: J 25 SER cc_start: 0.1051 (OUTLIER) cc_final: 0.0447 (t) REVERT: J 98 GLU cc_start: 0.3073 (OUTLIER) cc_final: 0.2858 (pm20) REVERT: N 90 GLN cc_start: 0.1889 (OUTLIER) cc_final: 0.1596 (pp30) REVERT: N 207 LYS cc_start: 0.2884 (OUTLIER) cc_final: 0.2620 (ptmm) outliers start: 141 outliers final: 96 residues processed: 300 average time/residue: 0.3855 time to fit residues: 196.7910 Evaluate side-chains 262 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 154 time to evaluate : 3.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 472 ILE 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 552 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 607 GLN Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain H residue 102 PHE Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 197 ILE Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain K residue 56 SER Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain J residue 102 PHE Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 90 GLN Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 207 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 356 optimal weight: 40.0000 chunk 41 optimal weight: 8.9990 chunk 210 optimal weight: 9.9990 chunk 269 optimal weight: 7.9990 chunk 209 optimal weight: 0.9980 chunk 311 optimal weight: 50.0000 chunk 206 optimal weight: 10.0000 chunk 368 optimal weight: 20.0000 chunk 230 optimal weight: 20.0000 chunk 224 optimal weight: 0.9980 chunk 169 optimal weight: 10.0000 overall best weight: 5.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 360 ASN ** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN B 99 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.5245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 31553 Z= 0.466 Angle : 0.776 11.901 42912 Z= 0.381 Chirality : 0.052 0.684 5087 Planarity : 0.005 0.062 5444 Dihedral : 8.435 68.777 5616 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.80 % Favored : 90.99 % Rotamer: Outliers : 5.45 % Allowed : 23.09 % Favored : 71.45 % 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: -1.62 (0.13), residues: 3786 helix: 0.75 (0.20), residues: 679 sheet: -0.33 (0.15), residues: 1066 loop : -2.23 (0.12), residues: 2041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP J 36 HIS 0.006 0.001 HIS B1048 PHE 0.022 0.002 PHE B 65 TYR 0.022 0.002 TYR K 87 ARG 0.008 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 157 time to evaluate : 3.406 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 335 LEU cc_start: 0.5624 (OUTLIER) cc_final: 0.5380 (pp) REVERT: A 571 ASP cc_start: 0.6895 (t70) cc_final: 0.6666 (t0) REVERT: B 47 VAL cc_start: 0.8657 (OUTLIER) cc_final: 0.8441 (t) REVERT: B 88 ASP cc_start: 0.6312 (t0) cc_final: 0.6043 (t0) REVERT: B 153 MET cc_start: 0.3888 (OUTLIER) cc_final: 0.1376 (mmm) REVERT: B 473 TYR cc_start: 0.3973 (OUTLIER) cc_final: 0.2958 (m-80) REVERT: B 560 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7542 (mp) REVERT: B 569 ILE cc_start: 0.3495 (OUTLIER) cc_final: 0.3192 (mm) REVERT: B 1029 MET cc_start: 0.8937 (tpp) cc_final: 0.8593 (ttm) REVERT: C 424 LYS cc_start: 0.5100 (tttm) cc_final: 0.3632 (ttmt) REVERT: H 45 LEU cc_start: 0.1211 (mm) cc_final: 0.0936 (mt) REVERT: H 102 PHE cc_start: -0.3187 (OUTLIER) cc_final: -0.3954 (m-80) REVERT: H 194 GLN cc_start: 0.2064 (OUTLIER) cc_final: 0.1372 (mt0) REVERT: K 90 GLN cc_start: 0.3711 (OUTLIER) cc_final: 0.2020 (mm110) REVERT: K 145 LYS cc_start: 0.1648 (mtpt) cc_final: -0.0155 (tttp) REVERT: J 25 SER cc_start: 0.1332 (OUTLIER) cc_final: 0.0736 (t) REVERT: J 98 GLU cc_start: 0.2841 (OUTLIER) cc_final: 0.2624 (pm20) REVERT: N 65 SER cc_start: -0.3553 (OUTLIER) cc_final: -0.4087 (t) REVERT: N 206 THR cc_start: 0.4364 (OUTLIER) cc_final: 0.4008 (p) REVERT: N 207 LYS cc_start: 0.2937 (OUTLIER) cc_final: 0.2688 (ptmm) outliers start: 183 outliers final: 141 residues processed: 326 average time/residue: 0.3593 time to fit residues: 202.0936 Evaluate side-chains 301 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 146 time to evaluate : 3.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 607 GLN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 102 PHE Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 197 ILE Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain K residue 39 LYS Chi-restraints excluded: chain K residue 56 SER Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 27 PHE Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain J residue 102 PHE Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 194 GLN Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 206 THR Chi-restraints excluded: chain N residue 207 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 227 optimal weight: 2.9990 chunk 147 optimal weight: 10.0000 chunk 219 optimal weight: 0.0270 chunk 110 optimal weight: 7.9990 chunk 72 optimal weight: 0.1980 chunk 71 optimal weight: 0.9990 chunk 234 optimal weight: 20.0000 chunk 250 optimal weight: 0.6980 chunk 182 optimal weight: 2.9990 chunk 34 optimal weight: 20.0000 chunk 289 optimal weight: 0.7980 overall best weight: 0.5440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS B 317 ASN B 370 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 31553 Z= 0.158 Angle : 0.643 12.159 42912 Z= 0.312 Chirality : 0.047 0.561 5087 Planarity : 0.004 0.063 5444 Dihedral : 7.907 64.400 5616 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.31 % Favored : 93.48 % Rotamer: Outliers : 3.34 % Allowed : 25.18 % 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: -1.22 (0.13), residues: 3786 helix: 1.25 (0.21), residues: 682 sheet: -0.06 (0.16), residues: 1032 loop : -2.02 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP J 105 HIS 0.002 0.000 HIS C 519 PHE 0.018 0.001 PHE A 86 TYR 0.019 0.001 TYR B1067 ARG 0.007 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 171 time to evaluate : 3.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 LEU cc_start: 0.5363 (OUTLIER) cc_final: 0.5133 (pp) REVERT: A 571 ASP cc_start: 0.6803 (t70) cc_final: 0.6545 (t0) REVERT: B 456 PHE cc_start: 0.4862 (OUTLIER) cc_final: 0.3318 (t80) REVERT: B 473 TYR cc_start: 0.3977 (OUTLIER) cc_final: 0.3171 (m-80) REVERT: B 569 ILE cc_start: 0.3118 (OUTLIER) cc_final: 0.2864 (mm) REVERT: B 1029 MET cc_start: 0.8832 (tpp) cc_final: 0.8463 (ttm) REVERT: C 41 LYS cc_start: 0.6972 (OUTLIER) cc_final: 0.6561 (mttm) REVERT: C 86 PHE cc_start: 0.4282 (OUTLIER) cc_final: 0.3213 (m-10) REVERT: C 424 LYS cc_start: 0.5003 (tttm) cc_final: 0.3657 (ttmt) REVERT: H 27 PHE cc_start: 0.3683 (OUTLIER) cc_final: 0.3186 (p90) REVERT: H 45 LEU cc_start: 0.1352 (mm) cc_final: 0.1128 (mt) REVERT: H 102 PHE cc_start: -0.3465 (OUTLIER) cc_final: -0.4126 (m-80) REVERT: K 90 GLN cc_start: 0.3589 (OUTLIER) cc_final: 0.2102 (mm110) REVERT: K 145 LYS cc_start: 0.1527 (mtpt) cc_final: -0.0240 (tttp) REVERT: J 25 SER cc_start: 0.1481 (OUTLIER) cc_final: 0.0915 (t) REVERT: N 206 THR cc_start: 0.4033 (OUTLIER) cc_final: 0.3776 (p) outliers start: 112 outliers final: 90 residues processed: 275 average time/residue: 0.3789 time to fit residues: 176.6926 Evaluate side-chains 254 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 153 time to evaluate : 3.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 102 PHE Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 197 ILE Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain K residue 56 SER Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain J residue 102 PHE Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 194 GLN Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 206 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 334 optimal weight: 20.0000 chunk 352 optimal weight: 30.0000 chunk 321 optimal weight: 20.0000 chunk 343 optimal weight: 20.0000 chunk 206 optimal weight: 0.3980 chunk 149 optimal weight: 9.9990 chunk 269 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 chunk 310 optimal weight: 30.0000 chunk 324 optimal weight: 0.6980 chunk 341 optimal weight: 0.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.5593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 31553 Z= 0.342 Angle : 0.719 11.906 42912 Z= 0.350 Chirality : 0.050 0.641 5087 Planarity : 0.005 0.066 5444 Dihedral : 8.209 65.031 5614 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.32 % Favored : 91.49 % Rotamer: Outliers : 3.96 % Allowed : 24.64 % Favored : 71.39 % 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: -1.39 (0.13), residues: 3786 helix: 1.05 (0.21), residues: 679 sheet: -0.22 (0.16), residues: 1061 loop : -2.10 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP J 36 HIS 0.004 0.001 HIS A1064 PHE 0.031 0.002 PHE A 201 TYR 0.023 0.002 TYR C 904 ARG 0.006 0.001 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 151 time to evaluate : 3.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 571 ASP cc_start: 0.6867 (t70) cc_final: 0.6641 (t0) REVERT: B 97 LYS cc_start: 0.6235 (OUTLIER) cc_final: 0.5419 (tmtt) REVERT: B 456 PHE cc_start: 0.4903 (OUTLIER) cc_final: 0.3285 (t80) REVERT: B 473 TYR cc_start: 0.4090 (OUTLIER) cc_final: 0.3072 (m-80) REVERT: B 569 ILE cc_start: 0.3440 (OUTLIER) cc_final: 0.3146 (mm) REVERT: B 960 ASN cc_start: 0.8436 (OUTLIER) cc_final: 0.7943 (t0) REVERT: B 1029 MET cc_start: 0.8945 (tpp) cc_final: 0.8557 (ttm) REVERT: C 424 LYS cc_start: 0.5075 (tttm) cc_final: 0.3739 (ttmt) REVERT: H 27 PHE cc_start: 0.3614 (OUTLIER) cc_final: 0.3087 (p90) REVERT: H 45 LEU cc_start: 0.1157 (mm) cc_final: 0.0909 (mt) REVERT: H 102 PHE cc_start: -0.3524 (OUTLIER) cc_final: -0.4299 (m-80) REVERT: K 90 GLN cc_start: 0.3777 (OUTLIER) cc_final: 0.2159 (mm110) REVERT: K 145 LYS cc_start: 0.1757 (mtpt) cc_final: 0.0113 (tttp) REVERT: J 25 SER cc_start: 0.1324 (OUTLIER) cc_final: 0.0758 (t) REVERT: N 65 SER cc_start: -0.3614 (OUTLIER) cc_final: -0.4161 (t) REVERT: N 90 GLN cc_start: 0.2636 (OUTLIER) cc_final: 0.2280 (pp30) REVERT: N 206 THR cc_start: 0.4178 (OUTLIER) cc_final: 0.3956 (p) outliers start: 133 outliers final: 108 residues processed: 273 average time/residue: 0.3656 time to fit residues: 170.1837 Evaluate side-chains 263 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 143 time to evaluate : 3.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 607 GLN Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 102 PHE Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 197 ILE Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain K residue 56 SER Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain J residue 102 PHE Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 194 GLN Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 90 GLN Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 206 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 225 optimal weight: 7.9990 chunk 362 optimal weight: 30.0000 chunk 221 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 chunk 252 optimal weight: 8.9990 chunk 380 optimal weight: 30.0000 chunk 350 optimal weight: 0.5980 chunk 303 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 234 optimal weight: 0.9990 chunk 185 optimal weight: 0.8980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 314 GLN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.5660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31553 Z= 0.186 Angle : 0.662 12.056 42912 Z= 0.319 Chirality : 0.048 0.575 5087 Planarity : 0.004 0.065 5444 Dihedral : 7.865 60.627 5614 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.97 % Favored : 92.84 % Rotamer: Outliers : 3.49 % Allowed : 25.27 % Favored : 71.25 % 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: 3786 helix: 1.23 (0.21), residues: 692 sheet: -0.07 (0.16), residues: 1038 loop : -2.04 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 105 HIS 0.002 0.000 HIS H 202 PHE 0.026 0.001 PHE C 32 TYR 0.025 0.001 TYR C 904 ARG 0.009 0.000 ARG A 319 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 156 time to evaluate : 3.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 LEU cc_start: 0.5407 (OUTLIER) cc_final: 0.5196 (pp) REVERT: A 571 ASP cc_start: 0.6817 (t70) cc_final: 0.6555 (t0) REVERT: A 957 GLN cc_start: 0.7443 (OUTLIER) cc_final: 0.7116 (mp10) REVERT: B 97 LYS cc_start: 0.6220 (OUTLIER) cc_final: 0.5457 (tmtt) REVERT: B 456 PHE cc_start: 0.4847 (OUTLIER) cc_final: 0.3324 (t80) REVERT: B 464 PHE cc_start: 0.6283 (OUTLIER) cc_final: 0.4737 (t80) REVERT: B 473 TYR cc_start: 0.4058 (OUTLIER) cc_final: 0.3187 (m-80) REVERT: B 569 ILE cc_start: 0.3319 (OUTLIER) cc_final: 0.3034 (mm) REVERT: B 1029 MET cc_start: 0.8878 (tpp) cc_final: 0.8492 (ttm) REVERT: C 86 PHE cc_start: 0.4501 (OUTLIER) cc_final: 0.3401 (m-10) REVERT: C 424 LYS cc_start: 0.5084 (tttm) cc_final: 0.3750 (ttmt) REVERT: H 27 PHE cc_start: 0.3628 (OUTLIER) cc_final: 0.3012 (p90) REVERT: H 102 PHE cc_start: -0.3631 (OUTLIER) cc_final: -0.4362 (m-80) REVERT: K 90 GLN cc_start: 0.3722 (OUTLIER) cc_final: 0.2179 (mm110) REVERT: K 145 LYS cc_start: 0.1603 (mtpt) cc_final: 0.0108 (tttp) REVERT: J 25 SER cc_start: 0.1243 (OUTLIER) cc_final: 0.0671 (t) REVERT: N 65 SER cc_start: -0.3482 (OUTLIER) cc_final: -0.4059 (t) REVERT: N 90 GLN cc_start: 0.2585 (OUTLIER) cc_final: 0.2171 (pp30) REVERT: N 206 THR cc_start: 0.3964 (OUTLIER) cc_final: 0.3743 (p) outliers start: 117 outliers final: 97 residues processed: 264 average time/residue: 0.3881 time to fit residues: 174.4141 Evaluate side-chains 259 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 147 time to evaluate : 3.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 102 PHE Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 197 ILE Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain K residue 56 SER Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 102 PHE Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 181 SER Chi-restraints excluded: chain J residue 194 GLN Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 90 GLN Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 206 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 240 optimal weight: 50.0000 chunk 322 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 chunk 279 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 303 optimal weight: 0.5980 chunk 127 optimal weight: 0.4980 chunk 311 optimal weight: 40.0000 chunk 38 optimal weight: 0.6980 chunk 55 optimal weight: 8.9990 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 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B1106 GLN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.185536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.141630 restraints weight = 57776.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.129650 restraints weight = 72260.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.126866 restraints weight = 67071.492| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.5775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31553 Z= 0.170 Angle : 0.629 11.317 42912 Z= 0.303 Chirality : 0.047 0.527 5087 Planarity : 0.004 0.065 5444 Dihedral : 7.316 57.744 5614 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.29 % Favored : 92.53 % Rotamer: Outliers : 3.55 % Allowed : 25.30 % Favored : 71.16 % 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: -1.07 (0.13), residues: 3786 helix: 1.42 (0.21), residues: 693 sheet: 0.07 (0.16), residues: 1020 loop : -1.97 (0.13), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 105 HIS 0.002 0.000 HIS H 202 PHE 0.020 0.001 PHE A 201 TYR 0.020 0.001 TYR B1067 ARG 0.009 0.000 ARG A 319 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5976.79 seconds wall clock time: 111 minutes 3.31 seconds (6663.31 seconds total)