Starting phenix.real_space_refine on Fri Apr 12 15:13:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d0b_30529/04_2024/7d0b_30529.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d0b_30529/04_2024/7d0b_30529.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d0b_30529/04_2024/7d0b_30529.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d0b_30529/04_2024/7d0b_30529.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d0b_30529/04_2024/7d0b_30529.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d0b_30529/04_2024/7d0b_30529.pdb" } resolution = 3.9 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= 0.003 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 113 5.16 5 C 16589 2.51 5 N 4232 2.21 5 O 5131 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 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 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B ARG 246": "NH1" <-> "NH2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B GLU 324": "OE1" <-> "OE2" 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 554": "OE1" <-> "OE2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B GLU 748": "OE1" <-> "OE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B GLU 918": "OE1" <-> "OE2" Residue "B GLU 1072": "OE1" <-> "OE2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C ARG 246": "NH1" <-> "NH2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C ARG 509": "NH1" <-> "NH2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C GLU 725": "OE1" <-> "OE2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C GLU 1031": "OE1" <-> "OE2" Residue "C GLU 1072": "OE1" <-> "OE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 26065 Number of models: 1 Model: "" Number of chains: 29 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: 7692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 981, 7692 Classifications: {'peptide': 981} Link IDs: {'PTRANS': 48, 'TRANS': 932} Chain breaks: 11 Chain: "C" Number of atoms: 7692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 981, 7692 Classifications: {'peptide': 981} Link IDs: {'PTRANS': 48, 'TRANS': 932} Chain breaks: 11 Chain: "H" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 972 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain: "L" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 880 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} 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: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 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 Time building chain proxies: 14.16, per 1000 atoms: 0.54 Number of scatterers: 26065 At special positions: 0 Unit cell: (135.875, 166.311, 194.573, 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 113 16.00 O 5131 8.00 N 4232 7.00 C 16589 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, 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=2.54 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.33 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.05 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 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=2.50 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.58 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.05 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.12 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=1.95 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=1.98 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " 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 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 J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " NAG-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 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 343 " " NAG C1407 " - " ASN C 603 " " NAG C1408 " - " ASN C 616 " " NAG C1409 " - " 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 J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG M 1 " - " ASN B 331 " " NAG N 1 " - " ASN B 709 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN B1098 " " NAG R 1 " - " ASN B1134 " " NAG S 1 " - " ASN C 331 " " NAG T 1 " - " ASN C 709 " " NAG U 1 " - " ASN C 717 " " NAG V 1 " - " ASN C 801 " " NAG W 1 " - " ASN C1074 " " NAG X 1 " - " ASN C1098 " " NAG Y 1 " - " ASN C1134 " " NAG Z 1 " - " ASN B1074 " Time building additional restraints: 11.25 Conformation dependent library (CDL) restraints added in 4.5 seconds 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6024 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 50 sheets defined 21.9% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.99 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 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: 4.256A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.624A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.739A 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: 3.630A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.772A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.635A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 815' Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.647A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.552A 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: 3.992A 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: 3.647A 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: 4.633A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.646A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 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 416 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 removed outlier: 3.696A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.964A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.544A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.604A 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: 3.846A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.010A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.246A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.674A 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 338 through 343 Processing helix chain 'C' and resid 364 through 370 removed outlier: 3.615A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (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: 3.562A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.606A 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: 3.589A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.355A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.220A 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: 3.816A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'H' and resid 88 through 92 Processing helix chain 'H' and resid 103 through 106 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.857A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.729A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.776A 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=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.270A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 326 through 328 Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.542A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 448 through 454 removed outlier: 5.864A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 551 through 554 removed outlier: 4.789A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 653 through 655 removed outlier: 6.689A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.943A 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 711 through 728 removed outlier: 6.588A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.606A 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: 6.244A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.606A 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: 6.244A 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: 4.730A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.506A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.713A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.570A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC2, first strand: chain 'B' and resid 116 through 121 removed outlier: 3.731A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 309 through 319 removed outlier: 5.938A pdb=" N LYS B 310 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLY B 601 " --> pdb=" O LYS B 310 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.674A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 539 through 543 removed outlier: 5.339A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.250A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.167A 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=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, 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=AD2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.552A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD6, first strand: chain 'C' and resid 116 through 121 removed outlier: 3.731A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN C 134 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 316 removed outlier: 4.316A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.673A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 539 through 543 Processing sheet with id=AE1, first strand: chain 'C' and resid 553 through 554 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.246A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE3, 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: 6.842A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.592A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.881A 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=AE5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.568A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE7, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AE8, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AE9, first strand: chain 'H' and resid 59 through 61 removed outlier: 6.308A pdb=" N TRP H 38 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU H 52 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL H 36 " --> pdb=" O LEU H 52 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TYR H 54 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL H 34 " --> pdb=" O TYR H 54 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 69 through 74 Processing sheet with id=AF2, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AF3, first strand: chain 'L' and resid 11 through 14 removed outlier: 5.718A pdb=" N LEU L 11 " --> pdb=" O GLU L 111 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LYS L 113 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL L 13 " --> pdb=" O LYS L 113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'L' and resid 19 through 20 removed outlier: 3.882A pdb=" N ILE L 81 " --> pdb=" O ALA L 19 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 59 through 60 removed outlier: 6.595A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) 918 hydrogen bonds defined for protein. 2487 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.00 Time building geometry restraints manager: 12.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5009 1.32 - 1.45: 7859 1.45 - 1.58: 13616 1.58 - 1.71: 0 1.71 - 1.84: 143 Bond restraints: 26627 Sorted by residual: bond pdb=" CA SER A 698 " pdb=" C SER A 698 " ideal model delta sigma weight residual 1.522 1.443 0.079 1.20e-02 6.94e+03 4.31e+01 bond pdb=" CA ILE A 692 " pdb=" C ILE A 692 " ideal model delta sigma weight residual 1.523 1.460 0.063 1.16e-02 7.43e+03 2.97e+01 bond pdb=" CA ILE A 693 " pdb=" CB ILE A 693 " ideal model delta sigma weight residual 1.544 1.472 0.072 1.49e-02 4.50e+03 2.34e+01 bond pdb=" C THR C 588 " pdb=" N PRO C 589 " ideal model delta sigma weight residual 1.330 1.389 -0.058 1.23e-02 6.61e+03 2.26e+01 bond pdb=" N ILE A 692 " pdb=" CA ILE A 692 " ideal model delta sigma weight residual 1.458 1.403 0.055 1.17e-02 7.31e+03 2.22e+01 ... (remaining 26622 not shown) Histogram of bond angle deviations from ideal: 97.52 - 105.79: 534 105.79 - 114.05: 15628 114.05 - 122.32: 15585 122.32 - 130.58: 4390 130.58 - 138.85: 78 Bond angle restraints: 36215 Sorted by residual: angle pdb=" N ILE A 692 " pdb=" CA ILE A 692 " pdb=" C ILE A 692 " ideal model delta sigma weight residual 109.55 100.43 9.12 1.38e+00 5.25e-01 4.37e+01 angle pdb=" CA ILE A 692 " pdb=" C ILE A 692 " pdb=" N ILE A 693 " ideal model delta sigma weight residual 115.82 124.84 -9.02 1.52e+00 4.33e-01 3.52e+01 angle pdb=" C PHE B 86 " pdb=" N ASN B 87 " pdb=" CA ASN B 87 " ideal model delta sigma weight residual 121.54 132.74 -11.20 1.91e+00 2.74e-01 3.44e+01 angle pdb=" C PHE C 86 " pdb=" N ASN C 87 " pdb=" CA ASN C 87 " ideal model delta sigma weight residual 121.54 132.74 -11.20 1.91e+00 2.74e-01 3.44e+01 angle pdb=" C PHE A 86 " pdb=" N ASN A 87 " pdb=" CA ASN A 87 " ideal model delta sigma weight residual 121.54 132.72 -11.18 1.91e+00 2.74e-01 3.43e+01 ... (remaining 36210 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 14359 17.94 - 35.87: 1636 35.87 - 53.81: 543 53.81 - 71.75: 169 71.75 - 89.69: 52 Dihedral angle restraints: 16759 sinusoidal: 7420 harmonic: 9339 Sorted by residual: dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.03 71.97 1 1.00e+01 1.00e-02 6.63e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.06 71.94 1 1.00e+01 1.00e-02 6.62e+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 21.11 71.89 1 1.00e+01 1.00e-02 6.62e+01 ... (remaining 16756 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.329: 4318 0.329 - 0.659: 5 0.659 - 0.988: 3 0.988 - 1.318: 0 1.318 - 1.647: 2 Chirality restraints: 4328 Sorted by residual: chirality pdb=" C1 NAG Z 2 " pdb=" O4 NAG Z 1 " pdb=" C2 NAG Z 2 " pdb=" O5 NAG Z 2 " both_signs ideal model delta sigma weight residual False -2.40 -3.08 0.68 2.00e-02 2.50e+03 1.16e+03 chirality pdb=" C1 NAG Y 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG Y 1 " pdb=" O5 NAG Y 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.75 -1.65 2.00e-01 2.50e+01 6.78e+01 chirality pdb=" C1 NAG C1404 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG C1404 " pdb=" O5 NAG C1404 " both_signs ideal model delta sigma weight residual False -2.40 -0.93 -1.47 2.00e-01 2.50e+01 5.38e+01 ... (remaining 4325 not shown) Planarity restraints: 4621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 234 " -0.161 2.00e-02 2.50e+03 2.13e-01 5.65e+02 pdb=" CG ASN C 234 " 0.066 2.00e-02 2.50e+03 pdb=" OD1 ASN C 234 " -0.024 2.00e-02 2.50e+03 pdb=" ND2 ASN C 234 " 0.366 2.00e-02 2.50e+03 pdb=" C1 NAG C1404 " -0.247 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " 0.119 2.00e-02 2.50e+03 1.72e-01 3.69e+02 pdb=" CG ASN C 331 " -0.052 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " 0.040 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " -0.302 2.00e-02 2.50e+03 pdb=" C1 NAG S 1 " 0.195 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 709 " -0.047 2.00e-02 2.50e+03 5.85e-02 4.28e+01 pdb=" CG ASN A 709 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 709 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN A 709 " 0.100 2.00e-02 2.50e+03 pdb=" C1 NAG A1409 " -0.068 2.00e-02 2.50e+03 ... (remaining 4618 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 245 2.51 - 3.11: 18851 3.11 - 3.71: 37675 3.71 - 4.30: 56929 4.30 - 4.90: 93867 Nonbonded interactions: 207567 Sorted by model distance: nonbonded pdb=" O SER A 530 " pdb=" OG1 THR A 531 " model vdw 1.913 2.440 nonbonded pdb=" O ALA C 372 " pdb=" OG SER C 373 " model vdw 1.919 2.440 nonbonded pdb=" NH1 ARG A 346 " pdb=" O PHE A 347 " model vdw 1.983 2.520 nonbonded pdb=" O LYS A 529 " pdb=" OG SER A 530 " model vdw 1.986 2.440 nonbonded pdb=" O GLN C 564 " pdb=" O PHE C 565 " model vdw 2.004 3.040 ... (remaining 207562 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 939 or resid 944 through 1146 or resid 1401 through \ 1409)) selection = (chain 'B' and (resid 27 through 826 or resid 855 through 1146 or resid 1401 thr \ ough 1409)) selection = (chain 'C' and (resid 27 through 826 or resid 855 through 1146 or resid 1401 thr \ ough 1409)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } 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: 1.300 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: 6.680 Check model and map are aligned: 0.400 Set scattering table: 0.250 Process input model: 72.560 Find NCS groups from input model: 2.000 Set up NCS constraints: 0.340 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.117 26627 Z= 0.699 Angle : 1.047 13.846 36215 Z= 0.604 Chirality : 0.075 1.647 4328 Planarity : 0.007 0.093 4573 Dihedral : 17.961 89.686 10621 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 23.14 Ramachandran Plot: Outliers : 2.10 % Allowed : 10.55 % Favored : 87.34 % Rotamer: Outliers : 12.29 % Allowed : 18.36 % Favored : 69.35 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.01 (0.12), residues: 3136 helix: -2.08 (0.17), residues: 631 sheet: -2.21 (0.17), residues: 763 loop : -3.21 (0.12), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP B 104 HIS 0.009 0.002 HIS A1048 PHE 0.035 0.003 PHE H 24 TYR 0.028 0.003 TYR B1067 ARG 0.007 0.001 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 346 poor density : 458 time to evaluate : 3.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ASN cc_start: 0.5027 (OUTLIER) cc_final: 0.4495 (m110) REVERT: A 164 ASN cc_start: 0.5832 (OUTLIER) cc_final: 0.5501 (m-40) REVERT: A 389 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.8001 (p0) REVERT: A 517 LEU cc_start: 0.5208 (OUTLIER) cc_final: 0.3535 (tp) REVERT: A 900 MET cc_start: 0.7691 (mtp) cc_final: 0.7385 (mtp) REVERT: A 976 VAL cc_start: 0.8280 (OUTLIER) cc_final: 0.7975 (t) REVERT: A 1051 SER cc_start: 0.9396 (m) cc_final: 0.9026 (p) REVERT: B 153 MET cc_start: 0.0157 (mpp) cc_final: -0.0751 (mmm) REVERT: B 587 ILE cc_start: 0.8272 (mt) cc_final: 0.8028 (mt) REVERT: B 710 ASN cc_start: 0.8324 (OUTLIER) cc_final: 0.8091 (p0) REVERT: B 902 MET cc_start: 0.8760 (tpt) cc_final: 0.8497 (tpp) REVERT: B 916 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8854 (tp) REVERT: B 968 SER cc_start: 0.8277 (OUTLIER) cc_final: 0.7957 (p) REVERT: C 54 LEU cc_start: 0.4583 (mt) cc_final: 0.4341 (mt) REVERT: C 366 SER cc_start: 0.6875 (m) cc_final: 0.6413 (t) REVERT: C 369 TYR cc_start: 0.7173 (OUTLIER) cc_final: 0.6088 (p90) REVERT: C 382 VAL cc_start: 0.7411 (OUTLIER) cc_final: 0.7118 (p) REVERT: C 583 GLU cc_start: 0.3771 (OUTLIER) cc_final: 0.3562 (tp30) REVERT: C 690 GLN cc_start: 0.6749 (OUTLIER) cc_final: 0.6544 (pm20) REVERT: C 699 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7948 (mt) REVERT: C 900 MET cc_start: 0.8482 (mtp) cc_final: 0.8280 (mtm) REVERT: C 975 SER cc_start: 0.8634 (OUTLIER) cc_final: 0.8394 (p) REVERT: C 1050 MET cc_start: 0.8354 (ptm) cc_final: 0.8064 (ptm) REVERT: H 114 PHE cc_start: 0.0253 (OUTLIER) cc_final: -0.0370 (m-80) outliers start: 346 outliers final: 52 residues processed: 745 average time/residue: 0.3978 time to fit residues: 462.3581 Evaluate side-chains 254 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 187 time to evaluate : 4.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 58 ASP Chi-restraints excluded: chain H residue 114 PHE Chi-restraints excluded: chain H residue 116 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 269 optimal weight: 1.9990 chunk 241 optimal weight: 8.9990 chunk 134 optimal weight: 10.0000 chunk 82 optimal weight: 0.4980 chunk 163 optimal weight: 4.9990 chunk 129 optimal weight: 7.9990 chunk 250 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 186 optimal weight: 0.9980 chunk 289 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS A 134 GLN A 137 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN A 440 ASN A 540 ASN A 613 GLN A 644 GLN A 658 ASN A 856 ASN A 901 GLN A 913 GLN A 914 ASN A 919 ASN A 926 GLN A 935 GLN A 955 ASN A 969 ASN A 992 GLN A1101 HIS ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 188 ASN B 239 GLN B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN B 644 GLN B 710 ASN B 901 GLN B 914 ASN B 919 ASN B 920 GLN B 926 GLN B 957 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS C 137 ASN C 188 ASN C 196 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN C 409 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN C 607 GLN C 644 GLN C 658 ASN C 675 GLN C 703 ASN C 751 ASN C 784 GLN C 804 GLN C 901 GLN C 914 ASN C 926 GLN C 935 GLN C 969 ASN C 992 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN C1071 GLN C1101 HIS ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** L 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 26627 Z= 0.267 Angle : 0.786 10.777 36215 Z= 0.395 Chirality : 0.051 0.526 4328 Planarity : 0.006 0.056 4573 Dihedral : 10.175 73.075 4996 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.62 % Favored : 92.22 % Rotamer: Outliers : 5.68 % Allowed : 22.51 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.14), residues: 3136 helix: 0.09 (0.21), residues: 641 sheet: -1.47 (0.17), residues: 799 loop : -2.69 (0.13), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 104 HIS 0.006 0.001 HIS A 49 PHE 0.022 0.002 PHE B 135 TYR 0.023 0.002 TYR C 453 ARG 0.010 0.001 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 214 time to evaluate : 2.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ASN cc_start: 0.5014 (OUTLIER) cc_final: 0.4211 (m110) REVERT: A 164 ASN cc_start: 0.5965 (OUTLIER) cc_final: 0.5437 (m-40) REVERT: A 900 MET cc_start: 0.7831 (mtp) cc_final: 0.7535 (mtp) REVERT: B 153 MET cc_start: -0.0456 (mpp) cc_final: -0.2072 (ptp) REVERT: B 417 LYS cc_start: 0.5924 (OUTLIER) cc_final: 0.4638 (mmmt) REVERT: C 369 TYR cc_start: 0.6839 (OUTLIER) cc_final: 0.6560 (p90) REVERT: C 402 ILE cc_start: 0.5390 (OUTLIER) cc_final: 0.4862 (tt) REVERT: C 583 GLU cc_start: 0.3965 (OUTLIER) cc_final: 0.3565 (tp30) REVERT: C 699 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8326 (mt) REVERT: C 975 SER cc_start: 0.8519 (t) cc_final: 0.8156 (p) REVERT: C 1126 CYS cc_start: 0.5865 (OUTLIER) cc_final: 0.5607 (p) REVERT: C 1132 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8603 (pp) outliers start: 160 outliers final: 82 residues processed: 355 average time/residue: 0.3591 time to fit residues: 209.4049 Evaluate side-chains 244 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 153 time to evaluate : 3.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL 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 969 ASN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 58 ASP Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 100 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 160 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 241 optimal weight: 2.9990 chunk 197 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 290 optimal weight: 7.9990 chunk 313 optimal weight: 20.0000 chunk 258 optimal weight: 3.9990 chunk 287 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 232 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 856 ASN A 926 GLN B 49 HIS B 134 GLN B 354 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 207 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN C 414 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 542 ASN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26627 Z= 0.200 Angle : 0.682 11.658 36215 Z= 0.336 Chirality : 0.048 0.536 4328 Planarity : 0.004 0.060 4573 Dihedral : 8.729 65.870 4934 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.11 % Favored : 92.73 % Rotamer: Outliers : 5.01 % Allowed : 24.08 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.14), residues: 3136 helix: 0.81 (0.21), residues: 642 sheet: -1.11 (0.17), residues: 801 loop : -2.39 (0.13), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 104 HIS 0.004 0.001 HIS H 99 PHE 0.023 0.001 PHE C 456 TYR 0.022 0.001 TYR A 473 ARG 0.006 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 177 time to evaluate : 3.022 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 164 ASN cc_start: 0.5946 (OUTLIER) cc_final: 0.5630 (m-40) REVERT: A 822 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8541 (mm) REVERT: A 900 MET cc_start: 0.7857 (mtp) cc_final: 0.7611 (mtp) REVERT: B 153 MET cc_start: -0.1143 (mpp) cc_final: -0.2991 (ptp) REVERT: C 277 LEU cc_start: 0.6313 (OUTLIER) cc_final: 0.6102 (mt) REVERT: C 369 TYR cc_start: 0.7090 (OUTLIER) cc_final: 0.6431 (p90) REVERT: C 402 ILE cc_start: 0.5446 (OUTLIER) cc_final: 0.4906 (tt) REVERT: C 699 LEU cc_start: 0.8647 (mp) cc_final: 0.8269 (mt) REVERT: C 973 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.8114 (mt) REVERT: C 975 SER cc_start: 0.8681 (t) cc_final: 0.8289 (p) REVERT: C 1126 CYS cc_start: 0.5995 (OUTLIER) cc_final: 0.5792 (p) REVERT: C 1132 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8571 (pp) REVERT: L 104 PHE cc_start: 0.2084 (m-80) cc_final: 0.1818 (m-80) outliers start: 141 outliers final: 89 residues processed: 301 average time/residue: 0.3247 time to fit residues: 168.0601 Evaluate side-chains 235 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 138 time to evaluate : 3.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 49 TRP Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain L residue 102 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 286 optimal weight: 7.9990 chunk 218 optimal weight: 0.0970 chunk 150 optimal weight: 5.9990 chunk 32 optimal weight: 30.0000 chunk 138 optimal weight: 30.0000 chunk 194 optimal weight: 2.9990 chunk 291 optimal weight: 3.9990 chunk 308 optimal weight: 6.9990 chunk 152 optimal weight: 3.9990 chunk 276 optimal weight: 0.7980 chunk 83 optimal weight: 9.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 211 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN A 856 ASN A1005 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN C 115 GLN C 207 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN C1135 ASN ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26627 Z= 0.224 Angle : 0.678 16.595 36215 Z= 0.329 Chirality : 0.048 0.536 4328 Planarity : 0.004 0.048 4573 Dihedral : 8.113 59.875 4918 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.33 % Favored : 92.54 % Rotamer: Outliers : 5.89 % Allowed : 22.76 % Favored : 71.34 % 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: -1.64 (0.14), residues: 3136 helix: 1.28 (0.21), residues: 635 sheet: -0.95 (0.18), residues: 792 loop : -2.17 (0.13), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 104 HIS 0.012 0.001 HIS C 207 PHE 0.028 0.001 PHE C 464 TYR 0.025 0.001 TYR L 97 ARG 0.005 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 157 time to evaluate : 3.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 ASN cc_start: 0.5955 (OUTLIER) cc_final: 0.5525 (m-40) REVERT: A 822 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8552 (mm) REVERT: B 153 MET cc_start: -0.1274 (mpp) cc_final: -0.2795 (ptp) REVERT: C 66 HIS cc_start: 0.5918 (OUTLIER) cc_final: 0.5518 (t-90) REVERT: C 369 TYR cc_start: 0.7197 (OUTLIER) cc_final: 0.6580 (p90) REVERT: C 402 ILE cc_start: 0.5580 (OUTLIER) cc_final: 0.4990 (tt) REVERT: C 611 LEU cc_start: 0.8370 (tp) cc_final: 0.8161 (tt) REVERT: C 697 MET cc_start: 0.8097 (ptm) cc_final: 0.7821 (ptp) REVERT: C 699 LEU cc_start: 0.8546 (mp) cc_final: 0.8108 (mt) REVERT: C 973 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8305 (mt) REVERT: C 975 SER cc_start: 0.8538 (t) cc_final: 0.8207 (p) REVERT: C 1132 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8648 (pp) REVERT: C 1135 ASN cc_start: 0.8106 (OUTLIER) cc_final: 0.7901 (t0) outliers start: 166 outliers final: 97 residues processed: 307 average time/residue: 0.3667 time to fit residues: 191.1490 Evaluate side-chains 242 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 137 time to evaluate : 3.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain L residue 102 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 256 optimal weight: 2.9990 chunk 175 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 chunk 229 optimal weight: 10.0000 chunk 127 optimal weight: 20.0000 chunk 263 optimal weight: 0.9990 chunk 213 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 157 optimal weight: 1.9990 chunk 276 optimal weight: 0.0670 chunk 77 optimal weight: 7.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN A 856 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 207 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 ASN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.4897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26627 Z= 0.211 Angle : 0.661 13.443 36215 Z= 0.320 Chirality : 0.047 0.481 4328 Planarity : 0.004 0.046 4573 Dihedral : 7.602 59.631 4906 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.86 % Favored : 92.98 % Rotamer: Outliers : 5.22 % Allowed : 23.40 % Favored : 71.38 % 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: -1.40 (0.14), residues: 3136 helix: 1.51 (0.22), residues: 636 sheet: -0.80 (0.18), residues: 779 loop : -2.03 (0.13), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP H 49 HIS 0.016 0.001 HIS C 207 PHE 0.022 0.001 PHE A 135 TYR 0.030 0.001 TYR A 200 ARG 0.004 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 161 time to evaluate : 3.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 ASN cc_start: 0.6014 (OUTLIER) cc_final: 0.5623 (m-40) REVERT: A 822 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8451 (mm) REVERT: B 153 MET cc_start: -0.1134 (mpp) cc_final: -0.2400 (ptp) REVERT: B 1037 SER cc_start: 0.8796 (OUTLIER) cc_final: 0.8366 (p) REVERT: C 52 GLN cc_start: 0.7654 (mm-40) cc_final: 0.7379 (tp-100) REVERT: C 66 HIS cc_start: 0.5965 (OUTLIER) cc_final: 0.5599 (t-90) REVERT: C 277 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.6659 (mt) REVERT: C 369 TYR cc_start: 0.7348 (OUTLIER) cc_final: 0.6587 (p90) REVERT: C 402 ILE cc_start: 0.5448 (OUTLIER) cc_final: 0.5024 (tt) REVERT: C 611 LEU cc_start: 0.8476 (tp) cc_final: 0.8256 (tt) REVERT: C 697 MET cc_start: 0.8196 (ptm) cc_final: 0.7929 (ptp) REVERT: C 699 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8128 (mt) REVERT: C 973 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8449 (mt) REVERT: C 1132 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8632 (pp) REVERT: C 1135 ASN cc_start: 0.7982 (OUTLIER) cc_final: 0.7154 (m-40) outliers start: 147 outliers final: 96 residues processed: 293 average time/residue: 0.3308 time to fit residues: 166.5051 Evaluate side-chains 249 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 142 time to evaluate : 3.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 49 TRP Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain L residue 102 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 103 optimal weight: 6.9990 chunk 277 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 181 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 chunk 308 optimal weight: 8.9990 chunk 256 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 25 optimal weight: 20.0000 chunk 102 optimal weight: 3.9990 chunk 162 optimal weight: 0.5980 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN B 121 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN B 969 ASN B1002 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.5313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26627 Z= 0.219 Angle : 0.652 11.607 36215 Z= 0.315 Chirality : 0.047 0.464 4328 Planarity : 0.004 0.049 4573 Dihedral : 7.275 59.162 4902 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.89 % Favored : 92.92 % Rotamer: Outliers : 5.11 % Allowed : 23.83 % Favored : 71.06 % 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: -1.21 (0.15), residues: 3136 helix: 1.65 (0.22), residues: 638 sheet: -0.60 (0.18), residues: 791 loop : -1.96 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 104 HIS 0.013 0.001 HIS C 207 PHE 0.023 0.001 PHE A 92 TYR 0.022 0.001 TYR L 97 ARG 0.006 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 150 time to evaluate : 2.885 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 164 ASN cc_start: 0.6053 (OUTLIER) cc_final: 0.5718 (m-40) REVERT: A 765 ARG cc_start: 0.7210 (ttm-80) cc_final: 0.6833 (ttm-80) REVERT: A 822 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8369 (mm) REVERT: B 153 MET cc_start: -0.0746 (mpp) cc_final: -0.1831 (ptm) REVERT: C 66 HIS cc_start: 0.6255 (OUTLIER) cc_final: 0.5824 (t-90) REVERT: C 277 LEU cc_start: 0.7011 (OUTLIER) cc_final: 0.6798 (mt) REVERT: C 369 TYR cc_start: 0.7340 (OUTLIER) cc_final: 0.6543 (p90) REVERT: C 402 ILE cc_start: 0.5519 (OUTLIER) cc_final: 0.5099 (tt) REVERT: C 697 MET cc_start: 0.8187 (ptm) cc_final: 0.7888 (ptp) REVERT: C 699 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8132 (mt) REVERT: C 1132 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8651 (pp) REVERT: C 1135 ASN cc_start: 0.8187 (OUTLIER) cc_final: 0.7338 (m-40) outliers start: 144 outliers final: 107 residues processed: 281 average time/residue: 0.3280 time to fit residues: 156.2708 Evaluate side-chains 251 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 135 time to evaluate : 2.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 49 TRP Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain L residue 102 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 297 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 175 optimal weight: 7.9990 chunk 225 optimal weight: 0.6980 chunk 174 optimal weight: 0.9980 chunk 259 optimal weight: 10.0000 chunk 172 optimal weight: 7.9990 chunk 307 optimal weight: 20.0000 chunk 192 optimal weight: 1.9990 chunk 187 optimal weight: 7.9990 chunk 141 optimal weight: 20.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 856 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN C1135 ASN ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.5637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26627 Z= 0.216 Angle : 0.648 16.409 36215 Z= 0.313 Chirality : 0.047 0.465 4328 Planarity : 0.004 0.055 4573 Dihedral : 7.159 58.899 4900 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.73 % Favored : 93.14 % Rotamer: Outliers : 4.79 % Allowed : 24.29 % Favored : 70.92 % 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 (0.15), residues: 3136 helix: 1.73 (0.22), residues: 638 sheet: -0.43 (0.18), residues: 782 loop : -1.89 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 104 HIS 0.005 0.001 HIS C 207 PHE 0.030 0.001 PHE A 92 TYR 0.023 0.001 TYR L 97 ARG 0.003 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 140 time to evaluate : 2.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 ASN cc_start: 0.6148 (OUTLIER) cc_final: 0.5782 (m-40) REVERT: A 765 ARG cc_start: 0.7264 (ttm-80) cc_final: 0.6933 (ttm-80) REVERT: A 822 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8327 (mm) REVERT: B 153 MET cc_start: -0.0655 (mpp) cc_final: -0.1673 (ptm) REVERT: B 900 MET cc_start: 0.7351 (OUTLIER) cc_final: 0.7114 (mtm) REVERT: C 66 HIS cc_start: 0.6353 (OUTLIER) cc_final: 0.5834 (t-90) REVERT: C 369 TYR cc_start: 0.7373 (OUTLIER) cc_final: 0.6518 (p90) REVERT: C 398 ASP cc_start: 0.5473 (m-30) cc_final: 0.5204 (t70) REVERT: C 402 ILE cc_start: 0.5708 (OUTLIER) cc_final: 0.5327 (tt) REVERT: C 697 MET cc_start: 0.8238 (ptm) cc_final: 0.7933 (ptp) REVERT: C 699 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8087 (mt) REVERT: C 1132 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8625 (pp) REVERT: C 1135 ASN cc_start: 0.8113 (OUTLIER) cc_final: 0.7839 (t0) REVERT: H 116 TYR cc_start: 0.4557 (OUTLIER) cc_final: 0.4087 (t80) outliers start: 135 outliers final: 106 residues processed: 262 average time/residue: 0.3592 time to fit residues: 161.2782 Evaluate side-chains 247 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 131 time to evaluate : 3.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain L residue 102 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 190 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 195 optimal weight: 0.9980 chunk 209 optimal weight: 10.0000 chunk 152 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 241 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN B 125 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 207 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 409 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 965 GLN ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.6214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 26627 Z= 0.288 Angle : 0.692 15.576 36215 Z= 0.337 Chirality : 0.048 0.481 4328 Planarity : 0.004 0.049 4573 Dihedral : 7.414 58.393 4899 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.37 % Favored : 92.51 % Rotamer: Outliers : 5.08 % Allowed : 24.04 % Favored : 70.88 % 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 (0.15), residues: 3136 helix: 1.64 (0.21), residues: 639 sheet: -0.33 (0.18), residues: 793 loop : -1.91 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP H 49 HIS 0.004 0.001 HIS C 207 PHE 0.027 0.002 PHE H 114 TYR 0.032 0.002 TYR L 97 ARG 0.005 0.001 ARG C 577 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 135 time to evaluate : 2.958 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 765 ARG cc_start: 0.7279 (ttm-80) cc_final: 0.6966 (ttm-80) REVERT: A 822 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8420 (mm) REVERT: A 1002 GLN cc_start: 0.7491 (tm-30) cc_final: 0.7210 (tm-30) REVERT: B 153 MET cc_start: -0.0046 (mpp) cc_final: -0.0905 (ptm) REVERT: B 900 MET cc_start: 0.7523 (OUTLIER) cc_final: 0.7308 (mtm) REVERT: C 66 HIS cc_start: 0.6114 (OUTLIER) cc_final: 0.5754 (t-90) REVERT: C 369 TYR cc_start: 0.7359 (OUTLIER) cc_final: 0.6363 (p90) REVERT: C 402 ILE cc_start: 0.5987 (OUTLIER) cc_final: 0.5649 (tt) REVERT: C 573 THR cc_start: 0.7998 (m) cc_final: 0.7710 (t) REVERT: C 697 MET cc_start: 0.8184 (ptm) cc_final: 0.7873 (ptp) REVERT: C 699 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8142 (mt) REVERT: C 856 ASN cc_start: 0.7827 (OUTLIER) cc_final: 0.7147 (p0) outliers start: 143 outliers final: 110 residues processed: 266 average time/residue: 0.3342 time to fit residues: 150.8970 Evaluate side-chains 244 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 127 time to evaluate : 2.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 49 TRP Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain L residue 102 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 279 optimal weight: 0.0020 chunk 294 optimal weight: 6.9990 chunk 268 optimal weight: 0.0980 chunk 286 optimal weight: 5.9990 chunk 172 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 224 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 258 optimal weight: 0.9990 chunk 270 optimal weight: 1.9990 chunk 285 optimal weight: 6.9990 overall best weight: 0.8192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1071 GLN C 207 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN C 394 ASN C 409 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 935 GLN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.6310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 26627 Z= 0.152 Angle : 0.630 16.016 36215 Z= 0.304 Chirality : 0.047 0.463 4328 Planarity : 0.004 0.050 4573 Dihedral : 7.096 56.626 4896 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.06 % Favored : 93.81 % Rotamer: Outliers : 3.59 % Allowed : 25.60 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.15), residues: 3136 helix: 1.83 (0.22), residues: 642 sheet: -0.17 (0.19), residues: 782 loop : -1.79 (0.14), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP H 49 HIS 0.010 0.001 HIS H 99 PHE 0.027 0.001 PHE C 562 TYR 0.023 0.001 TYR A 200 ARG 0.004 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 143 time to evaluate : 2.857 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 765 ARG cc_start: 0.7237 (ttm-80) cc_final: 0.6903 (ttm-80) REVERT: A 822 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8252 (mm) REVERT: A 869 MET cc_start: 0.8683 (mpp) cc_final: 0.7744 (ptp) REVERT: A 1002 GLN cc_start: 0.7362 (tm-30) cc_final: 0.7077 (tm-30) REVERT: B 153 MET cc_start: 0.0131 (mpp) cc_final: -0.0770 (ptm) REVERT: C 66 HIS cc_start: 0.6228 (OUTLIER) cc_final: 0.5896 (t-90) REVERT: C 369 TYR cc_start: 0.7311 (OUTLIER) cc_final: 0.6411 (p90) REVERT: C 402 ILE cc_start: 0.5956 (OUTLIER) cc_final: 0.5665 (tt) REVERT: C 573 THR cc_start: 0.7916 (m) cc_final: 0.7637 (t) REVERT: C 699 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.7939 (mt) REVERT: C 856 ASN cc_start: 0.7779 (OUTLIER) cc_final: 0.7174 (p0) outliers start: 101 outliers final: 80 residues processed: 231 average time/residue: 0.3467 time to fit residues: 135.1261 Evaluate side-chains 219 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 133 time to evaluate : 3.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 49 TRP Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain L residue 102 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 188 optimal weight: 2.9990 chunk 302 optimal weight: 20.0000 chunk 184 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 210 optimal weight: 3.9990 chunk 317 optimal weight: 20.0000 chunk 292 optimal weight: 0.8980 chunk 253 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 chunk 195 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.6318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 26627 Z= 0.195 Angle : 0.742 59.198 36215 Z= 0.390 Chirality : 0.047 0.464 4328 Planarity : 0.004 0.065 4573 Dihedral : 7.025 56.667 4891 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.22 % Favored : 93.69 % Rotamer: Outliers : 3.41 % Allowed : 25.39 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.15), residues: 3136 helix: 1.82 (0.22), residues: 642 sheet: -0.15 (0.19), residues: 782 loop : -1.80 (0.14), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP H 49 HIS 0.074 0.002 HIS C 207 PHE 0.026 0.001 PHE C 562 TYR 0.021 0.001 TYR L 97 ARG 0.003 0.000 ARG C 466 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 133 time to evaluate : 2.824 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 765 ARG cc_start: 0.7243 (ttm-80) cc_final: 0.6908 (ttm-80) REVERT: A 822 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8262 (mm) REVERT: A 869 MET cc_start: 0.8677 (mpp) cc_final: 0.7756 (ptp) REVERT: A 1002 GLN cc_start: 0.7369 (tm-30) cc_final: 0.7076 (tm-30) REVERT: B 153 MET cc_start: 0.0135 (mpp) cc_final: -0.0767 (ptm) REVERT: C 66 HIS cc_start: 0.6176 (OUTLIER) cc_final: 0.5898 (t-90) REVERT: C 369 TYR cc_start: 0.7320 (OUTLIER) cc_final: 0.6417 (p90) REVERT: C 402 ILE cc_start: 0.5944 (OUTLIER) cc_final: 0.5668 (tt) REVERT: C 573 THR cc_start: 0.7941 (m) cc_final: 0.7647 (t) REVERT: C 699 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.7941 (mt) REVERT: C 856 ASN cc_start: 0.7777 (OUTLIER) cc_final: 0.7178 (p0) outliers start: 96 outliers final: 85 residues processed: 214 average time/residue: 0.3458 time to fit residues: 125.3110 Evaluate side-chains 220 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 129 time to evaluate : 2.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 49 TRP Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain L residue 102 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 201 optimal weight: 1.9990 chunk 269 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 233 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 253 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 260 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 81 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.098004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.067710 restraints weight = 96382.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.069523 restraints weight = 57179.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.069463 restraints weight = 37766.653| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.6517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 26627 Z= 0.275 Angle : 0.672 17.814 36215 Z= 0.325 Chirality : 0.048 0.472 4328 Planarity : 0.004 0.049 4573 Dihedral : 7.087 56.832 4891 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.21 % Favored : 92.70 % Rotamer: Outliers : 3.66 % Allowed : 25.14 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.15), residues: 3136 helix: 1.79 (0.22), residues: 639 sheet: -0.20 (0.18), residues: 791 loop : -1.79 (0.14), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP C 353 HIS 0.005 0.001 HIS B1048 PHE 0.031 0.002 PHE C 329 TYR 0.026 0.002 TYR A 200 ARG 0.018 0.001 ARG C 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5039.84 seconds wall clock time: 94 minutes 11.48 seconds (5651.48 seconds total)