Starting phenix.real_space_refine on Fri Mar 22 18:10:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xid_33203/03_2024/7xid_33203.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xid_33203/03_2024/7xid_33203.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xid_33203/03_2024/7xid_33203.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xid_33203/03_2024/7xid_33203.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xid_33203/03_2024/7xid_33203.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xid_33203/03_2024/7xid_33203.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.078 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 164 5.16 5 C 21850 2.51 5 N 5566 2.21 5 O 6676 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ARG 493": "NH1" <-> "NH2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ARG 493": "NH1" <-> "NH2" Residue "C GLU 516": "OE1" <-> "OE2" Residue "D GLU 22": "OE1" <-> "OE2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 145": "OE1" <-> "OE2" Residue "D GLU 160": "OE1" <-> "OE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D GLU 189": "OE1" <-> "OE2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D ARG 245": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "D GLU 312": "OE1" <-> "OE2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D GLU 430": "OE1" <-> "OE2" Residue "D GLU 435": "OE1" <-> "OE2" Residue "D GLU 457": "OE1" <-> "OE2" Residue "D ARG 518": "NH1" <-> "NH2" Residue "D GLU 536": "OE1" <-> "OE2" Residue "D GLU 564": "OE1" <-> "OE2" Residue "E GLU 22": "OE1" <-> "OE2" Residue "E GLU 57": "OE1" <-> "OE2" Residue "E GLU 110": "OE1" <-> "OE2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 145": "OE1" <-> "OE2" Residue "E GLU 160": "OE1" <-> "OE2" Residue "E ARG 169": "NH1" <-> "NH2" Residue "E ARG 177": "NH1" <-> "NH2" Residue "E GLU 189": "OE1" <-> "OE2" Residue "E ARG 192": "NH1" <-> "NH2" Residue "E ARG 245": "NH1" <-> "NH2" Residue "E ARG 273": "NH1" <-> "NH2" Residue "E GLU 312": "OE1" <-> "OE2" Residue "E ARG 357": "NH1" <-> "NH2" Residue "E GLU 430": "OE1" <-> "OE2" Residue "E GLU 435": "OE1" <-> "OE2" Residue "E GLU 457": "OE1" <-> "OE2" Residue "E ARG 518": "NH1" <-> "NH2" Residue "E GLU 536": "OE1" <-> "OE2" Residue "E GLU 564": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 34256 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 7558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 963, 7558 Classifications: {'peptide': 963} Link IDs: {'PTRANS': 52, 'TRANS': 910} Chain breaks: 10 Chain: "B" Number of atoms: 7842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7842 Classifications: {'peptide': 998} Link IDs: {'PTRANS': 54, 'TRANS': 943} Chain breaks: 9 Chain: "C" Number of atoms: 7842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7842 Classifications: {'peptide': 998} Link IDs: {'PTRANS': 54, 'TRANS': 943} Chain breaks: 9 Chain: "D" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Chain: "E" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 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: "D" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "E" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 17.56, per 1000 atoms: 0.51 Number of scatterers: 34256 At special positions: 0 Unit cell: (135.875, 196.747, 246.749, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 164 16.00 O 6676 8.00 N 5566 7.00 C 21850 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.19 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=1.97 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.39 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.15 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.15 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.12 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.18 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.07 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.14 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.09 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.02 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.20 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=1.99 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.17 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.26 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=1.97 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.17 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.10 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.09 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.18 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.09 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.01 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.06 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.05 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.08 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.20 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.15 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.19 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.02 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.14 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.19 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A1406 " - " NAG A1407 " " NAG B1410 " - " NAG B1411 " " NAG D 905 " - " NAG D 906 " " NAG D 906 " - " NAG D 907 " " NAG E 905 " - " NAG E 906 " " NAG E 906 " - " NAG E 907 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " NAG B1406 " " 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 T 2 " - " NAG C1406 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 343 " " NAG A1408 " - " ASN A 603 " " NAG A1409 " - " ASN A 616 " " NAG A1410 " - " ASN A 657 " " NAG A1411 " - " 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 B1407 " - " ASN B 603 " " NAG B1408 " - " ASN B 616 " " NAG B1409 " - " ASN B 657 " " NAG B1410 " - " ASN B1074 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 282 " " NAG C1407 " - " ASN C 603 " " NAG C1408 " - " ASN C 616 " " NAG C1409 " - " ASN C 657 " " NAG D 901 " - " ASN D 90 " " NAG D 902 " - " ASN D 103 " " NAG D 903 " - " ASN D 322 " " NAG D 904 " - " ASN D 432 " " NAG D 905 " - " ASN D 546 " " NAG E 901 " - " ASN E 90 " " NAG E 902 " - " ASN E 103 " " NAG E 903 " - " ASN E 322 " " NAG E 904 " - " ASN E 432 " " NAG E 905 " - " ASN E 546 " " NAG F 1 " - " ASN A 331 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1074 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG L 1 " - " ASN B 331 " " NAG M 1 " - " ASN B 343 " " 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 343 " " NAG U 1 " - " ASN C 709 " " NAG V 1 " - " ASN C 717 " " NAG W 1 " - " ASN C 801 " " NAG X 1 " - " ASN C1074 " " NAG Y 1 " - " ASN C1098 " " NAG Z 1 " - " ASN C1134 " " NAG a 1 " - " ASN D 53 " " NAG b 1 " - " ASN E 53 " Time building additional restraints: 13.19 Conformation dependent library (CDL) restraints added in 5.4 seconds 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7824 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 47 sheets defined 37.2% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.95 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.491A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.542A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.529A 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: 3.791A pdb=" N LYS A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.701A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.252A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 932 Processing helix chain 'A' and resid 933 through 940 Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.761A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 968 removed outlier: 3.703A pdb=" N SER A 968 " --> pdb=" O GLN A 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 965 through 968' Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.758A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.982A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (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 349 through 353 removed outlier: 3.801A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 404 through 410 removed outlier: 4.158A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 removed outlier: 4.087A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.872A 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: 3.985A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 removed outlier: 3.590A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.515A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.576A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.650A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.591A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 4.078A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.758A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 983 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.323A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.536A 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 349 through 353 removed outlier: 3.802A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 388 Processing helix chain 'C' and resid 404 through 410 removed outlier: 4.158A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 753 Processing helix chain 'C' and resid 754 through 756 No H-bonds generated for 'chain 'C' and resid 754 through 756' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.612A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.655A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 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 933 Processing helix chain 'C' and resid 933 through 939 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.322A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (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 976 through 981 removed outlier: 3.810A pdb=" N PHE C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.931A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'D' and resid 21 through 53 removed outlier: 4.081A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 removed outlier: 3.694A pdb=" N GLN D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 83 No H-bonds generated for 'chain 'D' and resid 82 through 83' Processing helix chain 'D' and resid 84 through 88 removed outlier: 4.522A pdb=" N GLU D 87 " --> pdb=" O PRO D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 101 removed outlier: 3.585A pdb=" N LYS D 94 " --> pdb=" O ASN D 90 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN D 96 " --> pdb=" O THR D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 removed outlier: 3.562A pdb=" N SER D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 154 removed outlier: 3.932A pdb=" N MET D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 193 removed outlier: 3.935A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU D 171 " --> pdb=" O SER D 167 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.598A pdb=" N GLU D 189 " --> pdb=" O VAL D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.641A pdb=" N TYR D 202 " --> pdb=" O ASP D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 221 through 231 removed outlier: 4.100A pdb=" N ASP D 225 " --> pdb=" O GLN D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 247 removed outlier: 3.550A pdb=" N TYR D 237 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TYR D 243 " --> pdb=" O HIS D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 319 removed outlier: 3.732A pdb=" N ILE D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE D 315 " --> pdb=" O ALA D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.527A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN D 330 " --> pdb=" O GLY D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.809A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.592A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.555A pdb=" N ALA D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU D 410 " --> pdb=" O GLU D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 466 removed outlier: 3.608A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLY D 448 " --> pdb=" O LEU D 444 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N THR D 449 " --> pdb=" O THR D 445 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU D 450 " --> pdb=" O ILE D 446 " (cutoff:3.500A) Proline residue: D 451 - end of helix Processing helix chain 'D' and resid 472 through 482 removed outlier: 4.546A pdb=" N TRP D 478 " --> pdb=" O MET D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 502 removed outlier: 3.769A pdb=" N ALA D 501 " --> pdb=" O CYS D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 529 removed outlier: 4.750A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU D 527 " --> pdb=" O PHE D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.628A pdb=" N LYS D 541 " --> pdb=" O PRO D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.753A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 removed outlier: 4.382A pdb=" N ASP D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 602 No H-bonds generated for 'chain 'D' and resid 600 through 602' Processing helix chain 'E' and resid 21 through 53 removed outlier: 4.081A pdb=" N HIS E 34 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU E 39 " --> pdb=" O GLU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 removed outlier: 3.694A pdb=" N GLN E 81 " --> pdb=" O SER E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 removed outlier: 3.585A pdb=" N LYS E 94 " --> pdb=" O ASN E 90 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 129 removed outlier: 3.562A pdb=" N SER E 113 " --> pdb=" O SER E 109 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS E 114 " --> pdb=" O GLU E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 154 removed outlier: 3.932A pdb=" N MET E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 193 removed outlier: 3.935A pdb=" N ARG E 169 " --> pdb=" O TRP E 165 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU E 171 " --> pdb=" O SER E 167 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LYS E 174 " --> pdb=" O SER E 170 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN E 175 " --> pdb=" O GLU E 171 " (cutoff:3.500A) Proline residue: E 178 - end of helix removed outlier: 3.597A pdb=" N GLU E 189 " --> pdb=" O VAL E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 removed outlier: 3.641A pdb=" N TYR E 202 " --> pdb=" O ASP E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 221 through 231 removed outlier: 4.100A pdb=" N ASP E 225 " --> pdb=" O GLN E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 247 removed outlier: 3.551A pdb=" N TYR E 237 " --> pdb=" O ILE E 233 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TYR E 243 " --> pdb=" O HIS E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 277 No H-bonds generated for 'chain 'E' and resid 275 through 277' Processing helix chain 'E' and resid 278 through 283 Processing helix chain 'E' and resid 293 through 300 Processing helix chain 'E' and resid 303 through 319 removed outlier: 3.732A pdb=" N ILE E 307 " --> pdb=" O ASP E 303 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE E 308 " --> pdb=" O ALA E 304 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE E 315 " --> pdb=" O ALA E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 331 removed outlier: 3.527A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN E 330 " --> pdb=" O GLY E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.810A pdb=" N HIS E 378 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 393 removed outlier: 3.592A pdb=" N ARG E 393 " --> pdb=" O PHE E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 413 removed outlier: 3.555A pdb=" N ALA E 403 " --> pdb=" O GLY E 399 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE E 407 " --> pdb=" O ALA E 403 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N SER E 409 " --> pdb=" O GLY E 405 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU E 410 " --> pdb=" O GLU E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 466 removed outlier: 3.608A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR E 445 " --> pdb=" O LYS E 441 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLY E 448 " --> pdb=" O LEU E 444 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N THR E 449 " --> pdb=" O THR E 445 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU E 450 " --> pdb=" O ILE E 446 " (cutoff:3.500A) Proline residue: E 451 - end of helix Processing helix chain 'E' and resid 472 through 482 removed outlier: 4.547A pdb=" N TRP E 478 " --> pdb=" O MET E 474 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 502 removed outlier: 3.768A pdb=" N ALA E 501 " --> pdb=" O CYS E 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 513 through 529 removed outlier: 4.751A pdb=" N THR E 519 " --> pdb=" O TYR E 515 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU E 520 " --> pdb=" O TYR E 516 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU E 527 " --> pdb=" O PHE E 523 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 removed outlier: 3.628A pdb=" N LYS E 541 " --> pdb=" O PRO E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.752A pdb=" N GLY E 551 " --> pdb=" O SER E 547 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 572 Processing helix chain 'E' and resid 581 through 588 Processing helix chain 'E' and resid 588 through 599 removed outlier: 4.383A pdb=" N ASP E 597 " --> pdb=" O THR E 593 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 602 No H-bonds generated for 'chain 'E' and resid 600 through 602' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.515A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 7.395A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.326A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 92 removed outlier: 6.306A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.468A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 323 through 328 removed outlier: 5.675A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.777A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.174A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.292A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.752A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.752A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.485A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.769A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.850A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.590A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 49 through 55 removed outlier: 7.471A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.512A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.696A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER B 596 " --> pdb=" O LEU B 611 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU B 611 " --> pdb=" O SER B 596 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 323 through 328 removed outlier: 5.857A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.550A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC5, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.577A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.546A pdb=" N ASN B 703 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.152A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.152A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.498A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.944A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.686A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 49 through 55 removed outlier: 7.498A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.924A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU C 117 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLU C 132 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 90 through 92 removed outlier: 3.739A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.478A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 323 through 328 removed outlier: 5.456A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.551A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.307A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.892A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.892A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.301A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE6, first strand: chain 'D' and resid 131 through 133 Processing sheet with id=AE7, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.367A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.174A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 131 through 133 Processing sheet with id=AF1, first strand: chain 'E' and resid 262 through 263 removed outlier: 5.368A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.175A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 1382 hydrogen bonds defined for protein. 3867 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.52 Time building geometry restraints manager: 14.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7165 1.33 - 1.45: 9149 1.45 - 1.58: 18523 1.58 - 1.70: 0 1.70 - 1.83: 233 Bond restraints: 35070 Sorted by residual: bond pdb=" CA SER A 698 " pdb=" C SER A 698 " ideal model delta sigma weight residual 1.522 1.443 0.080 1.20e-02 6.94e+03 4.40e+01 bond pdb=" C THR C 208 " pdb=" N PRO C 209 " ideal model delta sigma weight residual 1.329 1.386 -0.058 1.20e-02 6.94e+03 2.31e+01 bond pdb=" C THR B 208 " pdb=" N PRO B 209 " ideal model delta sigma weight residual 1.329 1.386 -0.057 1.25e-02 6.40e+03 2.08e+01 bond pdb=" C THR A 208 " pdb=" N PRO A 209 " ideal model delta sigma weight residual 1.329 1.386 -0.057 1.25e-02 6.40e+03 2.08e+01 bond pdb=" N PRO A1143 " pdb=" CD PRO A1143 " ideal model delta sigma weight residual 1.473 1.412 0.061 1.40e-02 5.10e+03 1.90e+01 ... (remaining 35065 not shown) Histogram of bond angle deviations from ideal: 98.85 - 106.86: 1195 106.86 - 114.86: 20851 114.86 - 122.87: 22411 122.87 - 130.88: 3053 130.88 - 138.89: 161 Bond angle restraints: 47671 Sorted by residual: angle pdb=" N ASN D 432 " pdb=" CA ASN D 432 " pdb=" C ASN D 432 " ideal model delta sigma weight residual 111.82 120.40 -8.58 1.16e+00 7.43e-01 5.47e+01 angle pdb=" N ASN E 432 " pdb=" CA ASN E 432 " pdb=" C ASN E 432 " ideal model delta sigma weight residual 111.82 120.39 -8.57 1.16e+00 7.43e-01 5.45e+01 angle pdb=" N ILE A 794 " pdb=" CA ILE A 794 " pdb=" C ILE A 794 " ideal model delta sigma weight residual 110.05 103.19 6.86 1.09e+00 8.42e-01 3.96e+01 angle pdb=" C THR C 208 " pdb=" N PRO C 209 " pdb=" CA PRO C 209 " ideal model delta sigma weight residual 120.31 114.37 5.94 9.80e-01 1.04e+00 3.68e+01 angle pdb=" C SER A 31 " pdb=" N PHE A 32 " pdb=" CA PHE A 32 " ideal model delta sigma weight residual 122.44 115.30 7.14 1.19e+00 7.06e-01 3.60e+01 ... (remaining 47666 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 20417 17.73 - 35.46: 1243 35.46 - 53.18: 252 53.18 - 70.91: 103 70.91 - 88.64: 37 Dihedral angle restraints: 22052 sinusoidal: 9916 harmonic: 12136 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 175.44 -82.44 1 1.00e+01 1.00e-02 8.34e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 175.40 -82.40 1 1.00e+01 1.00e-02 8.33e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -16.73 -69.27 1 1.00e+01 1.00e-02 6.20e+01 ... (remaining 22049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.335: 5515 0.335 - 0.669: 14 0.669 - 1.004: 4 1.004 - 1.339: 0 1.339 - 1.673: 6 Chirality restraints: 5539 Sorted by residual: chirality pdb=" C1 NAG B1406 " pdb=" O4 NAG M 2 " pdb=" C2 NAG B1406 " pdb=" O5 NAG B1406 " both_signs ideal model delta sigma weight residual False -2.40 -0.97 -1.43 2.00e-02 2.50e+03 5.13e+03 chirality pdb=" C1 NAG C1406 " pdb=" O4 NAG T 2 " pdb=" C2 NAG C1406 " pdb=" O5 NAG C1406 " both_signs ideal model delta sigma weight residual False -2.40 -0.97 -1.43 2.00e-02 2.50e+03 5.12e+03 chirality pdb=" C1 NAG A1407 " pdb=" O4 NAG A1406 " pdb=" C2 NAG A1407 " pdb=" O5 NAG A1407 " both_signs ideal model delta sigma weight residual False -2.40 -1.40 -1.00 2.00e-02 2.50e+03 2.52e+03 ... (remaining 5536 not shown) Planarity restraints: 6091 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.193 2.00e-02 2.50e+03 2.92e-01 1.06e+03 pdb=" CG ASN A 331 " 0.092 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.057 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.505 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " -0.348 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " -0.197 2.00e-02 2.50e+03 2.43e-01 7.40e+02 pdb=" CG ASN A 343 " 0.077 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " 0.415 2.00e-02 2.50e+03 pdb=" C1 NAG A1406 " -0.281 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 902 " 0.285 2.00e-02 2.50e+03 2.39e-01 7.16e+02 pdb=" C7 NAG D 902 " -0.074 2.00e-02 2.50e+03 pdb=" C8 NAG D 902 " 0.185 2.00e-02 2.50e+03 pdb=" N2 NAG D 902 " -0.407 2.00e-02 2.50e+03 pdb=" O7 NAG D 902 " 0.010 2.00e-02 2.50e+03 ... (remaining 6088 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 117 2.44 - 3.05: 21588 3.05 - 3.67: 48690 3.67 - 4.28: 74325 4.28 - 4.90: 120869 Nonbonded interactions: 265589 Sorted by model distance: nonbonded pdb=" O LYS A 528 " pdb=" CG LYS A 529 " model vdw 1.822 3.440 nonbonded pdb=" O PRO A 330 " pdb=" CG ASN A 331 " model vdw 2.040 3.270 nonbonded pdb=" O LEU B 335 " pdb=" O CYS B 336 " model vdw 2.062 3.040 nonbonded pdb=" O PRO B 39 " pdb=" CG ASP B 40 " model vdw 2.088 3.270 nonbonded pdb=" O LYS C 528 " pdb=" O LYS C 529 " model vdw 2.120 3.040 ... (remaining 265584 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 939 or resid 944 through 1146 or resid 1401 thr \ ough 1409)) selection = (chain 'B' and (resid 27 through 454 or resid 491 through 1146 or resid 1401 thr \ ough 1409)) selection = (chain 'C' and (resid 27 through 454 or resid 491 through 1146 or resid 1401 thr \ ough 1409)) } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 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: 6.990 Check model and map are aligned: 0.520 Set scattering table: 0.320 Process input model: 82.480 Find NCS groups from input model: 2.620 Set up NCS constraints: 0.510 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5990 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.103 35070 Z= 0.535 Angle : 1.042 13.891 47671 Z= 0.625 Chirality : 0.085 1.673 5539 Planarity : 0.007 0.239 6031 Dihedral : 12.613 88.639 14096 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 1.59 % Allowed : 5.99 % Favored : 92.41 % Rotamer: Outliers : 1.12 % Allowed : 3.88 % Favored : 95.00 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.94 % 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: -2.95 (0.11), residues: 4087 helix: -1.68 (0.12), residues: 1304 sheet: -0.68 (0.19), residues: 688 loop : -2.63 (0.12), residues: 2095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 163 HIS 0.007 0.001 HIS D 493 PHE 0.038 0.001 PHE A 377 TYR 0.027 0.002 TYR D 183 ARG 0.004 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 3658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 570 time to evaluate : 3.516 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: A 374 PHE cc_start: 0.1325 (OUTLIER) cc_final: 0.0545 (m-10) REVERT: B 153 MET cc_start: 0.1988 (mtp) cc_final: 0.0153 (ppp) REVERT: B 1123 SER cc_start: 0.7587 (t) cc_final: 0.7341 (m) REVERT: D 82 MET cc_start: 0.0480 (mmt) cc_final: 0.0209 (tmm) REVERT: D 376 MET cc_start: 0.2872 (ttm) cc_final: 0.2286 (ptt) REVERT: D 594 TRP cc_start: 0.0336 (t60) cc_final: -0.0990 (t-100) REVERT: D 596 LYS cc_start: 0.2288 (mttt) cc_final: 0.1749 (tttm) REVERT: E 114 LYS cc_start: 0.4617 (mmtm) cc_final: 0.3609 (mmmm) REVERT: E 127 TYR cc_start: -0.0004 (t80) cc_final: -0.2135 (t80) REVERT: E 480 MET cc_start: 0.0395 (mtp) cc_final: -0.0211 (ttp) outliers start: 41 outliers final: 7 residues processed: 611 average time/residue: 0.5054 time to fit residues: 491.7124 Evaluate side-chains 275 residues out of total 3658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 267 time to evaluate : 3.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain D residue 610 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 347 optimal weight: 5.9990 chunk 312 optimal weight: 8.9990 chunk 173 optimal weight: 2.9990 chunk 106 optimal weight: 20.0000 chunk 210 optimal weight: 0.8980 chunk 166 optimal weight: 1.9990 chunk 322 optimal weight: 20.0000 chunk 124 optimal weight: 30.0000 chunk 196 optimal weight: 3.9990 chunk 240 optimal weight: 7.9990 chunk 374 optimal weight: 9.9990 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 49 HIS A 121 ASN A 953 ASN A 957 GLN A1010 GLN A1011 GLN B 207 HIS B 218 GLN B 354 ASN B 360 ASN B 388 ASN B 487 ASN B 556 ASN B 613 GLN B 914 ASN B1088 HIS C 354 ASN C 360 ASN C 388 ASN C 448 ASN C 487 ASN C 607 GLN C 901 GLN D 61 ASN D 98 GLN D 149 ASN D 241 HIS E 42 GLN E 194 ASN E 241 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6363 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 35070 Z= 0.351 Angle : 0.796 19.774 47671 Z= 0.399 Chirality : 0.053 0.612 5539 Planarity : 0.005 0.051 6031 Dihedral : 7.353 60.411 6377 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.12 % Favored : 93.49 % Rotamer: Outliers : 2.35 % Allowed : 9.32 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.12), residues: 4087 helix: -0.14 (0.14), residues: 1299 sheet: -0.71 (0.21), residues: 585 loop : -2.19 (0.12), residues: 2203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP D 271 HIS 0.012 0.002 HIS A1064 PHE 0.027 0.002 PHE C 970 TYR 0.032 0.002 TYR E 41 ARG 0.008 0.001 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 273 time to evaluate : 3.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 PHE cc_start: 0.7633 (m-80) cc_final: 0.7334 (m-10) REVERT: A 374 PHE cc_start: 0.1520 (OUTLIER) cc_final: 0.0256 (m-10) REVERT: B 122 ASN cc_start: 0.3056 (OUTLIER) cc_final: 0.2141 (m110) REVERT: B 153 MET cc_start: 0.2576 (mtp) cc_final: 0.0313 (ppp) REVERT: B 336 CYS cc_start: -0.3071 (OUTLIER) cc_final: -0.3616 (t) REVERT: B 984 LEU cc_start: 0.7049 (tp) cc_final: 0.6804 (tp) REVERT: C 867 ASP cc_start: 0.6280 (OUTLIER) cc_final: 0.5972 (m-30) REVERT: D 152 MET cc_start: 0.1143 (tpp) cc_final: 0.0113 (ptt) REVERT: D 288 LYS cc_start: 0.3466 (mptt) cc_final: 0.3116 (mmtt) REVERT: D 474 MET cc_start: 0.1279 (OUTLIER) cc_final: 0.0558 (mtm) REVERT: D 594 TRP cc_start: 0.0379 (t60) cc_final: -0.1160 (t-100) REVERT: D 596 LYS cc_start: 0.2094 (mttt) cc_final: 0.1443 (tmtt) REVERT: E 82 MET cc_start: 0.0370 (tpp) cc_final: -0.0290 (mmt) REVERT: E 127 TYR cc_start: 0.0156 (t80) cc_final: -0.2075 (t80) REVERT: E 227 GLU cc_start: 0.1936 (OUTLIER) cc_final: 0.1603 (pt0) REVERT: E 323 MET cc_start: 0.1898 (mpp) cc_final: -0.1695 (mmm) REVERT: E 332 MET cc_start: 0.2165 (tmm) cc_final: 0.1390 (tmm) REVERT: E 360 MET cc_start: -0.2349 (mtt) cc_final: -0.2566 (mtt) REVERT: E 400 PHE cc_start: 0.1256 (OUTLIER) cc_final: -0.0768 (m-10) REVERT: E 480 MET cc_start: 0.0999 (mtp) cc_final: 0.0303 (ttt) REVERT: E 514 ARG cc_start: 0.4934 (ptt180) cc_final: 0.4227 (ptt-90) REVERT: E 557 MET cc_start: 0.1018 (OUTLIER) cc_final: 0.0623 (ttp) outliers start: 86 outliers final: 40 residues processed: 339 average time/residue: 0.4499 time to fit residues: 250.0662 Evaluate side-chains 260 residues out of total 3658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 212 time to evaluate : 3.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1139 ASP Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 400 PHE Chi-restraints excluded: chain E residue 557 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 207 optimal weight: 9.9990 chunk 116 optimal weight: 0.8980 chunk 311 optimal weight: 9.9990 chunk 254 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 374 optimal weight: 30.0000 chunk 404 optimal weight: 20.0000 chunk 333 optimal weight: 8.9990 chunk 371 optimal weight: 6.9990 chunk 127 optimal weight: 8.9990 chunk 300 optimal weight: 10.0000 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 901 GLN A1010 GLN A1011 GLN A1088 HIS ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 544 ASN B 556 ASN B 564 GLN B 955 ASN C 477 ASN C 505 HIS C 762 GLN E 33 ASN E 96 GLN E 442 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6521 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 35070 Z= 0.395 Angle : 0.750 17.086 47671 Z= 0.375 Chirality : 0.051 0.530 5539 Planarity : 0.005 0.046 6031 Dihedral : 6.892 59.336 6372 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.70 % Favored : 93.05 % Rotamer: Outliers : 2.71 % Allowed : 11.43 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.12), residues: 4087 helix: 0.44 (0.14), residues: 1318 sheet: -0.67 (0.20), residues: 649 loop : -2.20 (0.12), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 473 HIS 0.011 0.001 HIS B1064 PHE 0.025 0.002 PHE A 238 TYR 0.023 0.002 TYR E 385 ARG 0.009 0.001 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 237 time to evaluate : 4.026 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: A 153 MET cc_start: 0.2417 (pmm) cc_final: 0.1332 (mtt) REVERT: A 374 PHE cc_start: 0.1141 (OUTLIER) cc_final: 0.0238 (p90) REVERT: B 122 ASN cc_start: 0.2670 (OUTLIER) cc_final: 0.1559 (m110) REVERT: B 153 MET cc_start: 0.3063 (mtp) cc_final: 0.0423 (ppp) REVERT: B 270 LEU cc_start: 0.6867 (mt) cc_final: 0.6422 (mp) REVERT: B 402 ILE cc_start: -0.2388 (OUTLIER) cc_final: -0.2622 (pt) REVERT: D 152 MET cc_start: 0.1081 (tpp) cc_final: -0.0118 (ptt) REVERT: D 288 LYS cc_start: 0.3450 (mptt) cc_final: 0.3120 (mmtt) REVERT: D 474 MET cc_start: 0.0071 (mtm) cc_final: -0.0280 (mpp) REVERT: E 33 ASN cc_start: 0.5887 (OUTLIER) cc_final: 0.4314 (m-40) REVERT: E 127 TYR cc_start: 0.0485 (t80) cc_final: -0.1971 (t80) REVERT: E 227 GLU cc_start: 0.2061 (OUTLIER) cc_final: 0.1755 (pt0) REVERT: E 285 PHE cc_start: 0.0142 (m-80) cc_final: -0.0136 (m-80) REVERT: E 323 MET cc_start: 0.1622 (mpp) cc_final: -0.1552 (mmm) REVERT: E 332 MET cc_start: 0.3008 (OUTLIER) cc_final: 0.2100 (tmm) REVERT: E 357 ARG cc_start: 0.2623 (OUTLIER) cc_final: 0.2346 (mpt-90) REVERT: E 442 GLN cc_start: -0.1126 (mm-40) cc_final: -0.2063 (tm-30) REVERT: E 480 MET cc_start: 0.1070 (mtp) cc_final: -0.0146 (ttt) REVERT: E 514 ARG cc_start: 0.5093 (ptt180) cc_final: 0.4381 (ptt-90) REVERT: E 557 MET cc_start: 0.1186 (tpt) cc_final: 0.0531 (ttp) outliers start: 99 outliers final: 61 residues processed: 318 average time/residue: 0.4338 time to fit residues: 230.9161 Evaluate side-chains 268 residues out of total 3658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 200 time to evaluate : 3.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1011 GLN Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 477 ASN Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 103 ASN Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 357 ARG Chi-restraints excluded: chain E residue 366 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 370 optimal weight: 10.0000 chunk 281 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 178 optimal weight: 10.0000 chunk 251 optimal weight: 0.8980 chunk 376 optimal weight: 1.9990 chunk 398 optimal weight: 40.0000 chunk 196 optimal weight: 6.9990 chunk 356 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 675 GLN B 955 ASN C 437 ASN C 762 GLN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 ASN E 33 ASN E 149 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 35070 Z= 0.286 Angle : 0.665 14.609 47671 Z= 0.332 Chirality : 0.048 0.445 5539 Planarity : 0.004 0.044 6031 Dihedral : 6.504 59.558 6372 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.07 % Favored : 93.69 % Rotamer: Outliers : 2.79 % Allowed : 11.89 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % 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: -1.27 (0.13), residues: 4087 helix: 0.85 (0.14), residues: 1306 sheet: -0.66 (0.19), residues: 683 loop : -2.09 (0.12), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP D 473 HIS 0.006 0.001 HIS B1064 PHE 0.025 0.002 PHE D 314 TYR 0.023 0.001 TYR A1067 ARG 0.004 0.000 ARG C 815 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 210 time to evaluate : 3.602 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: A 153 MET cc_start: 0.2171 (pmm) cc_final: 0.1274 (mtp) REVERT: A 374 PHE cc_start: 0.0844 (OUTLIER) cc_final: 0.0068 (p90) REVERT: B 153 MET cc_start: 0.3284 (mtp) cc_final: 0.0517 (ppp) REVERT: B 270 LEU cc_start: 0.6750 (mt) cc_final: 0.6368 (mp) REVERT: B 336 CYS cc_start: -0.2627 (OUTLIER) cc_final: -0.3221 (t) REVERT: C 918 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6893 (mp0) REVERT: D 21 ILE cc_start: -0.1301 (OUTLIER) cc_final: -0.1747 (mt) REVERT: D 152 MET cc_start: 0.0965 (tpp) cc_final: -0.0106 (ptt) REVERT: D 376 MET cc_start: 0.2243 (ttm) cc_final: 0.1941 (ttp) REVERT: D 474 MET cc_start: -0.0184 (mtm) cc_final: -0.0617 (mpp) REVERT: D 549 GLU cc_start: 0.0910 (OUTLIER) cc_final: 0.0226 (tm-30) REVERT: E 33 ASN cc_start: 0.5203 (OUTLIER) cc_final: 0.4362 (m-40) REVERT: E 82 MET cc_start: 0.2949 (tpt) cc_final: 0.1722 (mmt) REVERT: E 127 TYR cc_start: 0.0620 (t80) cc_final: -0.1977 (t80) REVERT: E 227 GLU cc_start: 0.2041 (OUTLIER) cc_final: 0.1724 (pt0) REVERT: E 285 PHE cc_start: -0.0220 (m-80) cc_final: -0.0485 (m-80) REVERT: E 323 MET cc_start: 0.1481 (mpp) cc_final: -0.1588 (mmm) REVERT: E 332 MET cc_start: 0.3221 (OUTLIER) cc_final: 0.2201 (tmm) REVERT: E 442 GLN cc_start: -0.0987 (mm-40) cc_final: -0.1866 (tm-30) REVERT: E 474 MET cc_start: -0.0294 (mmp) cc_final: -0.0954 (mtp) REVERT: E 514 ARG cc_start: 0.5069 (ptt180) cc_final: 0.4315 (ptt-90) outliers start: 102 outliers final: 63 residues processed: 298 average time/residue: 0.4275 time to fit residues: 213.8950 Evaluate side-chains 262 residues out of total 3658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 191 time to evaluate : 3.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 471 ASP Chi-restraints excluded: chain D residue 549 GLU Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 103 ASN Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 471 ASP Chi-restraints excluded: chain E residue 513 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 331 optimal weight: 0.5980 chunk 226 optimal weight: 20.0000 chunk 5 optimal weight: 2.9990 chunk 296 optimal weight: 20.0000 chunk 164 optimal weight: 0.6980 chunk 339 optimal weight: 20.0000 chunk 275 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 203 optimal weight: 2.9990 chunk 357 optimal weight: 30.0000 chunk 100 optimal weight: 7.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN B 239 GLN C 477 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6538 moved from start: 0.4855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 35070 Z= 0.289 Angle : 0.637 12.886 47671 Z= 0.319 Chirality : 0.048 0.453 5539 Planarity : 0.004 0.045 6031 Dihedral : 6.237 59.055 6370 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.44 % Favored : 93.34 % Rotamer: Outliers : 3.06 % Allowed : 12.55 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % 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: -1.13 (0.13), residues: 4087 helix: 1.06 (0.15), residues: 1305 sheet: -0.61 (0.19), residues: 671 loop : -2.06 (0.13), residues: 2111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 594 HIS 0.005 0.001 HIS B1058 PHE 0.020 0.002 PHE A 855 TYR 0.027 0.001 TYR D 510 ARG 0.003 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 202 time to evaluate : 3.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.2078 (pmm) cc_final: 0.0044 (ptt) REVERT: A 374 PHE cc_start: 0.0138 (OUTLIER) cc_final: -0.0406 (p90) REVERT: A 995 ARG cc_start: 0.6569 (OUTLIER) cc_final: 0.6183 (mtm-85) REVERT: B 66 HIS cc_start: 0.5761 (OUTLIER) cc_final: 0.5267 (t-90) REVERT: B 153 MET cc_start: 0.3473 (mtp) cc_final: 0.0541 (ppp) REVERT: B 336 CYS cc_start: -0.2407 (OUTLIER) cc_final: -0.2967 (t) REVERT: C 153 MET cc_start: 0.4073 (tmm) cc_final: 0.3670 (tmm) REVERT: D 152 MET cc_start: 0.0800 (tpp) cc_final: -0.0188 (ptt) REVERT: D 288 LYS cc_start: 0.3382 (mptt) cc_final: 0.2564 (mttm) REVERT: D 376 MET cc_start: 0.2148 (ttm) cc_final: 0.1938 (ttp) REVERT: D 549 GLU cc_start: 0.1412 (OUTLIER) cc_final: 0.0550 (tp30) REVERT: E 33 ASN cc_start: 0.5440 (OUTLIER) cc_final: 0.4661 (m-40) REVERT: E 127 TYR cc_start: 0.0633 (t80) cc_final: -0.1925 (t80) REVERT: E 227 GLU cc_start: 0.1950 (OUTLIER) cc_final: 0.1707 (pt0) REVERT: E 285 PHE cc_start: -0.0207 (m-80) cc_final: -0.0481 (m-80) REVERT: E 323 MET cc_start: 0.1860 (mpp) cc_final: -0.1175 (mmm) REVERT: E 442 GLN cc_start: -0.0860 (mm-40) cc_final: -0.1796 (tm-30) REVERT: E 474 MET cc_start: -0.0051 (mmp) cc_final: -0.0777 (mtp) REVERT: E 480 MET cc_start: 0.1137 (mtp) cc_final: -0.0159 (ttt) REVERT: E 514 ARG cc_start: 0.4866 (OUTLIER) cc_final: 0.4220 (ptt-90) REVERT: E 559 ARG cc_start: 0.4309 (tmt170) cc_final: 0.1406 (ptp-170) outliers start: 112 outliers final: 77 residues processed: 298 average time/residue: 0.4423 time to fit residues: 219.2391 Evaluate side-chains 278 residues out of total 3658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 193 time to evaluate : 3.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 373 HIS Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 471 ASP Chi-restraints excluded: chain D residue 549 GLU Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 103 ASN Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 357 ARG Chi-restraints excluded: chain E residue 400 PHE Chi-restraints excluded: chain E residue 471 ASP Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain E residue 514 ARG Chi-restraints excluded: chain E residue 519 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 133 optimal weight: 2.9990 chunk 358 optimal weight: 30.0000 chunk 78 optimal weight: 8.9990 chunk 233 optimal weight: 30.0000 chunk 98 optimal weight: 3.9990 chunk 398 optimal weight: 20.0000 chunk 330 optimal weight: 20.0000 chunk 184 optimal weight: 1.9990 chunk 33 optimal weight: 20.0000 chunk 131 optimal weight: 0.8980 chunk 209 optimal weight: 9.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 804 GLN C 115 GLN C 164 ASN C 644 GLN ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 moved from start: 0.5350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 35070 Z= 0.365 Angle : 0.680 11.192 47671 Z= 0.341 Chirality : 0.049 0.472 5539 Planarity : 0.005 0.053 6031 Dihedral : 6.326 58.666 6370 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.17 % Favored : 92.59 % Rotamer: Outliers : 3.17 % Allowed : 13.26 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % 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: -1.18 (0.13), residues: 4087 helix: 1.09 (0.15), residues: 1309 sheet: -0.75 (0.19), residues: 688 loop : -2.11 (0.13), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 594 HIS 0.006 0.001 HIS B1058 PHE 0.049 0.002 PHE B 429 TYR 0.030 0.002 TYR D 587 ARG 0.003 0.001 ARG C 905 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 201 time to evaluate : 3.581 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: A 153 MET cc_start: 0.2176 (pmm) cc_final: 0.0001 (ptt) REVERT: A 374 PHE cc_start: 0.0358 (OUTLIER) cc_final: -0.0532 (p90) REVERT: A 995 ARG cc_start: 0.6479 (OUTLIER) cc_final: 0.5902 (mtm-85) REVERT: B 66 HIS cc_start: 0.5837 (OUTLIER) cc_final: 0.5133 (t-90) REVERT: B 153 MET cc_start: 0.3747 (mtp) cc_final: 0.0642 (ppp) REVERT: B 270 LEU cc_start: 0.6815 (mt) cc_final: 0.6562 (mp) REVERT: B 336 CYS cc_start: -0.2560 (OUTLIER) cc_final: -0.3083 (t) REVERT: C 153 MET cc_start: 0.4417 (tmm) cc_final: 0.4148 (tmm) REVERT: C 347 PHE cc_start: 0.2185 (OUTLIER) cc_final: 0.1228 (m-80) REVERT: D 21 ILE cc_start: -0.1350 (OUTLIER) cc_final: -0.1745 (mt) REVERT: D 152 MET cc_start: 0.0822 (tpp) cc_final: -0.0403 (ptt) REVERT: D 288 LYS cc_start: 0.3496 (mptt) cc_final: 0.2622 (mttm) REVERT: E 41 TYR cc_start: 0.2723 (t80) cc_final: 0.2305 (t80) REVERT: E 81 GLN cc_start: 0.2706 (tp40) cc_final: 0.1336 (mt0) REVERT: E 127 TYR cc_start: 0.0729 (t80) cc_final: -0.1960 (t80) REVERT: E 285 PHE cc_start: -0.0178 (m-80) cc_final: -0.0427 (m-80) REVERT: E 318 VAL cc_start: -0.1379 (OUTLIER) cc_final: -0.1590 (t) REVERT: E 323 MET cc_start: 0.1708 (mpp) cc_final: -0.1523 (mmm) REVERT: E 442 GLN cc_start: -0.0704 (mm-40) cc_final: -0.1782 (tm-30) REVERT: E 474 MET cc_start: -0.0202 (mmp) cc_final: -0.0892 (mtp) REVERT: E 559 ARG cc_start: 0.4200 (tmt170) cc_final: 0.1316 (ptp-170) outliers start: 116 outliers final: 81 residues processed: 298 average time/residue: 0.4269 time to fit residues: 212.1104 Evaluate side-chains 277 residues out of total 3658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 189 time to evaluate : 3.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 373 HIS Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 471 ASP Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 103 ASN Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 400 PHE Chi-restraints excluded: chain E residue 471 ASP Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain E residue 519 THR Chi-restraints excluded: chain E residue 604 VAL Chi-restraints excluded: chain E residue 609 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 384 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 227 optimal weight: 20.0000 chunk 291 optimal weight: 0.0670 chunk 225 optimal weight: 9.9990 chunk 335 optimal weight: 20.0000 chunk 222 optimal weight: 9.9990 chunk 397 optimal weight: 30.0000 chunk 248 optimal weight: 2.9990 chunk 242 optimal weight: 0.7980 chunk 183 optimal weight: 0.9980 overall best weight: 1.3722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 ASN C 762 GLN D 61 ASN ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 325 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6521 moved from start: 0.5447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35070 Z= 0.175 Angle : 0.588 10.037 47671 Z= 0.292 Chirality : 0.046 0.488 5539 Planarity : 0.004 0.065 6031 Dihedral : 5.848 59.374 6370 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.58 % Favored : 94.15 % Rotamer: Outliers : 2.24 % Allowed : 14.38 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % 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: -0.87 (0.13), residues: 4087 helix: 1.38 (0.15), residues: 1313 sheet: -0.59 (0.19), residues: 713 loop : -1.97 (0.13), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 594 HIS 0.004 0.001 HIS D 265 PHE 0.021 0.001 PHE B 92 TYR 0.020 0.001 TYR C1067 ARG 0.005 0.000 ARG B 646 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 197 time to evaluate : 3.716 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: A 153 MET cc_start: 0.2290 (pmm) cc_final: 0.0488 (ptt) REVERT: A 374 PHE cc_start: 0.0326 (OUTLIER) cc_final: -0.0448 (p90) REVERT: A 995 ARG cc_start: 0.6272 (OUTLIER) cc_final: 0.5711 (mtm-85) REVERT: B 66 HIS cc_start: 0.5789 (OUTLIER) cc_final: 0.5113 (t-90) REVERT: B 153 MET cc_start: 0.3886 (mtp) cc_final: 0.0698 (ppp) REVERT: B 336 CYS cc_start: -0.2475 (OUTLIER) cc_final: -0.2947 (t) REVERT: C 153 MET cc_start: 0.4164 (tmm) cc_final: 0.2700 (ttm) REVERT: C 237 ARG cc_start: 0.6597 (mtp-110) cc_final: 0.6317 (mtm110) REVERT: D 21 ILE cc_start: -0.1519 (OUTLIER) cc_final: -0.1837 (mp) REVERT: D 152 MET cc_start: 0.0764 (tpp) cc_final: -0.0489 (ptt) REVERT: D 259 ILE cc_start: 0.4278 (OUTLIER) cc_final: 0.4072 (tp) REVERT: D 288 LYS cc_start: 0.3630 (mptt) cc_final: 0.2431 (mttm) REVERT: E 41 TYR cc_start: 0.2735 (t80) cc_final: 0.2332 (t80) REVERT: E 81 GLN cc_start: 0.2810 (tp40) cc_final: 0.1474 (mt0) REVERT: E 82 MET cc_start: 0.2146 (tpt) cc_final: 0.1090 (mmt) REVERT: E 127 TYR cc_start: 0.0606 (t80) cc_final: -0.1896 (t80) REVERT: E 285 PHE cc_start: -0.0183 (m-80) cc_final: -0.0473 (m-80) REVERT: E 318 VAL cc_start: -0.1349 (OUTLIER) cc_final: -0.1586 (t) REVERT: E 323 MET cc_start: 0.1406 (mpp) cc_final: -0.1501 (mmm) REVERT: E 408 MET cc_start: 0.2377 (mmt) cc_final: 0.1930 (mmt) REVERT: E 442 GLN cc_start: -0.0858 (mm-40) cc_final: -0.1871 (tm-30) REVERT: E 474 MET cc_start: 0.0529 (mmp) cc_final: -0.0517 (mtp) REVERT: E 480 MET cc_start: 0.1363 (mtp) cc_final: 0.0046 (ttt) REVERT: E 559 ARG cc_start: 0.4250 (tmt170) cc_final: 0.1326 (ptp-170) outliers start: 82 outliers final: 55 residues processed: 272 average time/residue: 0.4288 time to fit residues: 196.3221 Evaluate side-chains 243 residues out of total 3658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 181 time to evaluate : 3.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 373 HIS Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 471 ASP Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain E residue 103 ASN Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 355 ASP Chi-restraints excluded: chain E residue 400 PHE Chi-restraints excluded: chain E residue 471 ASP Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain E residue 519 THR Chi-restraints excluded: chain E residue 604 VAL Chi-restraints excluded: chain E residue 609 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 245 optimal weight: 3.9990 chunk 158 optimal weight: 8.9990 chunk 237 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 252 optimal weight: 6.9990 chunk 270 optimal weight: 0.4980 chunk 196 optimal weight: 7.9990 chunk 37 optimal weight: 30.0000 chunk 312 optimal weight: 50.0000 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6598 moved from start: 0.5720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 35070 Z= 0.340 Angle : 0.661 10.366 47671 Z= 0.328 Chirality : 0.048 0.476 5539 Planarity : 0.004 0.064 6031 Dihedral : 6.019 59.729 6370 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.17 % Favored : 92.56 % Rotamer: Outliers : 2.62 % Allowed : 14.52 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % 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: -1.03 (0.13), residues: 4087 helix: 1.20 (0.15), residues: 1311 sheet: -0.68 (0.19), residues: 717 loop : -2.03 (0.13), residues: 2059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP D 594 HIS 0.010 0.001 HIS B 207 PHE 0.025 0.002 PHE B 898 TYR 0.024 0.002 TYR A1067 ARG 0.004 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 195 time to evaluate : 3.455 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: A 153 MET cc_start: 0.1807 (pmm) cc_final: 0.0155 (ptt) REVERT: A 374 PHE cc_start: 0.0413 (OUTLIER) cc_final: -0.0544 (p90) REVERT: A 995 ARG cc_start: 0.6357 (OUTLIER) cc_final: 0.5658 (mtm-85) REVERT: B 66 HIS cc_start: 0.5861 (OUTLIER) cc_final: 0.5275 (t-90) REVERT: B 153 MET cc_start: 0.3558 (mtp) cc_final: 0.0544 (ppp) REVERT: B 270 LEU cc_start: 0.6795 (mt) cc_final: 0.6528 (mp) REVERT: B 336 CYS cc_start: -0.2044 (OUTLIER) cc_final: -0.2442 (t) REVERT: C 153 MET cc_start: 0.4146 (tmm) cc_final: 0.3871 (mmt) REVERT: C 237 ARG cc_start: 0.6736 (mtp-110) cc_final: 0.6486 (mtm110) REVERT: D 21 ILE cc_start: -0.1346 (OUTLIER) cc_final: -0.1685 (mp) REVERT: D 152 MET cc_start: 0.0710 (tpp) cc_final: -0.0581 (ptt) REVERT: D 259 ILE cc_start: 0.4261 (OUTLIER) cc_final: 0.4050 (tp) REVERT: D 288 LYS cc_start: 0.3353 (mptt) cc_final: 0.3043 (mmtt) REVERT: D 462 MET cc_start: 0.4357 (mmp) cc_final: 0.3118 (mmm) REVERT: D 483 GLU cc_start: 0.0980 (pt0) cc_final: 0.0180 (tt0) REVERT: E 41 TYR cc_start: 0.2766 (t80) cc_final: 0.2375 (t80) REVERT: E 81 GLN cc_start: 0.2496 (tp40) cc_final: 0.1202 (mt0) REVERT: E 285 PHE cc_start: -0.0092 (m-80) cc_final: -0.0353 (m-80) REVERT: E 323 MET cc_start: 0.1252 (mpp) cc_final: -0.1831 (mmm) REVERT: E 408 MET cc_start: 0.2464 (mmt) cc_final: 0.2027 (mmt) REVERT: E 442 GLN cc_start: -0.0554 (mm-40) cc_final: -0.1758 (tm-30) REVERT: E 474 MET cc_start: 0.0464 (mmp) cc_final: -0.0512 (mtp) REVERT: E 480 MET cc_start: 0.1517 (mtp) cc_final: 0.0112 (ttt) REVERT: E 559 ARG cc_start: 0.4332 (tmt170) cc_final: 0.1408 (ptp-170) outliers start: 96 outliers final: 71 residues processed: 280 average time/residue: 0.4343 time to fit residues: 203.0289 Evaluate side-chains 263 residues out of total 3658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 186 time to evaluate : 3.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 373 HIS Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 103 ASN Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 355 ASP Chi-restraints excluded: chain E residue 400 PHE Chi-restraints excluded: chain E residue 471 ASP Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain E residue 519 THR Chi-restraints excluded: chain E residue 604 VAL Chi-restraints excluded: chain E residue 609 ASP Chi-restraints excluded: chain E residue 613 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 361 optimal weight: 5.9990 chunk 380 optimal weight: 40.0000 chunk 347 optimal weight: 20.0000 chunk 370 optimal weight: 7.9990 chunk 222 optimal weight: 10.0000 chunk 161 optimal weight: 4.9990 chunk 290 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 334 optimal weight: 0.9990 chunk 349 optimal weight: 8.9990 chunk 368 optimal weight: 50.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 0.5917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 35070 Z= 0.291 Angle : 0.633 10.458 47671 Z= 0.314 Chirality : 0.047 0.476 5539 Planarity : 0.004 0.062 6031 Dihedral : 5.941 57.941 6370 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.31 % Favored : 93.44 % Rotamer: Outliers : 2.38 % Allowed : 14.84 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.13), residues: 4087 helix: 1.21 (0.15), residues: 1323 sheet: -0.69 (0.19), residues: 705 loop : -2.02 (0.13), residues: 2059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP D 594 HIS 0.004 0.001 HIS B 207 PHE 0.031 0.002 PHE A 65 TYR 0.023 0.001 TYR A1067 ARG 0.003 0.000 ARG B 646 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 190 time to evaluate : 3.757 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: A 153 MET cc_start: 0.1821 (pmm) cc_final: 0.0230 (ptt) REVERT: A 374 PHE cc_start: 0.0667 (OUTLIER) cc_final: -0.0125 (p90) REVERT: A 995 ARG cc_start: 0.6294 (OUTLIER) cc_final: 0.5642 (mtm-85) REVERT: B 66 HIS cc_start: 0.5818 (OUTLIER) cc_final: 0.5241 (t-90) REVERT: B 153 MET cc_start: 0.3818 (mtp) cc_final: 0.0671 (ppp) REVERT: B 336 CYS cc_start: -0.2210 (OUTLIER) cc_final: -0.2641 (t) REVERT: D 21 ILE cc_start: -0.1361 (OUTLIER) cc_final: -0.1747 (mt) REVERT: D 152 MET cc_start: 0.0483 (tpp) cc_final: -0.0810 (ptt) REVERT: D 259 ILE cc_start: 0.4288 (OUTLIER) cc_final: 0.4082 (tp) REVERT: D 288 LYS cc_start: 0.3346 (mptt) cc_final: 0.2997 (mmtt) REVERT: D 462 MET cc_start: 0.3938 (mmp) cc_final: 0.2716 (mmm) REVERT: D 483 GLU cc_start: 0.1172 (pt0) cc_final: 0.0228 (tt0) REVERT: E 33 ASN cc_start: 0.5437 (OUTLIER) cc_final: 0.3851 (m-40) REVERT: E 41 TYR cc_start: 0.2682 (t80) cc_final: 0.2215 (t80) REVERT: E 81 GLN cc_start: 0.2400 (tp40) cc_final: 0.1196 (mt0) REVERT: E 127 TYR cc_start: 0.0514 (t80) cc_final: 0.0248 (p90) REVERT: E 323 MET cc_start: 0.1272 (mpp) cc_final: -0.1327 (mmm) REVERT: E 408 MET cc_start: 0.2644 (mmt) cc_final: 0.2176 (mmt) REVERT: E 442 GLN cc_start: -0.0396 (mm-40) cc_final: -0.1703 (tm-30) REVERT: E 474 MET cc_start: 0.0767 (mmp) cc_final: 0.0032 (mmm) REVERT: E 480 MET cc_start: 0.1616 (mtp) cc_final: 0.0445 (tpt) REVERT: E 571 GLU cc_start: 0.3754 (OUTLIER) cc_final: 0.3553 (tt0) outliers start: 87 outliers final: 68 residues processed: 269 average time/residue: 0.4315 time to fit residues: 198.0470 Evaluate side-chains 255 residues out of total 3658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 179 time to evaluate : 3.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 373 HIS Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 471 ASP Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 103 ASN Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 355 ASP Chi-restraints excluded: chain E residue 400 PHE Chi-restraints excluded: chain E residue 471 ASP Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain E residue 519 THR Chi-restraints excluded: chain E residue 571 GLU Chi-restraints excluded: chain E residue 604 VAL Chi-restraints excluded: chain E residue 613 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.9167 > 50: distance: 68 - 73: 4.771 distance: 73 - 74: 16.744 distance: 74 - 75: 4.696 distance: 75 - 76: 16.726 distance: 75 - 77: 19.853 distance: 76 - 98: 24.745 distance: 77 - 78: 8.812 distance: 78 - 79: 4.400 distance: 78 - 81: 24.246 distance: 79 - 80: 10.752 distance: 79 - 85: 14.826 distance: 80 - 106: 26.668 distance: 81 - 82: 21.228 distance: 82 - 83: 15.532 distance: 85 - 86: 25.151 distance: 86 - 87: 22.397 distance: 86 - 89: 23.177 distance: 87 - 88: 11.411 distance: 87 - 93: 9.751 distance: 88 - 118: 34.246 distance: 89 - 90: 10.070 distance: 89 - 91: 21.244 distance: 90 - 92: 13.486 distance: 93 - 94: 21.338 distance: 94 - 95: 9.423 distance: 94 - 97: 9.223 distance: 95 - 98: 8.145 distance: 98 - 99: 16.282 distance: 99 - 100: 12.076 distance: 99 - 102: 37.033 distance: 100 - 101: 9.575 distance: 100 - 106: 7.332 distance: 102 - 103: 15.195 distance: 103 - 104: 10.890 distance: 103 - 105: 3.389 distance: 106 - 107: 12.340 distance: 107 - 108: 4.291 distance: 107 - 110: 11.041 distance: 108 - 109: 20.225 distance: 108 - 118: 21.403 distance: 110 - 111: 11.315 distance: 111 - 112: 6.616 distance: 111 - 113: 7.365 distance: 112 - 114: 9.362 distance: 113 - 115: 9.120 distance: 114 - 116: 9.781 distance: 115 - 116: 11.500 distance: 116 - 117: 7.677 distance: 118 - 119: 15.170 distance: 119 - 120: 16.197 distance: 119 - 122: 5.162 distance: 120 - 121: 12.165 distance: 120 - 126: 12.654 distance: 122 - 123: 15.538 distance: 123 - 124: 13.711 distance: 123 - 125: 8.398 distance: 126 - 127: 11.646 distance: 127 - 128: 8.196 distance: 127 - 130: 11.040 distance: 128 - 129: 10.386 distance: 128 - 138: 11.462 distance: 131 - 132: 9.413 distance: 131 - 133: 17.843 distance: 132 - 134: 10.733 distance: 133 - 135: 8.538 distance: 134 - 136: 15.628 distance: 135 - 136: 6.301 distance: 136 - 137: 14.056 distance: 138 - 139: 8.259 distance: 139 - 140: 11.831 distance: 139 - 142: 22.322 distance: 140 - 141: 15.740 distance: 140 - 147: 18.854 distance: 142 - 143: 9.648 distance: 143 - 144: 7.403 distance: 144 - 145: 8.607 distance: 145 - 146: 25.423 distance: 147 - 148: 8.638 distance: 148 - 149: 10.391 distance: 148 - 151: 22.548 distance: 149 - 150: 9.770 distance: 149 - 155: 23.894 distance: 151 - 152: 19.964 distance: 152 - 153: 14.464 distance: 152 - 154: 25.898