Starting phenix.real_space_refine on Mon Jun 23 03:01:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ybk_33724/06_2025/7ybk_33724.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ybk_33724/06_2025/7ybk_33724.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ybk_33724/06_2025/7ybk_33724.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ybk_33724/06_2025/7ybk_33724.map" model { file = "/net/cci-nas-00/data/ceres_data/7ybk_33724/06_2025/7ybk_33724.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ybk_33724/06_2025/7ybk_33724.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 16823 2.51 5 N 4291 2.21 5 O 5263 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.82s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26491 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 8411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1074, 8411 Classifications: {'peptide': 1074} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1021} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 8431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8431 Classifications: {'peptide': 1077} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 52, 'TRANS': 1024} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 8405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1074, 8405 Classifications: {'peptide': 1074} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1021} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 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: 17.54, per 1000 atoms: 0.66 Number of scatterers: 26491 At special positions: 0 Unit cell: (155.15, 153.01, 218.28, 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 114 16.00 O 5263 8.00 N 4291 7.00 C 16823 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 ALPHA1-4 " NAG J 2 " - " MAN J 3 " " NAG K 2 " - " MAN K 3 " " NAG T 2 " - " MAN T 3 " " NAG U 2 " - " MAN U 3 " " NAG e 2 " - " MAN e 3 " " NAG f 2 " - " MAN f 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " BETA1-6 " NAG I 1 " - " FUC I 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG S 1 " - " FUC S 3 " " NAG d 1 " - " FUC d 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 149 " " NAG A1404 " - " ASN A 165 " " NAG A1405 " - " ASN A 282 " " NAG A1407 " - " ASN A 603 " " NAG A1408 " - " ASN A 657 " " NAG A1409 " - " ASN A 709 " " NAG A1410 " - " ASN A1158 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 149 " " NAG B1403 " - " ASN B 234 " " NAG B1404 " - " ASN B 331 " " NAG B1405 " - " ASN B 343 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 657 " " NAG B1408 " - " ASN B 709 " " NAG B1409 " - " ASN B1158 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 149 " " NAG C1403 " - " ASN C 331 " " NAG C1404 " - " ASN C 603 " " NAG C1405 " - " ASN C 657 " " NAG C1406 " - " ASN C 709 " " NAG C1407 " - " ASN C1158 " " NAG D 1 " - " ASN A 17 " " NAG F 1 " - " ASN A 616 " " 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 17 " " NAG M 1 " - " ASN B 122 " " NAG N 1 " - " ASN B 165 " " NAG O 1 " - " ASN B 282 " " NAG P 1 " - " ASN B 616 " " NAG Q 1 " - " ASN B 717 " " NAG R 1 " - " ASN B 801 " " NAG S 1 " - " ASN B1074 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN C 17 " " NAG X 1 " - " ASN C 165 " " NAG Y 1 " - " ASN C 234 " " NAG Z 1 " - " ASN C 282 " " NAG a 1 " - " ASN C 616 " " NAG b 1 " - " ASN C 717 " " NAG c 1 " - " ASN C 801 " " NAG d 1 " - " ASN C1074 " " NAG e 1 " - " ASN C1098 " " NAG f 1 " - " ASN C1134 " Time building additional restraints: 7.50 Conformation dependent library (CDL) restraints added in 3.6 seconds 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6040 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 50 sheets defined 26.0% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.59 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.898A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.959A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.022A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.522A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 623 removed outlier: 3.684A pdb=" N GLU A 619 " --> pdb=" O ASN A 616 " (cutoff:3.500A) Proline residue: A 621 - end of helix Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.527A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 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: 3.699A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 826 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.501A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR A 873 " --> pdb=" O MET A 869 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER A 875 " --> pdb=" O ALA A 871 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 876 " --> pdb=" O GLN A 872 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR A 881 " --> pdb=" O LEU A 877 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.604A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.985A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY A 908 " --> pdb=" O TYR A 904 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.867A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.648A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.909A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.632A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.510A pdb=" N GLU A 990 " --> pdb=" O LYS A 986 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1160 removed outlier: 4.010A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS A1154 " --> pdb=" O GLU A1150 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A1160 " --> pdb=" O PHE A1156 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 386 through 390 Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.462A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA B 411 " --> pdb=" O ARG B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 618 through 623 removed outlier: 3.963A pdb=" N VAL B 622 " --> pdb=" O THR B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 753 Processing helix chain 'B' and resid 754 through 757 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.631A pdb=" N ILE B 770 " --> pdb=" O ALA B 766 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA B 783 " --> pdb=" O GLN B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.557A pdb=" N ASP B 820 " --> pdb=" O SER B 816 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 882 removed outlier: 3.773A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER B 875 " --> pdb=" O ALA B 871 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B 876 " --> pdb=" O GLN B 872 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR B 881 " --> pdb=" O LEU B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.586A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.833A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG B 905 " --> pdb=" O GLN B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 4.045A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.595A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.633A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.547A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 1033 removed outlier: 3.686A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR B1006 " --> pdb=" O GLN B1002 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1161 removed outlier: 3.917A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER B1161 " --> pdb=" O LYS B1157 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 386 through 390 Processing helix chain 'C' and resid 405 through 411 removed outlier: 5.074A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLN C 409 " --> pdb=" O GLU C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.541A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.701A pdb=" N ILE C 882 " --> pdb=" O LEU C 878 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 910 removed outlier: 3.556A pdb=" N MET C 902 " --> pdb=" O PHE C 898 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN C 907 " --> pdb=" O ALA C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 4.061A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.600A pdb=" N LYS C 933 " --> pdb=" O SER C 929 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.524A pdb=" N ASP C 950 " --> pdb=" O GLY C 946 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.557A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.772A pdb=" N GLU C 990 " --> pdb=" O LYS C 986 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU C1001 " --> pdb=" O ILE C 997 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN C1005 " --> pdb=" O LEU C1001 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR C1006 " --> pdb=" O GLN C1002 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN C1010 " --> pdb=" O THR C1006 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1140 through 1159 removed outlier: 4.101A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 9.234A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.254A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.035A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 168 removed outlier: 3.756A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 143 removed outlier: 6.891A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.513A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 610 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 651 " --> pdb=" O VAL A 610 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 318 through 319 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.662A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 539 through 543 removed outlier: 3.595A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 565 through 566 removed outlier: 5.995A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.577A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY A 667 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.351A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 removed outlier: 3.718A pdb=" N SER A 735 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 788 removed outlier: 3.763A pdb=" N ILE A 788 " --> pdb=" O ALA C 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.386A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.801A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY B 268 " --> pdb=" O TYR B 91 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.801A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY B 268 " --> pdb=" O TYR B 91 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.643A pdb=" N PHE B 55 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN B 271 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.546A pdb=" N GLN B 239 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 142 through 143 removed outlier: 5.893A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.272A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL B 595 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 324 through 325 removed outlier: 7.826A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.726A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.868A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 542 through 543 removed outlier: 3.755A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.919A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.568A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.568A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 6.018A pdb=" N VAL B1122 " --> pdb=" O PHE B1089 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N PHE B1089 " --> pdb=" O VAL B1122 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N GLY B1124 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.659A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE C 197 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 50 through 51 removed outlier: 3.626A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.713A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 9.703A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 142 through 143 removed outlier: 6.604A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.476A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.451A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.661A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.750A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.516A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 642 through 645 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.624A pdb=" N TYR C 695 " --> pdb=" O CYS C 671 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE C 666 " --> pdb=" O ILE C 670 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 715 removed outlier: 5.289A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.537A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1120 through 1122 897 hydrogen bonds defined for protein. 2448 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.64 Time building geometry restraints manager: 8.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8292 1.34 - 1.46: 6792 1.46 - 1.59: 11842 1.59 - 1.71: 3 1.71 - 1.83: 144 Bond restraints: 27073 Sorted by residual: bond pdb=" C VAL A 991 " pdb=" N GLN A 992 " ideal model delta sigma weight residual 1.334 1.471 -0.136 1.27e-02 6.20e+03 1.15e+02 bond pdb=" CG PRO C 322 " pdb=" CD PRO C 322 " ideal model delta sigma weight residual 1.503 1.256 0.247 3.40e-02 8.65e+02 5.26e+01 bond pdb=" CG PRO A 330 " pdb=" CD PRO A 330 " ideal model delta sigma weight residual 1.503 1.273 0.230 3.40e-02 8.65e+02 4.56e+01 bond pdb=" C LEU A 977 " pdb=" N ASN A 978 " ideal model delta sigma weight residual 1.334 1.432 -0.098 1.49e-02 4.50e+03 4.35e+01 bond pdb=" N ILE C 332 " pdb=" CA ILE C 332 " ideal model delta sigma weight residual 1.456 1.504 -0.048 1.23e-02 6.61e+03 1.55e+01 ... (remaining 27068 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 36545 3.05 - 6.09: 237 6.09 - 9.14: 22 9.14 - 12.19: 6 12.19 - 15.24: 4 Bond angle restraints: 36814 Sorted by residual: angle pdb=" CA PRO A 330 " pdb=" N PRO A 330 " pdb=" CD PRO A 330 " ideal model delta sigma weight residual 112.00 96.76 15.24 1.40e+00 5.10e-01 1.18e+02 angle pdb=" CA PRO C 322 " pdb=" N PRO C 322 " pdb=" CD PRO C 322 " ideal model delta sigma weight residual 112.00 98.56 13.44 1.40e+00 5.10e-01 9.21e+01 angle pdb=" N PRO A 330 " pdb=" CD PRO A 330 " pdb=" CG PRO A 330 " ideal model delta sigma weight residual 103.20 88.83 14.37 1.50e+00 4.44e-01 9.18e+01 angle pdb=" N PRO C 322 " pdb=" CD PRO C 322 " pdb=" CG PRO C 322 " ideal model delta sigma weight residual 103.20 89.55 13.65 1.50e+00 4.44e-01 8.28e+01 angle pdb=" O LEU A 977 " pdb=" C LEU A 977 " pdb=" N ASN A 978 " ideal model delta sigma weight residual 122.39 111.73 10.66 1.30e+00 5.92e-01 6.72e+01 ... (remaining 36809 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.82: 16277 24.82 - 49.65: 814 49.65 - 74.47: 129 74.47 - 99.30: 59 99.30 - 124.12: 18 Dihedral angle restraints: 17297 sinusoidal: 7906 harmonic: 9391 Sorted by residual: dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -174.61 88.61 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual 93.00 -178.40 -88.60 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual 93.00 169.40 -76.40 1 1.00e+01 1.00e-02 7.34e+01 ... (remaining 17294 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 4298 0.112 - 0.224: 104 0.224 - 0.336: 10 0.336 - 0.448: 1 0.448 - 0.560: 3 Chirality restraints: 4416 Sorted by residual: chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN B 801 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.83e+00 chirality pdb=" C1 NAG Z 1 " pdb=" ND2 ASN C 282 " pdb=" C2 NAG Z 1 " pdb=" O5 NAG Z 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.23e+00 chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.45e+00 ... (remaining 4413 not shown) Planarity restraints: 4692 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 801 " -0.001 2.00e-02 2.50e+03 4.30e-02 2.31e+01 pdb=" CG ASN B 801 " 0.043 2.00e-02 2.50e+03 pdb=" OD1 ASN B 801 " -0.050 2.00e-02 2.50e+03 pdb=" ND2 ASN B 801 " 0.053 2.00e-02 2.50e+03 pdb=" C1 NAG R 1 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN C 321 " 0.080 5.00e-02 4.00e+02 1.10e-01 1.94e+01 pdb=" N PRO C 322 " -0.190 5.00e-02 4.00e+02 pdb=" CA PRO C 322 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 322 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C1078 " 0.071 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO C1079 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO C1079 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO C1079 " 0.057 5.00e-02 4.00e+02 ... (remaining 4689 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 513 2.66 - 3.22: 25266 3.22 - 3.78: 38787 3.78 - 4.34: 51894 4.34 - 4.90: 83903 Nonbonded interactions: 200363 Sorted by model distance: nonbonded pdb=" O ASP C 290 " pdb=" OG SER C 297 " model vdw 2.106 3.040 nonbonded pdb=" OH TYR B 396 " pdb=" OH TYR C 200 " model vdw 2.113 3.040 nonbonded pdb=" OD1 ASN A 439 " pdb=" OG SER A 443 " model vdw 2.181 3.040 nonbonded pdb=" O ASN A 99 " pdb=" NH1 ARG A 102 " model vdw 2.183 3.120 nonbonded pdb=" OG1 THR A 912 " pdb=" OD1 ASN A 914 " model vdw 2.184 3.040 ... (remaining 200358 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 826 or resid 855 through 1162 or resid 1401 thr \ ough 1407)) selection = (chain 'B' and (resid 14 through 623 or resid 641 through 826 or resid 855 throu \ gh 1162 or resid 1401 through 1407)) selection = (chain 'C' and (resid 14 through 623 or resid 641 through 826 or resid 855 throu \ gh 1162 or resid 1401 through 1407)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' } ncs_group { reference = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'f' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 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: 0.040 Extract box with map and model: 1.160 Check model and map are aligned: 0.210 Set scattering table: 0.230 Process input model: 68.820 Find NCS groups from input model: 2.370 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 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 : 0.005 0.247 27204 Z= 0.244 Angle : 0.816 19.568 37165 Z= 0.427 Chirality : 0.050 0.560 4416 Planarity : 0.005 0.110 4640 Dihedral : 15.428 124.123 11131 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.79 % Favored : 96.14 % Rotamer: Outliers : 0.32 % Allowed : 0.53 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.14), residues: 3189 helix: -0.10 (0.20), residues: 661 sheet: -0.65 (0.21), residues: 559 loop : -1.49 (0.13), residues: 1969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 436 HIS 0.011 0.001 HIS A 66 PHE 0.034 0.001 PHE B 135 TYR 0.017 0.001 TYR A 145 ARG 0.015 0.001 ARG C 457 Details of bonding type rmsd link_NAG-ASN : bond 0.01293 ( 52) link_NAG-ASN : angle 4.76086 ( 156) link_ALPHA1-4 : bond 0.00442 ( 6) link_ALPHA1-4 : angle 1.75582 ( 18) link_BETA1-4 : bond 0.00521 ( 28) link_BETA1-4 : angle 1.49025 ( 84) hydrogen bonds : bond 0.30171 ( 865) hydrogen bonds : angle 9.83884 ( 2448) link_BETA1-6 : bond 0.00485 ( 3) link_BETA1-6 : angle 1.58418 ( 9) SS BOND : bond 0.00290 ( 42) SS BOND : angle 1.17799 ( 84) covalent geometry : bond 0.00494 (27073) covalent geometry : angle 0.75262 (36814) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 340 time to evaluate : 3.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: -0.1291 (tpt) cc_final: -0.1712 (tpt) REVERT: A 461 LEU cc_start: 0.4209 (pp) cc_final: 0.3632 (mm) REVERT: A 508 TYR cc_start: 0.5571 (m-80) cc_final: 0.5242 (m-80) REVERT: B 258 TRP cc_start: -0.2661 (t60) cc_final: -0.3011 (t60) REVERT: B 663 ASP cc_start: 0.7290 (m-30) cc_final: 0.7032 (m-30) REVERT: C 99 ASN cc_start: 0.4809 (m-40) cc_final: 0.4150 (m110) REVERT: C 266 TYR cc_start: 0.5016 (m-80) cc_final: 0.4213 (m-80) REVERT: C 369 TYR cc_start: 0.5954 (t80) cc_final: 0.5683 (t80) REVERT: C 420 ASP cc_start: 0.5475 (t0) cc_final: 0.5085 (t70) REVERT: C 1115 ILE cc_start: 0.4105 (mm) cc_final: 0.3833 (mm) outliers start: 9 outliers final: 2 residues processed: 348 average time/residue: 0.3871 time to fit residues: 213.4136 Evaluate side-chains 193 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 191 time to evaluate : 3.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain C residue 332 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 271 optimal weight: 5.9990 chunk 243 optimal weight: 6.9990 chunk 135 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 164 optimal weight: 6.9990 chunk 129 optimal weight: 20.0000 chunk 251 optimal weight: 0.0980 chunk 97 optimal weight: 0.6980 chunk 152 optimal weight: 30.0000 chunk 187 optimal weight: 0.3980 chunk 291 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN B 207 HIS ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN C 81 ASN C 448 ASN C 481 ASN C 542 ASN C 606 ASN C 955 ASN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.164543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.126312 restraints weight = 63097.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.124247 restraints weight = 40948.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.125372 restraints weight = 41762.156| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27204 Z= 0.149 Angle : 0.714 17.675 37165 Z= 0.348 Chirality : 0.048 0.565 4416 Planarity : 0.005 0.055 4640 Dihedral : 11.791 110.637 5347 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.08 % Favored : 95.89 % Rotamer: Outliers : 0.89 % Allowed : 8.09 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.14), residues: 3189 helix: 0.53 (0.19), residues: 706 sheet: -0.22 (0.20), residues: 654 loop : -1.52 (0.13), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 353 HIS 0.006 0.001 HIS A1048 PHE 0.019 0.002 PHE C 201 TYR 0.024 0.002 TYR B1067 ARG 0.006 0.001 ARG C 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00807 ( 52) link_NAG-ASN : angle 4.10138 ( 156) link_ALPHA1-4 : bond 0.01061 ( 6) link_ALPHA1-4 : angle 2.51836 ( 18) link_BETA1-4 : bond 0.00536 ( 28) link_BETA1-4 : angle 1.46225 ( 84) hydrogen bonds : bond 0.07141 ( 865) hydrogen bonds : angle 6.91174 ( 2448) link_BETA1-6 : bond 0.01358 ( 3) link_BETA1-6 : angle 2.22166 ( 9) SS BOND : bond 0.00323 ( 42) SS BOND : angle 1.13919 ( 84) covalent geometry : bond 0.00315 (27073) covalent geometry : angle 0.65695 (36814) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 235 time to evaluate : 2.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: -0.2563 (tpt) cc_final: -0.2885 (tpt) REVERT: A 329 PHE cc_start: 0.6399 (OUTLIER) cc_final: 0.6066 (m-10) REVERT: A 451 TYR cc_start: 0.5734 (m-80) cc_final: 0.5531 (m-80) REVERT: A 461 LEU cc_start: 0.4272 (pp) cc_final: 0.3597 (mm) REVERT: B 258 TRP cc_start: -0.2672 (t60) cc_final: -0.3382 (t60) REVERT: B 663 ASP cc_start: 0.7704 (m-30) cc_final: 0.7372 (m-30) REVERT: B 753 LEU cc_start: 0.9059 (tp) cc_final: 0.8795 (tp) REVERT: B 1031 GLU cc_start: 0.8777 (tm-30) cc_final: 0.8507 (tm-30) REVERT: B 1034 LEU cc_start: 0.9215 (mt) cc_final: 0.8987 (mp) REVERT: C 102 ARG cc_start: 0.0291 (OUTLIER) cc_final: 0.0069 (pmt-80) REVERT: C 177 MET cc_start: -0.4668 (ttt) cc_final: -0.5434 (ttt) REVERT: C 1105 THR cc_start: 0.8534 (p) cc_final: 0.8183 (p) outliers start: 25 outliers final: 11 residues processed: 252 average time/residue: 0.3586 time to fit residues: 148.3490 Evaluate side-chains 197 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 184 time to evaluate : 2.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 737 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 164 optimal weight: 5.9990 chunk 33 optimal weight: 20.0000 chunk 202 optimal weight: 0.7980 chunk 187 optimal weight: 2.9990 chunk 31 optimal weight: 0.0870 chunk 116 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 172 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 191 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 overall best weight: 1.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 207 HIS A 965 GLN A1159 HIS B 207 HIS ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 498 GLN C 606 ASN C 675 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.162093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.123125 restraints weight = 63667.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.121873 restraints weight = 43394.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.122799 restraints weight = 43428.197| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 27204 Z= 0.165 Angle : 0.695 16.211 37165 Z= 0.334 Chirality : 0.048 0.499 4416 Planarity : 0.004 0.051 4640 Dihedral : 10.532 107.386 5347 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.39 % Favored : 95.58 % Rotamer: Outliers : 1.46 % Allowed : 10.93 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.14), residues: 3189 helix: 0.56 (0.19), residues: 730 sheet: -0.23 (0.20), residues: 639 loop : -1.56 (0.13), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 353 HIS 0.025 0.001 HIS B 207 PHE 0.023 0.002 PHE B 456 TYR 0.027 0.002 TYR C 91 ARG 0.005 0.000 ARG A1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00651 ( 52) link_NAG-ASN : angle 3.92947 ( 156) link_ALPHA1-4 : bond 0.01410 ( 6) link_ALPHA1-4 : angle 2.71181 ( 18) link_BETA1-4 : bond 0.00396 ( 28) link_BETA1-4 : angle 1.45974 ( 84) hydrogen bonds : bond 0.06129 ( 865) hydrogen bonds : angle 6.26922 ( 2448) link_BETA1-6 : bond 0.01424 ( 3) link_BETA1-6 : angle 2.68540 ( 9) SS BOND : bond 0.00351 ( 42) SS BOND : angle 1.24809 ( 84) covalent geometry : bond 0.00372 (27073) covalent geometry : angle 0.63960 (36814) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 196 time to evaluate : 3.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: -0.2441 (tpt) cc_final: -0.2694 (tpt) REVERT: A 329 PHE cc_start: 0.6798 (OUTLIER) cc_final: 0.6405 (m-10) REVERT: A 763 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8364 (mp) REVERT: A 1030 SER cc_start: 0.9035 (p) cc_final: 0.8801 (t) REVERT: B 228 ASP cc_start: 0.7702 (m-30) cc_final: 0.6949 (t70) REVERT: B 258 TRP cc_start: -0.2616 (t60) cc_final: -0.3438 (t60) REVERT: B 663 ASP cc_start: 0.7755 (m-30) cc_final: 0.7455 (m-30) REVERT: B 1034 LEU cc_start: 0.9245 (mt) cc_final: 0.9003 (mp) REVERT: C 168 PHE cc_start: 0.6664 (t80) cc_final: 0.6380 (t80) REVERT: C 965 GLN cc_start: 0.8841 (tp40) cc_final: 0.8309 (tm-30) REVERT: C 1105 THR cc_start: 0.8591 (p) cc_final: 0.8297 (p) outliers start: 41 outliers final: 20 residues processed: 228 average time/residue: 0.3379 time to fit residues: 129.3324 Evaluate side-chains 193 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 2.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 276 optimal weight: 5.9990 chunk 147 optimal weight: 20.0000 chunk 243 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 245 optimal weight: 10.0000 chunk 293 optimal weight: 5.9990 chunk 284 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 249 optimal weight: 10.0000 chunk 118 optimal weight: 0.6980 chunk 140 optimal weight: 8.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 955 ASN A 965 GLN B 188 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C 804 GLN C 935 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.154418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.114853 restraints weight = 62345.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.112503 restraints weight = 42788.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.113455 restraints weight = 48841.185| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 27204 Z= 0.259 Angle : 0.828 16.322 37165 Z= 0.396 Chirality : 0.051 0.501 4416 Planarity : 0.005 0.058 4640 Dihedral : 10.080 101.985 5345 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.71 % Favored : 94.26 % Rotamer: Outliers : 2.77 % Allowed : 12.96 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.14), residues: 3189 helix: 0.27 (0.19), residues: 728 sheet: -0.47 (0.20), residues: 618 loop : -1.73 (0.13), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 353 HIS 0.009 0.002 HIS A 655 PHE 0.028 0.002 PHE B 802 TYR 0.027 0.002 TYR B1067 ARG 0.005 0.001 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00704 ( 52) link_NAG-ASN : angle 4.25191 ( 156) link_ALPHA1-4 : bond 0.01208 ( 6) link_ALPHA1-4 : angle 3.00284 ( 18) link_BETA1-4 : bond 0.00600 ( 28) link_BETA1-4 : angle 1.93125 ( 84) hydrogen bonds : bond 0.06752 ( 865) hydrogen bonds : angle 6.37996 ( 2448) link_BETA1-6 : bond 0.01455 ( 3) link_BETA1-6 : angle 2.17601 ( 9) SS BOND : bond 0.00459 ( 42) SS BOND : angle 1.47396 ( 84) covalent geometry : bond 0.00602 (27073) covalent geometry : angle 0.77279 (36814) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 186 time to evaluate : 2.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 763 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8577 (mp) REVERT: A 1030 SER cc_start: 0.9200 (p) cc_final: 0.8969 (t) REVERT: B 228 ASP cc_start: 0.7867 (m-30) cc_final: 0.7398 (t70) REVERT: B 258 TRP cc_start: -0.2593 (t60) cc_final: -0.3527 (t60) REVERT: B 663 ASP cc_start: 0.7622 (m-30) cc_final: 0.7320 (m-30) REVERT: B 990 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7750 (pt0) REVERT: C 41 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7449 (tptp) REVERT: C 753 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8467 (tt) REVERT: C 965 GLN cc_start: 0.8984 (tp40) cc_final: 0.8165 (tm-30) REVERT: C 1105 THR cc_start: 0.8789 (p) cc_final: 0.8459 (p) outliers start: 78 outliers final: 41 residues processed: 251 average time/residue: 0.3406 time to fit residues: 143.0347 Evaluate side-chains 205 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 160 time to evaluate : 2.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 306 optimal weight: 0.5980 chunk 225 optimal weight: 10.0000 chunk 106 optimal weight: 20.0000 chunk 34 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 152 optimal weight: 4.9990 chunk 249 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 319 optimal weight: 0.8980 chunk 295 optimal weight: 0.7980 chunk 241 optimal weight: 0.8980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN B 564 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C 920 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.158442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.121472 restraints weight = 63135.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.118549 restraints weight = 48101.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.119739 restraints weight = 44781.850| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27204 Z= 0.141 Angle : 0.686 15.269 37165 Z= 0.325 Chirality : 0.047 0.469 4416 Planarity : 0.004 0.051 4640 Dihedral : 9.165 101.864 5345 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.23 % Favored : 95.74 % Rotamer: Outliers : 2.02 % Allowed : 15.12 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.14), residues: 3189 helix: 0.75 (0.20), residues: 721 sheet: -0.21 (0.20), residues: 620 loop : -1.73 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 436 HIS 0.009 0.001 HIS C 519 PHE 0.027 0.001 PHE C 201 TYR 0.020 0.001 TYR A1047 ARG 0.004 0.000 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00730 ( 52) link_NAG-ASN : angle 4.16216 ( 156) link_ALPHA1-4 : bond 0.01466 ( 6) link_ALPHA1-4 : angle 2.74916 ( 18) link_BETA1-4 : bond 0.00404 ( 28) link_BETA1-4 : angle 1.32555 ( 84) hydrogen bonds : bond 0.05551 ( 865) hydrogen bonds : angle 5.86152 ( 2448) link_BETA1-6 : bond 0.01574 ( 3) link_BETA1-6 : angle 1.92864 ( 9) SS BOND : bond 0.00334 ( 42) SS BOND : angle 1.21733 ( 84) covalent geometry : bond 0.00309 (27073) covalent geometry : angle 0.62408 (36814) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 186 time to evaluate : 2.952 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: B 228 ASP cc_start: 0.7977 (m-30) cc_final: 0.7543 (t70) REVERT: B 258 TRP cc_start: -0.2722 (t60) cc_final: -0.3533 (t60) REVERT: B 266 TYR cc_start: 0.8087 (m-80) cc_final: 0.7482 (m-80) REVERT: B 663 ASP cc_start: 0.7610 (m-30) cc_final: 0.7347 (m-30) REVERT: B 767 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8738 (mt) REVERT: B 819 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8398 (mp0) REVERT: C 354 ASN cc_start: 0.7457 (t0) cc_final: 0.7150 (t0) REVERT: C 452 LEU cc_start: 0.7980 (mm) cc_final: 0.7763 (mt) REVERT: C 965 GLN cc_start: 0.8799 (tp40) cc_final: 0.8456 (tm-30) REVERT: C 1105 THR cc_start: 0.8753 (p) cc_final: 0.8496 (p) outliers start: 57 outliers final: 41 residues processed: 229 average time/residue: 0.3627 time to fit residues: 136.2717 Evaluate side-chains 198 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 155 time to evaluate : 3.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 254 optimal weight: 8.9990 chunk 211 optimal weight: 0.8980 chunk 234 optimal weight: 0.0970 chunk 287 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 226 optimal weight: 7.9990 chunk 160 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 175 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 213 optimal weight: 5.9990 overall best weight: 2.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN A 965 GLN A1005 GLN B 564 GLN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.151955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.113397 restraints weight = 61930.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.110453 restraints weight = 51345.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.111614 restraints weight = 47241.008| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 27204 Z= 0.233 Angle : 0.764 15.504 37165 Z= 0.368 Chirality : 0.049 0.477 4416 Planarity : 0.005 0.063 4640 Dihedral : 9.015 99.761 5345 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.64 % Favored : 94.32 % Rotamer: Outliers : 2.84 % Allowed : 15.37 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.43 (0.14), residues: 3189 helix: 0.46 (0.19), residues: 731 sheet: -0.44 (0.20), residues: 656 loop : -1.82 (0.13), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 353 HIS 0.009 0.002 HIS B1083 PHE 0.023 0.002 PHE B 456 TYR 0.024 0.002 TYR B1067 ARG 0.014 0.001 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00653 ( 52) link_NAG-ASN : angle 4.07240 ( 156) link_ALPHA1-4 : bond 0.01477 ( 6) link_ALPHA1-4 : angle 2.95924 ( 18) link_BETA1-4 : bond 0.00418 ( 28) link_BETA1-4 : angle 1.49013 ( 84) hydrogen bonds : bond 0.06226 ( 865) hydrogen bonds : angle 6.06895 ( 2448) link_BETA1-6 : bond 0.01430 ( 3) link_BETA1-6 : angle 1.73738 ( 9) SS BOND : bond 0.00440 ( 42) SS BOND : angle 1.42809 ( 84) covalent geometry : bond 0.00546 (27073) covalent geometry : angle 0.71044 (36814) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 171 time to evaluate : 3.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 763 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8606 (mp) REVERT: A 1086 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8145 (mtmm) REVERT: B 258 TRP cc_start: -0.2583 (t60) cc_final: -0.3640 (t60) REVERT: B 398 ASP cc_start: 0.7251 (t0) cc_final: 0.7001 (t0) REVERT: B 580 GLN cc_start: 0.7457 (OUTLIER) cc_final: 0.7208 (mm-40) REVERT: B 663 ASP cc_start: 0.7646 (m-30) cc_final: 0.7370 (m-30) REVERT: C 354 ASN cc_start: 0.7521 (t0) cc_final: 0.7111 (t0) REVERT: C 965 GLN cc_start: 0.8949 (tp40) cc_final: 0.8406 (tm-30) REVERT: C 1105 THR cc_start: 0.8874 (p) cc_final: 0.8649 (p) outliers start: 80 outliers final: 55 residues processed: 237 average time/residue: 0.5403 time to fit residues: 218.6508 Evaluate side-chains 210 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 152 time to evaluate : 3.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1019 ARG Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 77 optimal weight: 1.9990 chunk 276 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 263 optimal weight: 9.9990 chunk 47 optimal weight: 20.0000 chunk 53 optimal weight: 4.9990 chunk 289 optimal weight: 2.9990 chunk 226 optimal weight: 1.9990 chunk 251 optimal weight: 5.9990 chunk 242 optimal weight: 5.9990 chunk 106 optimal weight: 30.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C1088 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.149059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.111644 restraints weight = 62333.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.108805 restraints weight = 53393.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.109809 restraints weight = 49573.585| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.5042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.169 27204 Z= 0.262 Angle : 0.815 19.599 37165 Z= 0.394 Chirality : 0.051 0.477 4416 Planarity : 0.005 0.057 4640 Dihedral : 9.102 101.345 5343 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.02 % Favored : 93.95 % Rotamer: Outliers : 3.44 % Allowed : 15.80 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.71 (0.14), residues: 3189 helix: 0.27 (0.19), residues: 734 sheet: -0.69 (0.20), residues: 617 loop : -1.96 (0.13), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 353 HIS 0.011 0.002 HIS B1083 PHE 0.064 0.003 PHE A 392 TYR 0.027 0.002 TYR B1067 ARG 0.005 0.001 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00660 ( 52) link_NAG-ASN : angle 4.05158 ( 156) link_ALPHA1-4 : bond 0.01392 ( 6) link_ALPHA1-4 : angle 2.87893 ( 18) link_BETA1-4 : bond 0.00415 ( 28) link_BETA1-4 : angle 1.48622 ( 84) hydrogen bonds : bond 0.06460 ( 865) hydrogen bonds : angle 6.13934 ( 2448) link_BETA1-6 : bond 0.01052 ( 3) link_BETA1-6 : angle 1.44682 ( 9) SS BOND : bond 0.00440 ( 42) SS BOND : angle 2.58858 ( 84) covalent geometry : bond 0.00620 (27073) covalent geometry : angle 0.75862 (36814) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 171 time to evaluate : 3.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7757 (ptt90) cc_final: 0.7096 (ptt90) REVERT: A 763 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8670 (mp) REVERT: A 904 TYR cc_start: 0.7673 (m-80) cc_final: 0.7434 (m-80) REVERT: A 926 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8211 (mt0) REVERT: A 1086 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8133 (mtmm) REVERT: A 1107 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7883 (tpp80) REVERT: B 258 TRP cc_start: -0.1927 (t60) cc_final: -0.3240 (t60) REVERT: B 266 TYR cc_start: 0.8639 (m-80) cc_final: 0.8110 (m-80) REVERT: B 342 PHE cc_start: 0.8179 (OUTLIER) cc_final: 0.7485 (m-80) REVERT: B 453 TYR cc_start: 0.7307 (p90) cc_final: 0.7015 (p90) REVERT: B 580 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.7365 (mm-40) REVERT: B 663 ASP cc_start: 0.7599 (m-30) cc_final: 0.7334 (m-30) REVERT: C 41 LYS cc_start: 0.7967 (tptm) cc_final: 0.7696 (tptm) REVERT: C 90 VAL cc_start: 0.9054 (t) cc_final: 0.8582 (m) REVERT: C 354 ASN cc_start: 0.7482 (t0) cc_final: 0.7103 (t0) REVERT: C 515 PHE cc_start: 0.8725 (OUTLIER) cc_final: 0.8496 (p90) REVERT: C 753 LEU cc_start: 0.9092 (tt) cc_final: 0.8672 (tt) REVERT: C 965 GLN cc_start: 0.8964 (tp40) cc_final: 0.8437 (tm-30) outliers start: 97 outliers final: 63 residues processed: 249 average time/residue: 0.4037 time to fit residues: 166.5815 Evaluate side-chains 221 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 151 time to evaluate : 2.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 926 GLN Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 303 optimal weight: 0.8980 chunk 287 optimal weight: 0.1980 chunk 208 optimal weight: 1.9990 chunk 128 optimal weight: 8.9990 chunk 86 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 136 optimal weight: 6.9990 chunk 282 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 310 optimal weight: 0.7980 chunk 183 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN A1005 GLN B 564 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.151866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.113990 restraints weight = 62120.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.111652 restraints weight = 49069.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.112740 restraints weight = 51178.218| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.5153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27204 Z= 0.125 Angle : 0.687 14.148 37165 Z= 0.327 Chirality : 0.047 0.446 4416 Planarity : 0.004 0.097 4640 Dihedral : 8.197 98.649 5343 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.64 % Favored : 95.33 % Rotamer: Outliers : 2.13 % Allowed : 17.86 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.14), residues: 3189 helix: 0.81 (0.20), residues: 727 sheet: -0.49 (0.21), residues: 613 loop : -1.77 (0.13), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP C 64 HIS 0.011 0.001 HIS B1083 PHE 0.023 0.001 PHE B 456 TYR 0.020 0.001 TYR A 369 ARG 0.009 0.000 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00684 ( 52) link_NAG-ASN : angle 3.78143 ( 156) link_ALPHA1-4 : bond 0.01622 ( 6) link_ALPHA1-4 : angle 2.67305 ( 18) link_BETA1-4 : bond 0.00438 ( 28) link_BETA1-4 : angle 1.26398 ( 84) hydrogen bonds : bond 0.05187 ( 865) hydrogen bonds : angle 5.63621 ( 2448) link_BETA1-6 : bond 0.01133 ( 3) link_BETA1-6 : angle 1.47218 ( 9) SS BOND : bond 0.00312 ( 42) SS BOND : angle 1.72397 ( 84) covalent geometry : bond 0.00264 (27073) covalent geometry : angle 0.63380 (36814) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 177 time to evaluate : 2.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 PHE cc_start: 0.7696 (m-80) cc_final: 0.7226 (t80) REVERT: A 904 TYR cc_start: 0.7467 (m-80) cc_final: 0.7001 (m-10) REVERT: A 968 SER cc_start: 0.9304 (m) cc_final: 0.8967 (p) REVERT: A 1115 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.8042 (mt) REVERT: B 258 TRP cc_start: -0.2222 (t60) cc_final: -0.3381 (t60) REVERT: B 266 TYR cc_start: 0.8564 (m-80) cc_final: 0.7955 (m-80) REVERT: B 453 TYR cc_start: 0.7053 (p90) cc_final: 0.6787 (p90) REVERT: B 663 ASP cc_start: 0.7590 (m-30) cc_final: 0.7367 (m-30) REVERT: B 973 ILE cc_start: 0.8988 (mm) cc_final: 0.8782 (mm) REVERT: B 1115 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7730 (mt) REVERT: C 41 LYS cc_start: 0.7986 (tptm) cc_final: 0.7743 (tptp) REVERT: C 90 VAL cc_start: 0.8942 (t) cc_final: 0.8394 (m) REVERT: C 354 ASN cc_start: 0.7554 (t0) cc_final: 0.7045 (t0) REVERT: C 552 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7962 (pp) REVERT: C 965 GLN cc_start: 0.8775 (tp40) cc_final: 0.8441 (tm-30) outliers start: 60 outliers final: 37 residues processed: 231 average time/residue: 0.3688 time to fit residues: 142.7321 Evaluate side-chains 195 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 155 time to evaluate : 3.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 941 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 301 optimal weight: 4.9990 chunk 164 optimal weight: 4.9990 chunk 43 optimal weight: 20.0000 chunk 134 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 chunk 148 optimal weight: 8.9990 chunk 260 optimal weight: 1.9990 chunk 297 optimal weight: 5.9990 chunk 243 optimal weight: 5.9990 chunk 271 optimal weight: 4.9990 chunk 202 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN B 564 GLN C 134 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS C 606 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.147914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.110762 restraints weight = 62427.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.108553 restraints weight = 47633.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.108910 restraints weight = 62542.970| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.5600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 27204 Z= 0.255 Angle : 0.806 14.179 37165 Z= 0.388 Chirality : 0.051 0.469 4416 Planarity : 0.005 0.088 4640 Dihedral : 8.369 96.957 5343 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.49 % Favored : 93.48 % Rotamer: Outliers : 2.09 % Allowed : 18.28 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.14), residues: 3189 helix: 0.36 (0.19), residues: 741 sheet: -0.67 (0.20), residues: 636 loop : -1.92 (0.13), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 64 HIS 0.011 0.002 HIS B1083 PHE 0.025 0.002 PHE B 800 TYR 0.027 0.002 TYR B1067 ARG 0.005 0.001 ARG A 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00655 ( 52) link_NAG-ASN : angle 3.99881 ( 156) link_ALPHA1-4 : bond 0.01537 ( 6) link_ALPHA1-4 : angle 2.96506 ( 18) link_BETA1-4 : bond 0.00409 ( 28) link_BETA1-4 : angle 1.47530 ( 84) hydrogen bonds : bond 0.06428 ( 865) hydrogen bonds : angle 6.02281 ( 2448) link_BETA1-6 : bond 0.00927 ( 3) link_BETA1-6 : angle 1.45573 ( 9) SS BOND : bond 0.00440 ( 42) SS BOND : angle 1.89425 ( 84) covalent geometry : bond 0.00596 (27073) covalent geometry : angle 0.75484 (36814) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 156 time to evaluate : 3.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 PHE cc_start: 0.7713 (m-80) cc_final: 0.7223 (t80) REVERT: A 904 TYR cc_start: 0.7900 (m-80) cc_final: 0.7565 (m-80) REVERT: A 1107 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7988 (tpp80) REVERT: A 1115 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.8181 (mt) REVERT: B 258 TRP cc_start: -0.1993 (t60) cc_final: -0.3309 (t60) REVERT: B 663 ASP cc_start: 0.7662 (m-30) cc_final: 0.7444 (m-30) REVERT: B 1115 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7871 (mt) REVERT: C 41 LYS cc_start: 0.7989 (tptm) cc_final: 0.7734 (tptm) REVERT: C 90 VAL cc_start: 0.9128 (t) cc_final: 0.8653 (m) REVERT: C 229 LEU cc_start: 0.8254 (mm) cc_final: 0.7967 (mp) REVERT: C 354 ASN cc_start: 0.7582 (t0) cc_final: 0.7108 (t0) outliers start: 59 outliers final: 45 residues processed: 205 average time/residue: 0.4608 time to fit residues: 159.3707 Evaluate side-chains 194 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 146 time to evaluate : 3.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 959 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 43 optimal weight: 20.0000 chunk 259 optimal weight: 20.0000 chunk 193 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 chunk 307 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 205 optimal weight: 0.8980 chunk 48 optimal weight: 0.0370 chunk 58 optimal weight: 8.9990 chunk 92 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.151354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.113790 restraints weight = 61657.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.111865 restraints weight = 45523.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.112821 restraints weight = 51076.583| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.5663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27204 Z= 0.128 Angle : 0.693 13.674 37165 Z= 0.328 Chirality : 0.047 0.445 4416 Planarity : 0.004 0.079 4640 Dihedral : 7.640 93.506 5343 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.45 % Favored : 95.52 % Rotamer: Outliers : 1.63 % Allowed : 18.96 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.14), residues: 3189 helix: 0.91 (0.20), residues: 723 sheet: -0.53 (0.20), residues: 633 loop : -1.78 (0.13), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 64 HIS 0.007 0.001 HIS B1083 PHE 0.025 0.001 PHE B 342 TYR 0.022 0.001 TYR A 369 ARG 0.006 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00672 ( 52) link_NAG-ASN : angle 3.70412 ( 156) link_ALPHA1-4 : bond 0.01658 ( 6) link_ALPHA1-4 : angle 2.84245 ( 18) link_BETA1-4 : bond 0.00435 ( 28) link_BETA1-4 : angle 1.25011 ( 84) hydrogen bonds : bond 0.05174 ( 865) hydrogen bonds : angle 5.58964 ( 2448) link_BETA1-6 : bond 0.00988 ( 3) link_BETA1-6 : angle 1.39128 ( 9) SS BOND : bond 0.00430 ( 42) SS BOND : angle 1.66549 ( 84) covalent geometry : bond 0.00274 (27073) covalent geometry : angle 0.64212 (36814) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 163 time to evaluate : 7.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 904 TYR cc_start: 0.7475 (m-80) cc_final: 0.7183 (m-80) REVERT: A 1115 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8124 (mt) REVERT: B 203 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8396 (mt) REVERT: B 258 TRP cc_start: -0.2215 (t60) cc_final: -0.3409 (t60) REVERT: B 266 TYR cc_start: 0.8677 (m-80) cc_final: 0.8096 (m-80) REVERT: B 663 ASP cc_start: 0.7658 (m-30) cc_final: 0.7421 (m-30) REVERT: B 973 ILE cc_start: 0.8992 (mm) cc_final: 0.8791 (mm) REVERT: B 1115 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7966 (mt) REVERT: C 41 LYS cc_start: 0.7838 (tptm) cc_final: 0.7597 (tptp) REVERT: C 90 VAL cc_start: 0.8940 (t) cc_final: 0.8389 (m) REVERT: C 204 TYR cc_start: 0.7222 (m-80) cc_final: 0.6982 (m-80) REVERT: C 229 LEU cc_start: 0.8094 (mm) cc_final: 0.7861 (mp) REVERT: C 354 ASN cc_start: 0.7595 (t0) cc_final: 0.7082 (t0) REVERT: C 965 GLN cc_start: 0.8767 (tp40) cc_final: 0.8553 (tm-30) outliers start: 46 outliers final: 38 residues processed: 204 average time/residue: 0.4979 time to fit residues: 175.9544 Evaluate side-chains 189 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 148 time to evaluate : 3.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 959 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 284 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 chunk 240 optimal weight: 0.9990 chunk 157 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 225 optimal weight: 5.9990 chunk 308 optimal weight: 3.9990 chunk 280 optimal weight: 2.9990 chunk 175 optimal weight: 0.3980 chunk 300 optimal weight: 4.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.149845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.112563 restraints weight = 62230.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.111373 restraints weight = 48614.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.111751 restraints weight = 55422.669| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.5857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27204 Z= 0.164 Angle : 0.709 13.451 37165 Z= 0.338 Chirality : 0.047 0.457 4416 Planarity : 0.005 0.077 4640 Dihedral : 7.393 87.029 5343 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.58 % Favored : 94.39 % Rotamer: Outliers : 1.77 % Allowed : 19.17 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.30 (0.14), residues: 3189 helix: 0.97 (0.20), residues: 713 sheet: -0.58 (0.20), residues: 646 loop : -1.80 (0.13), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 64 HIS 0.010 0.001 HIS B1083 PHE 0.030 0.002 PHE B 456 TYR 0.022 0.001 TYR C 873 ARG 0.011 0.001 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00605 ( 52) link_NAG-ASN : angle 3.72350 ( 156) link_ALPHA1-4 : bond 0.01669 ( 6) link_ALPHA1-4 : angle 3.14484 ( 18) link_BETA1-4 : bond 0.00365 ( 28) link_BETA1-4 : angle 1.29932 ( 84) hydrogen bonds : bond 0.05431 ( 865) hydrogen bonds : angle 5.60326 ( 2448) link_BETA1-6 : bond 0.00889 ( 3) link_BETA1-6 : angle 1.40295 ( 9) SS BOND : bond 0.00366 ( 42) SS BOND : angle 1.73900 ( 84) covalent geometry : bond 0.00378 (27073) covalent geometry : angle 0.65772 (36814) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8296.60 seconds wall clock time: 149 minutes 32.37 seconds (8972.37 seconds total)