Starting phenix.real_space_refine on Mon Jun 23 13:28:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sbl_24982/06_2025/7sbl_24982_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sbl_24982/06_2025/7sbl_24982.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sbl_24982/06_2025/7sbl_24982.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sbl_24982/06_2025/7sbl_24982.map" model { file = "/net/cci-nas-00/data/ceres_data/7sbl_24982/06_2025/7sbl_24982_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sbl_24982/06_2025/7sbl_24982_neut.cif" } resolution = 3.4 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= 0.003 sd= 0.044 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 117 5.16 5 C 17157 2.51 5 N 4385 2.21 5 O 5367 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 27026 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 8615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1102, 8615 Classifications: {'peptide': 1102} Link IDs: {'PTRANS': 52, 'TRANS': 1049} Chain breaks: 4 Chain: "B" Number of atoms: 8472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1081, 8472 Classifications: {'peptide': 1081} Link IDs: {'PTRANS': 52, 'TRANS': 1028} Chain breaks: 5 Chain: "C" Number of atoms: 8637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 8637 Classifications: {'peptide': 1103} Link IDs: {'PTRANS': 53, 'TRANS': 1049} Chain breaks: 4 Chain: "D" 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: "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: 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: "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: 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: "R" 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: "S" 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 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: "c" 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: "d" 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 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: 21.41, per 1000 atoms: 0.79 Number of scatterers: 27026 At special positions: 0 Unit cell: (146.037, 142.737, 216.168, 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 117 16.00 O 5367 8.00 N 4385 7.00 C 17157 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.06 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.05 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.02 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.05 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 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=2.04 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=2.05 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.06 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.01 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=2.02 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.05 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.06 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.00 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 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=2.05 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.05 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=2.01 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 D 2 " - " MAN D 3 " " NAG J 2 " - " MAN J 3 " " NAG K 2 " - " MAN K 3 " " NAG L 2 " - " MAN L 3 " " NAG R 2 " - " MAN R 3 " " NAG S 2 " - " MAN S 3 " " NAG T 2 " - " MAN T 3 " " NAG c 2 " - " MAN c 3 " " NAG d 2 " - " MAN d 3 " " NAG e 2 " - " MAN e 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 W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG 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 Q 1 " - " FUC Q 3 " " NAG b 1 " - " FUC b 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 149 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 603 " " NAG A1407 " - " ASN A 657 " " NAG A1408 " - " ASN A 709 " " NAG A1409 " - " ASN A1158 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 149 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 331 " " 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 165 " " NAG E 1 " - " ASN A 331 " " 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 A 343 " " NAG M 1 " - " ASN B 282 " " NAG N 1 " - " ASN B 616 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN B1074 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN B 343 " " NAG U 1 " - " ASN B 165 " " NAG V 1 " - " ASN C 717 " " NAG W 1 " - " ASN C 122 " " NAG X 1 " - " ASN C 234 " " NAG Y 1 " - " ASN C 282 " " NAG Z 1 " - " ASN C 616 " " NAG a 1 " - " ASN C 801 " " NAG b 1 " - " ASN C1074 " " NAG c 1 " - " ASN C1098 " " NAG d 1 " - " ASN C1134 " " NAG e 1 " - " ASN C 343 " " NAG f 1 " - " ASN C 165 " Time building additional restraints: 9.20 Conformation dependent library (CDL) restraints added in 3.9 seconds 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6150 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 46 sheets defined 27.6% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.33 Creating SS restraints... Processing helix chain 'A' and resid 180 through 185 removed outlier: 4.429A pdb=" N ASN A 185 " --> pdb=" O GLY A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.602A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 removed outlier: 3.879A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 411 removed outlier: 3.642A pdb=" N ILE A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA A 411 " --> pdb=" O VAL A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 411' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 619 through 623 Processing helix chain 'A' and resid 737 through 744 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: 4.023A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.509A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.624A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 848 Processing helix chain 'A' and resid 848 through 856 removed outlier: 3.909A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.652A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 889 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.590A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.930A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 987 through 1033 removed outlier: 4.278A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1161 removed outlier: 4.127A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER A1161 " --> pdb=" O LYS A1157 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.139A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.376A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.017A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.503A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 633 through 638 removed outlier: 3.784A pdb=" N TYR B 636 " --> pdb=" O TRP B 633 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER B 637 " --> pdb=" O ARG B 634 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR B 638 " --> pdb=" O VAL B 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 633 through 638' Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.875A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.089A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.630A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.537A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.127A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1159 removed outlier: 3.884A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B1152 " --> pdb=" O PHE B1148 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.526A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.025A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.032A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.726A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (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 616 through 620 Processing helix chain 'C' and resid 634 through 639 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 removed outlier: 4.015A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.465A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.544A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.694A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (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: 3.505A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.529A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.898A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1161 removed outlier: 4.260A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU C1152 " --> pdb=" O PHE C1148 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N TYR C1155 " --> pdb=" O GLU C1151 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER C1161 " --> pdb=" O LYS C1157 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.858A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.086A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.640A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.668A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.948A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.834A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.144A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.487A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.551A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.846A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.584A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.584A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.182A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790 removed outlier: 6.133A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.658A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 49 Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 49 removed outlier: 7.472A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.480A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.299A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.169A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.974A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.875A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.568A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.498A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 715 removed outlier: 4.083A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.907A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.254A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 5.484A pdb=" N VAL B1122 " --> pdb=" O PHE B1089 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N PHE B1089 " --> pdb=" O VAL B1122 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N GLY B1124 " --> pdb=" O ALA B1087 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 27 through 31 removed outlier: 8.915A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.988A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.167A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.456A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.985A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.183A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.507A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.550A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.236A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.615A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1092 hydrogen bonds defined for protein. 2973 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: 16.22 Time building geometry restraints manager: 10.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5129 1.32 - 1.45: 7299 1.45 - 1.58: 15042 1.58 - 1.71: 2 1.71 - 1.84: 147 Bond restraints: 27619 Sorted by residual: bond pdb=" CA ASN A 81 " pdb=" C ASN A 81 " ideal model delta sigma weight residual 1.524 1.586 -0.062 1.26e-02 6.30e+03 2.44e+01 bond pdb=" CA PRO A 25 " pdb=" C PRO A 25 " ideal model delta sigma weight residual 1.517 1.550 -0.033 6.70e-03 2.23e+04 2.43e+01 bond pdb=" C5 NAG S 1 " pdb=" O5 NAG S 1 " ideal model delta sigma weight residual 1.413 1.508 -0.095 2.00e-02 2.50e+03 2.28e+01 bond pdb=" C5 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.413 1.508 -0.095 2.00e-02 2.50e+03 2.27e+01 bond pdb=" C5 NAG A1409 " pdb=" O5 NAG A1409 " ideal model delta sigma weight residual 1.413 1.501 -0.088 2.00e-02 2.50e+03 1.94e+01 ... (remaining 27614 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 31397 2.56 - 5.11: 5722 5.11 - 7.67: 404 7.67 - 10.23: 31 10.23 - 12.78: 8 Bond angle restraints: 37562 Sorted by residual: angle pdb=" N ASN A 17 " pdb=" CA ASN A 17 " pdb=" C ASN A 17 " ideal model delta sigma weight residual 110.24 122.99 -12.75 1.41e+00 5.03e-01 8.18e+01 angle pdb=" N ASN C 17 " pdb=" CA ASN C 17 " pdb=" C ASN C 17 " ideal model delta sigma weight residual 110.23 123.01 -12.78 1.45e+00 4.76e-01 7.77e+01 angle pdb=" N ASN B 17 " pdb=" CA ASN B 17 " pdb=" C ASN B 17 " ideal model delta sigma weight residual 110.23 122.93 -12.70 1.45e+00 4.76e-01 7.67e+01 angle pdb=" N VAL A 143 " pdb=" CA VAL A 143 " pdb=" C VAL A 143 " ideal model delta sigma weight residual 108.89 98.80 10.09 1.32e+00 5.74e-01 5.84e+01 angle pdb=" N ARG A 19 " pdb=" CA ARG A 19 " pdb=" C ARG A 19 " ideal model delta sigma weight residual 110.68 100.07 10.61 1.39e+00 5.18e-01 5.83e+01 ... (remaining 37557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.23: 16937 25.23 - 50.46: 565 50.46 - 75.69: 128 75.69 - 100.92: 31 100.92 - 126.15: 34 Dihedral angle restraints: 17695 sinusoidal: 8130 harmonic: 9565 Sorted by residual: dihedral pdb=" CB CYS A 840 " pdb=" SG CYS A 840 " pdb=" SG CYS A 851 " pdb=" CB CYS A 851 " ideal model delta sinusoidal sigma weight residual -86.00 -154.93 68.93 1 1.00e+01 1.00e-02 6.15e+01 dihedral pdb=" C ASN A 603 " pdb=" N ASN A 603 " pdb=" CA ASN A 603 " pdb=" CB ASN A 603 " ideal model delta harmonic sigma weight residual -122.60 -141.47 18.87 0 2.50e+00 1.60e-01 5.70e+01 dihedral pdb=" N ASN A 603 " pdb=" C ASN A 603 " pdb=" CA ASN A 603 " pdb=" CB ASN A 603 " ideal model delta harmonic sigma weight residual 122.80 140.63 -17.83 0 2.50e+00 1.60e-01 5.09e+01 ... (remaining 17692 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.339: 4467 0.339 - 0.678: 32 0.678 - 1.016: 10 1.016 - 1.355: 6 1.355 - 1.694: 3 Chirality restraints: 4518 Sorted by residual: chirality pdb=" C1 NAG f 2 " pdb=" O4 NAG f 1 " pdb=" C2 NAG f 2 " pdb=" O5 NAG f 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.44e+02 chirality pdb=" C1 NAG e 2 " pdb=" O4 NAG e 1 " pdb=" C2 NAG e 2 " pdb=" O5 NAG e 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.05e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.33e+01 ... (remaining 4515 not shown) Planarity restraints: 4785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 343 " -0.181 2.00e-02 2.50e+03 1.96e-01 4.78e+02 pdb=" CG ASN B 343 " 0.114 2.00e-02 2.50e+03 pdb=" OD1 ASN B 343 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN B 343 " 0.300 2.00e-02 2.50e+03 pdb=" C1 NAG T 1 " -0.235 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " 0.181 2.00e-02 2.50e+03 1.95e-01 4.78e+02 pdb=" CG ASN A 343 " -0.114 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " -0.300 2.00e-02 2.50e+03 pdb=" C1 NAG L 1 " 0.235 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 165 " -0.101 2.00e-02 2.50e+03 1.37e-01 2.36e+02 pdb=" CG ASN B 165 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN B 165 " -0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN B 165 " 0.237 2.00e-02 2.50e+03 pdb=" C1 NAG U 1 " -0.160 2.00e-02 2.50e+03 ... (remaining 4782 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1027 2.74 - 3.28: 27152 3.28 - 3.82: 40951 3.82 - 4.36: 54890 4.36 - 4.90: 88246 Nonbonded interactions: 212266 Sorted by model distance: nonbonded pdb=" N GLN A 23 " pdb=" OE1 GLN A 23 " model vdw 2.197 3.120 nonbonded pdb=" N GLU B 281 " pdb=" OE1 GLU B 281 " model vdw 2.210 3.120 nonbonded pdb=" N GLU A 154 " pdb=" OE1 GLU A 154 " model vdw 2.220 3.120 nonbonded pdb=" CB GLN C 173 " pdb=" CD PRO C 174 " model vdw 2.238 3.840 nonbonded pdb=" CG2 THR C 33 " pdb=" CE1 PHE C 58 " model vdw 2.255 3.760 ... (remaining 212261 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 828 or resid 854 through 1162 or resid 1401 thr \ ough 1407)) selection = (chain 'B' and (resid 14 through 623 or resid 636 through 1162 or resid 1401 thr \ ough 1407)) selection = (chain 'C' and (resid 14 through 623 or resid 636 through 828 or resid 854 throu \ gh 1162 or resid 1401 through 1407)) } ncs_group { reference = (chain 'D' and resid 1 through 2) selection = (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 'L' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'b' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 55.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.050 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 80.320 Find NCS groups from input model: 2.780 Set up NCS constraints: 0.180 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: 0.020 Load rotamer database and sin/cos tables:3.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 144.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 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 : 0.014 0.095 27758 Z= 0.810 Angle : 2.020 43.792 37936 Z= 1.256 Chirality : 0.132 1.694 4518 Planarity : 0.013 0.124 4731 Dihedral : 14.917 126.149 11416 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.74 % Allowed : 7.81 % Favored : 91.46 % Rotamer: Outliers : 2.72 % Allowed : 4.43 % Favored : 92.84 % Cbeta Deviations : 0.62 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.13), residues: 3254 helix: -1.41 (0.16), residues: 736 sheet: 0.31 (0.21), residues: 580 loop : -1.78 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.122 0.021 TRP C 353 HIS 0.017 0.006 HIS C1083 PHE 0.107 0.015 PHE C 898 TYR 0.120 0.020 TYR C 489 ARG 0.013 0.001 ARG B 21 Details of bonding type rmsd link_NAG-ASN : bond 0.01662 ( 54) link_NAG-ASN : angle 11.16034 ( 162) link_ALPHA1-4 : bond 0.03024 ( 10) link_ALPHA1-4 : angle 4.66332 ( 30) link_BETA1-4 : bond 0.02030 ( 29) link_BETA1-4 : angle 3.80412 ( 87) hydrogen bonds : bond 0.18073 ( 1083) hydrogen bonds : angle 8.88679 ( 2973) link_BETA1-6 : bond 0.02603 ( 3) link_BETA1-6 : angle 2.45408 ( 9) SS BOND : bond 0.01350 ( 43) SS BOND : angle 2.05840 ( 86) covalent geometry : bond 0.01433 (27619) covalent geometry : angle 1.87619 (37562) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1065 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 987 time to evaluate : 2.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 VAL cc_start: 0.8848 (t) cc_final: 0.8557 (m) REVERT: A 114 THR cc_start: 0.7769 (p) cc_final: 0.7529 (p) REVERT: A 271 GLN cc_start: 0.7640 (mt0) cc_final: 0.7094 (mt0) REVERT: A 320 VAL cc_start: 0.9002 (t) cc_final: 0.8705 (m) REVERT: A 362 VAL cc_start: 0.7352 (t) cc_final: 0.6906 (t) REVERT: A 505 TYR cc_start: 0.5791 (t80) cc_final: 0.5577 (t80) REVERT: A 533 LEU cc_start: 0.8657 (tp) cc_final: 0.8268 (tt) REVERT: A 571 ASP cc_start: 0.7577 (t0) cc_final: 0.7242 (t0) REVERT: A 697 MET cc_start: 0.8406 (ptm) cc_final: 0.8142 (ptm) REVERT: A 737 ASP cc_start: 0.8018 (t0) cc_final: 0.7527 (t0) REVERT: A 740 MET cc_start: 0.8777 (ttt) cc_final: 0.8566 (ttm) REVERT: A 745 ASP cc_start: 0.7173 (m-30) cc_final: 0.6745 (m-30) REVERT: A 818 ILE cc_start: 0.9295 (mt) cc_final: 0.9054 (mt) REVERT: A 904 TYR cc_start: 0.7788 (m-80) cc_final: 0.7450 (m-80) REVERT: A 985 ASP cc_start: 0.7406 (p0) cc_final: 0.6998 (p0) REVERT: B 62 VAL cc_start: 0.8650 (m) cc_final: 0.8446 (t) REVERT: B 96 GLU cc_start: 0.5674 (OUTLIER) cc_final: 0.5206 (tp30) REVERT: B 128 ILE cc_start: 0.8248 (mt) cc_final: 0.7970 (mm) REVERT: B 178 ASP cc_start: 0.5843 (OUTLIER) cc_final: 0.4588 (m-30) REVERT: B 274 THR cc_start: 0.8850 (m) cc_final: 0.8141 (m) REVERT: B 329 PHE cc_start: 0.7814 (m-10) cc_final: 0.7557 (m-80) REVERT: B 396 TYR cc_start: 0.7707 (m-80) cc_final: 0.6898 (m-80) REVERT: B 696 THR cc_start: 0.9149 (m) cc_final: 0.8888 (p) REVERT: B 697 MET cc_start: 0.8427 (ptm) cc_final: 0.8089 (ptp) REVERT: B 808 ASP cc_start: 0.7841 (t0) cc_final: 0.7197 (t70) REVERT: B 824 ASN cc_start: 0.8664 (m-40) cc_final: 0.8442 (m-40) REVERT: B 976 VAL cc_start: 0.8993 (t) cc_final: 0.8451 (p) REVERT: B 979 ASP cc_start: 0.7563 (m-30) cc_final: 0.6971 (m-30) REVERT: C 46 SER cc_start: 0.9077 (m) cc_final: 0.8811 (p) REVERT: C 117 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.7021 (pp) REVERT: C 154 GLU cc_start: 0.5639 (OUTLIER) cc_final: 0.4950 (mp0) REVERT: C 179 LEU cc_start: 0.6238 (OUTLIER) cc_final: 0.5702 (tp) REVERT: C 186 PHE cc_start: 0.6022 (OUTLIER) cc_final: 0.5620 (m-80) REVERT: C 265 TYR cc_start: 0.6364 (p90) cc_final: 0.6100 (p90) REVERT: C 306 PHE cc_start: 0.8049 (m-80) cc_final: 0.7454 (m-80) REVERT: C 314 GLN cc_start: 0.8090 (tp40) cc_final: 0.7817 (tp40) REVERT: C 569 ILE cc_start: 0.8419 (mm) cc_final: 0.8018 (mt) REVERT: C 633 TRP cc_start: 0.7924 (p-90) cc_final: 0.7649 (p-90) REVERT: C 737 ASP cc_start: 0.8305 (t0) cc_final: 0.8069 (t0) REVERT: C 913 GLN cc_start: 0.8033 (pt0) cc_final: 0.7820 (pt0) REVERT: C 994 ASP cc_start: 0.7583 (t70) cc_final: 0.6941 (t0) REVERT: C 1023 ASN cc_start: 0.8182 (m-40) cc_final: 0.7883 (m110) outliers start: 78 outliers final: 22 residues processed: 1027 average time/residue: 0.5632 time to fit residues: 886.1306 Evaluate side-chains 747 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 719 time to evaluate : 3.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 515 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 276 optimal weight: 4.9990 chunk 248 optimal weight: 0.9990 chunk 137 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 167 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 257 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 156 optimal weight: 0.9990 chunk 191 optimal weight: 0.1980 chunk 297 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN A 658 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN B 125 ASN B 207 HIS B 211 ASN B 271 GLN B 437 ASN B 544 ASN B 563 GLN B 784 GLN B 856 ASN B 960 ASN B 965 GLN B1011 GLN C 125 ASN C 196 ASN C 271 GLN C 314 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C 919 ASN C 955 ASN C 957 GLN C 969 ASN C1119 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.098721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.078448 restraints weight = 68436.178| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 3.90 r_work: 0.3081 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 27758 Z= 0.189 Angle : 0.891 21.641 37936 Z= 0.434 Chirality : 0.052 0.512 4518 Planarity : 0.005 0.068 4731 Dihedral : 11.749 104.919 5561 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.01 % Favored : 94.90 % Rotamer: Outliers : 4.05 % Allowed : 12.43 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.14), residues: 3254 helix: 0.66 (0.19), residues: 760 sheet: 0.19 (0.19), residues: 682 loop : -1.59 (0.13), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 436 HIS 0.012 0.001 HIS B 207 PHE 0.037 0.002 PHE A 175 TYR 0.031 0.002 TYR C 904 ARG 0.008 0.001 ARG B 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00681 ( 54) link_NAG-ASN : angle 4.76862 ( 162) link_ALPHA1-4 : bond 0.01543 ( 10) link_ALPHA1-4 : angle 3.58463 ( 30) link_BETA1-4 : bond 0.00387 ( 29) link_BETA1-4 : angle 1.93836 ( 87) hydrogen bonds : bond 0.05049 ( 1083) hydrogen bonds : angle 6.61023 ( 2973) link_BETA1-6 : bond 0.01466 ( 3) link_BETA1-6 : angle 1.95629 ( 9) SS BOND : bond 0.00358 ( 43) SS BOND : angle 2.05223 ( 86) covalent geometry : bond 0.00421 (27619) covalent geometry : angle 0.82072 (37562) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 835 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 719 time to evaluate : 3.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.8569 (m) cc_final: 0.8150 (p) REVERT: A 80 ASP cc_start: 0.6932 (OUTLIER) cc_final: 0.5708 (m-30) REVERT: A 115 GLN cc_start: 0.8285 (mp10) cc_final: 0.8021 (mm-40) REVERT: A 138 ASP cc_start: 0.8657 (t0) cc_final: 0.8023 (p0) REVERT: A 140 PHE cc_start: 0.8289 (p90) cc_final: 0.8071 (p90) REVERT: A 214 ARG cc_start: 0.6661 (ttt90) cc_final: 0.6383 (ttt90) REVERT: A 224 GLU cc_start: 0.8165 (mp0) cc_final: 0.7958 (mp0) REVERT: A 319 ARG cc_start: 0.8756 (ptm-80) cc_final: 0.8476 (ptm160) REVERT: A 320 VAL cc_start: 0.9081 (t) cc_final: 0.8587 (m) REVERT: A 340 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8181 (mp0) REVERT: A 374 PHE cc_start: 0.7753 (m-80) cc_final: 0.7516 (m-80) REVERT: A 384 PRO cc_start: 0.8485 (Cg_endo) cc_final: 0.8160 (Cg_exo) REVERT: A 451 TYR cc_start: 0.7306 (m-80) cc_final: 0.6800 (m-80) REVERT: A 571 ASP cc_start: 0.8168 (t0) cc_final: 0.7741 (t0) REVERT: A 586 ASP cc_start: 0.8158 (m-30) cc_final: 0.7912 (m-30) REVERT: A 590 CYS cc_start: 0.7289 (OUTLIER) cc_final: 0.6976 (p) REVERT: A 591 SER cc_start: 0.8998 (t) cc_final: 0.8317 (p) REVERT: A 619 GLU cc_start: 0.8397 (mp0) cc_final: 0.8088 (mp0) REVERT: A 661 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7604 (tm-30) REVERT: A 697 MET cc_start: 0.8628 (ptm) cc_final: 0.8246 (ptm) REVERT: A 737 ASP cc_start: 0.8196 (t0) cc_final: 0.7983 (t0) REVERT: A 763 LEU cc_start: 0.9155 (mt) cc_final: 0.8927 (mp) REVERT: A 764 ASN cc_start: 0.8800 (m-40) cc_final: 0.8512 (m110) REVERT: A 819 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8190 (mt-10) REVERT: A 957 GLN cc_start: 0.8794 (tt0) cc_final: 0.8519 (tt0) REVERT: A 985 ASP cc_start: 0.8330 (p0) cc_final: 0.7945 (p0) REVERT: A 986 LYS cc_start: 0.9080 (tptt) cc_final: 0.8822 (tptp) REVERT: A 988 GLU cc_start: 0.8506 (tp30) cc_final: 0.8265 (tp30) REVERT: A 1037 SER cc_start: 0.9244 (t) cc_final: 0.8698 (p) REVERT: A 1119 ASN cc_start: 0.8613 (m-40) cc_final: 0.8392 (m-40) REVERT: B 90 VAL cc_start: 0.8750 (t) cc_final: 0.8523 (p) REVERT: B 96 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.6618 (tp30) REVERT: B 100 ILE cc_start: 0.8944 (mp) cc_final: 0.8507 (mp) REVERT: B 131 CYS cc_start: 0.2336 (OUTLIER) cc_final: 0.0678 (m) REVERT: B 195 LYS cc_start: 0.8722 (tttt) cc_final: 0.8465 (ttpt) REVERT: B 205 SER cc_start: 0.9207 (p) cc_final: 0.8706 (p) REVERT: B 218 GLN cc_start: 0.8610 (tt0) cc_final: 0.8385 (tt0) REVERT: B 271 GLN cc_start: 0.8792 (mt0) cc_final: 0.8555 (mt0) REVERT: B 290 ASP cc_start: 0.7882 (t0) cc_final: 0.7625 (t0) REVERT: B 319 ARG cc_start: 0.8890 (ttp-110) cc_final: 0.8582 (ttm-80) REVERT: B 353 TRP cc_start: 0.8331 (p-90) cc_final: 0.8078 (p-90) REVERT: B 396 TYR cc_start: 0.8306 (m-80) cc_final: 0.8090 (m-80) REVERT: B 437 ASN cc_start: 0.8146 (OUTLIER) cc_final: 0.7921 (m-40) REVERT: B 461 LEU cc_start: 0.9108 (pp) cc_final: 0.8838 (pp) REVERT: B 517 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7567 (mp) REVERT: B 528 LYS cc_start: 0.8936 (ttmm) cc_final: 0.8733 (ttmm) REVERT: B 651 ILE cc_start: 0.9182 (mt) cc_final: 0.8610 (pt) REVERT: B 696 THR cc_start: 0.9117 (m) cc_final: 0.8812 (p) REVERT: B 697 MET cc_start: 0.8709 (ptm) cc_final: 0.8076 (ptp) REVERT: B 740 MET cc_start: 0.8859 (ttp) cc_final: 0.8552 (ttp) REVERT: B 790 LYS cc_start: 0.8866 (tttt) cc_final: 0.8609 (ttpt) REVERT: B 808 ASP cc_start: 0.8174 (t0) cc_final: 0.7826 (t70) REVERT: B 824 ASN cc_start: 0.9158 (m-40) cc_final: 0.8767 (m-40) REVERT: B 979 ASP cc_start: 0.8307 (m-30) cc_final: 0.8080 (m-30) REVERT: B 1040 VAL cc_start: 0.9339 (m) cc_final: 0.9105 (p) REVERT: B 1111 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7577 (tm-30) REVERT: B 1113 GLN cc_start: 0.8723 (mt0) cc_final: 0.8402 (mt0) REVERT: C 41 LYS cc_start: 0.8758 (mttt) cc_final: 0.8441 (mmmt) REVERT: C 99 ASN cc_start: 0.8450 (t0) cc_final: 0.8230 (t0) REVERT: C 238 PHE cc_start: 0.8509 (p90) cc_final: 0.7922 (p90) REVERT: C 265 TYR cc_start: 0.6891 (p90) cc_final: 0.6420 (p90) REVERT: C 271 GLN cc_start: 0.8888 (mt0) cc_final: 0.8536 (mt0) REVERT: C 278 LYS cc_start: 0.8716 (tttt) cc_final: 0.8425 (ttpt) REVERT: C 313 TYR cc_start: 0.8659 (m-80) cc_final: 0.8268 (m-80) REVERT: C 377 PHE cc_start: 0.8398 (t80) cc_final: 0.7996 (t80) REVERT: C 473 TYR cc_start: 0.8570 (t80) cc_final: 0.8265 (t80) REVERT: C 562 PHE cc_start: 0.8227 (p90) cc_final: 0.7860 (p90) REVERT: C 602 THR cc_start: 0.9295 (m) cc_final: 0.9042 (p) REVERT: C 604 THR cc_start: 0.9030 (m) cc_final: 0.8629 (t) REVERT: C 711 SER cc_start: 0.9212 (t) cc_final: 0.8629 (p) REVERT: C 737 ASP cc_start: 0.8357 (t0) cc_final: 0.8138 (t0) REVERT: C 780 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8598 (mm-30) REVERT: C 790 LYS cc_start: 0.8882 (ttpt) cc_final: 0.8599 (ttmm) REVERT: C 900 MET cc_start: 0.9010 (tpp) cc_final: 0.8701 (mtp) REVERT: C 994 ASP cc_start: 0.8602 (t70) cc_final: 0.8295 (t0) REVERT: C 1041 ASP cc_start: 0.8714 (t0) cc_final: 0.8482 (t0) REVERT: C 1073 LYS cc_start: 0.9080 (mttt) cc_final: 0.8789 (mmmm) REVERT: C 1119 ASN cc_start: 0.8647 (m110) cc_final: 0.8201 (p0) REVERT: C 1148 PHE cc_start: 0.6866 (t80) cc_final: 0.6558 (t80) outliers start: 116 outliers final: 69 residues processed: 788 average time/residue: 0.5301 time to fit residues: 656.0580 Evaluate side-chains 697 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 622 time to evaluate : 6.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 154 optimal weight: 0.0980 chunk 95 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 chunk 321 optimal weight: 0.7980 chunk 268 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 221 optimal weight: 0.0670 chunk 296 optimal weight: 0.9990 overall best weight: 0.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN B 207 HIS B 658 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 317 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C 901 GLN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.097722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.077558 restraints weight = 68992.601| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 3.91 r_work: 0.3068 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 27758 Z= 0.171 Angle : 0.803 18.710 37936 Z= 0.390 Chirality : 0.048 0.400 4518 Planarity : 0.004 0.067 4731 Dihedral : 10.788 102.911 5541 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.44 % Favored : 94.44 % Rotamer: Outliers : 4.22 % Allowed : 14.80 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.14), residues: 3254 helix: 1.17 (0.19), residues: 765 sheet: 0.07 (0.19), residues: 664 loop : -1.50 (0.13), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 436 HIS 0.009 0.001 HIS B 207 PHE 0.034 0.002 PHE A1148 TYR 0.026 0.002 TYR C 904 ARG 0.007 0.001 ARG A 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00452 ( 54) link_NAG-ASN : angle 3.77514 ( 162) link_ALPHA1-4 : bond 0.01672 ( 10) link_ALPHA1-4 : angle 3.49656 ( 30) link_BETA1-4 : bond 0.00309 ( 29) link_BETA1-4 : angle 1.61611 ( 87) hydrogen bonds : bond 0.04570 ( 1083) hydrogen bonds : angle 6.27632 ( 2973) link_BETA1-6 : bond 0.01529 ( 3) link_BETA1-6 : angle 2.13988 ( 9) SS BOND : bond 0.00362 ( 43) SS BOND : angle 2.59877 ( 86) covalent geometry : bond 0.00383 (27619) covalent geometry : angle 0.74669 (37562) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 655 time to evaluate : 2.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.8852 (t0) cc_final: 0.8650 (t0) REVERT: A 53 ASP cc_start: 0.7457 (t0) cc_final: 0.7016 (t70) REVERT: A 63 THR cc_start: 0.8572 (m) cc_final: 0.8155 (p) REVERT: A 80 ASP cc_start: 0.6771 (OUTLIER) cc_final: 0.6119 (m-30) REVERT: A 138 ASP cc_start: 0.8615 (t0) cc_final: 0.7971 (p0) REVERT: A 140 PHE cc_start: 0.8289 (p90) cc_final: 0.8060 (p90) REVERT: A 320 VAL cc_start: 0.9144 (t) cc_final: 0.8665 (m) REVERT: A 340 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8216 (mp0) REVERT: A 374 PHE cc_start: 0.7662 (m-80) cc_final: 0.7396 (m-80) REVERT: A 387 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8841 (mp) REVERT: A 451 TYR cc_start: 0.7334 (m-80) cc_final: 0.6681 (m-80) REVERT: A 586 ASP cc_start: 0.8163 (m-30) cc_final: 0.7852 (m-30) REVERT: A 591 SER cc_start: 0.9091 (t) cc_final: 0.8562 (p) REVERT: A 619 GLU cc_start: 0.8315 (mp0) cc_final: 0.7987 (mp0) REVERT: A 697 MET cc_start: 0.8617 (ptm) cc_final: 0.8185 (ptm) REVERT: A 737 ASP cc_start: 0.8250 (t0) cc_final: 0.7935 (t0) REVERT: A 763 LEU cc_start: 0.9144 (mt) cc_final: 0.8908 (mp) REVERT: A 764 ASN cc_start: 0.8846 (m-40) cc_final: 0.8536 (m110) REVERT: A 819 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8275 (mt-10) REVERT: A 823 PHE cc_start: 0.8497 (m-10) cc_final: 0.8081 (m-10) REVERT: A 957 GLN cc_start: 0.8761 (tt0) cc_final: 0.8557 (tt0) REVERT: A 968 SER cc_start: 0.9265 (m) cc_final: 0.9056 (t) REVERT: A 985 ASP cc_start: 0.8277 (p0) cc_final: 0.7949 (p0) REVERT: A 988 GLU cc_start: 0.8523 (tp30) cc_final: 0.8274 (tp30) REVERT: A 1037 SER cc_start: 0.9274 (t) cc_final: 0.8745 (p) REVERT: A 1101 HIS cc_start: 0.7947 (m170) cc_final: 0.7702 (m90) REVERT: B 90 VAL cc_start: 0.8756 (OUTLIER) cc_final: 0.8509 (p) REVERT: B 96 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.6740 (tp30) REVERT: B 133 PHE cc_start: 0.7204 (m-80) cc_final: 0.6888 (m-80) REVERT: B 154 GLU cc_start: 0.6485 (OUTLIER) cc_final: 0.5217 (mp0) REVERT: B 195 LYS cc_start: 0.8833 (tttt) cc_final: 0.8611 (ttpt) REVERT: B 205 SER cc_start: 0.8983 (p) cc_final: 0.8635 (p) REVERT: B 218 GLN cc_start: 0.8604 (tt0) cc_final: 0.8365 (tt0) REVERT: B 271 GLN cc_start: 0.8788 (mt0) cc_final: 0.8513 (mt0) REVERT: B 290 ASP cc_start: 0.8001 (t0) cc_final: 0.7713 (t0) REVERT: B 303 LEU cc_start: 0.9403 (tp) cc_final: 0.9068 (tp) REVERT: B 304 LYS cc_start: 0.9279 (mmtp) cc_final: 0.9035 (mmmm) REVERT: B 319 ARG cc_start: 0.8855 (ttp-110) cc_final: 0.8535 (ttm-80) REVERT: B 329 PHE cc_start: 0.8580 (m-10) cc_final: 0.8322 (m-80) REVERT: B 353 TRP cc_start: 0.8272 (p-90) cc_final: 0.7741 (p-90) REVERT: B 398 ASP cc_start: 0.8022 (m-30) cc_final: 0.6475 (m-30) REVERT: B 461 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8425 (pp) REVERT: B 517 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7528 (mp) REVERT: B 607 GLN cc_start: 0.8804 (mm-40) cc_final: 0.8546 (mt0) REVERT: B 675 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7487 (mt0) REVERT: B 697 MET cc_start: 0.8685 (ptm) cc_final: 0.8251 (ptm) REVERT: B 762 GLN cc_start: 0.8975 (mt0) cc_final: 0.8586 (mt0) REVERT: B 790 LYS cc_start: 0.8889 (tttt) cc_final: 0.8615 (ttpt) REVERT: B 808 ASP cc_start: 0.8166 (t0) cc_final: 0.7725 (t70) REVERT: B 824 ASN cc_start: 0.9111 (m-40) cc_final: 0.8723 (m-40) REVERT: B 918 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8614 (mt-10) REVERT: B 935 GLN cc_start: 0.8509 (tm-30) cc_final: 0.8169 (tm-30) REVERT: B 979 ASP cc_start: 0.8353 (m-30) cc_final: 0.8081 (m-30) REVERT: B 995 ARG cc_start: 0.8810 (mtt-85) cc_final: 0.8385 (mtt-85) REVERT: B 1111 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7549 (tm-30) REVERT: B 1113 GLN cc_start: 0.8781 (mt0) cc_final: 0.8466 (mt0) REVERT: C 117 LEU cc_start: 0.7345 (pp) cc_final: 0.7025 (pp) REVERT: C 125 ASN cc_start: 0.7737 (m-40) cc_final: 0.7270 (m110) REVERT: C 173 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8050 (mm-40) REVERT: C 238 PHE cc_start: 0.8531 (p90) cc_final: 0.7923 (p90) REVERT: C 271 GLN cc_start: 0.8921 (mt0) cc_final: 0.8486 (mt0) REVERT: C 273 ARG cc_start: 0.8629 (ttm-80) cc_final: 0.8418 (ttm-80) REVERT: C 278 LYS cc_start: 0.8747 (tttt) cc_final: 0.8418 (ttpt) REVERT: C 313 TYR cc_start: 0.8686 (m-80) cc_final: 0.8370 (m-80) REVERT: C 377 PHE cc_start: 0.8413 (t80) cc_final: 0.7731 (t80) REVERT: C 465 GLU cc_start: 0.8083 (tp30) cc_final: 0.7869 (tp30) REVERT: C 516 GLU cc_start: 0.7597 (pt0) cc_final: 0.7318 (pt0) REVERT: C 558 LYS cc_start: 0.9031 (mtmt) cc_final: 0.8795 (mtmm) REVERT: C 582 LEU cc_start: 0.8635 (mt) cc_final: 0.8375 (mt) REVERT: C 584 ILE cc_start: 0.8739 (mm) cc_final: 0.8492 (mm) REVERT: C 602 THR cc_start: 0.9328 (m) cc_final: 0.9122 (p) REVERT: C 604 THR cc_start: 0.9019 (m) cc_final: 0.8606 (t) REVERT: C 654 GLU cc_start: 0.8395 (tp30) cc_final: 0.8089 (tp30) REVERT: C 711 SER cc_start: 0.9241 (t) cc_final: 0.8696 (p) REVERT: C 737 ASP cc_start: 0.8405 (t0) cc_final: 0.8129 (t0) REVERT: C 780 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8463 (mm-30) REVERT: C 790 LYS cc_start: 0.8903 (ttpt) cc_final: 0.8622 (ttmm) REVERT: C 804 GLN cc_start: 0.8827 (mm-40) cc_final: 0.8572 (mm110) REVERT: C 994 ASP cc_start: 0.8648 (t70) cc_final: 0.8187 (t0) REVERT: C 1073 LYS cc_start: 0.9074 (mttt) cc_final: 0.8770 (mmtp) REVERT: C 1092 GLU cc_start: 0.8308 (mp0) cc_final: 0.8080 (mp0) REVERT: C 1119 ASN cc_start: 0.8575 (OUTLIER) cc_final: 0.8138 (p0) outliers start: 121 outliers final: 72 residues processed: 728 average time/residue: 0.3790 time to fit residues: 432.1505 Evaluate side-chains 692 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 611 time to evaluate : 2.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 124 optimal weight: 0.9990 chunk 229 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 234 optimal weight: 0.0670 chunk 117 optimal weight: 0.9980 chunk 298 optimal weight: 0.9990 chunk 264 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 215 optimal weight: 0.9980 chunk 197 optimal weight: 2.9990 overall best weight: 0.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN A 658 ASN A 836 GLN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 388 ASN B 658 ASN C 314 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.097556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.077235 restraints weight = 69371.851| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 3.92 r_work: 0.3054 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27758 Z= 0.166 Angle : 0.770 17.536 37936 Z= 0.370 Chirality : 0.047 0.354 4518 Planarity : 0.004 0.058 4731 Dihedral : 10.159 101.542 5539 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.22 % Favored : 94.68 % Rotamer: Outliers : 4.26 % Allowed : 17.03 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.14), residues: 3254 helix: 1.35 (0.19), residues: 774 sheet: -0.00 (0.19), residues: 664 loop : -1.59 (0.13), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 436 HIS 0.003 0.001 HIS B 519 PHE 0.036 0.002 PHE A1148 TYR 0.035 0.002 TYR A 421 ARG 0.009 0.001 ARG B 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 54) link_NAG-ASN : angle 3.33726 ( 162) link_ALPHA1-4 : bond 0.01678 ( 10) link_ALPHA1-4 : angle 3.47058 ( 30) link_BETA1-4 : bond 0.00323 ( 29) link_BETA1-4 : angle 1.48594 ( 87) hydrogen bonds : bond 0.04205 ( 1083) hydrogen bonds : angle 6.07804 ( 2973) link_BETA1-6 : bond 0.01633 ( 3) link_BETA1-6 : angle 2.36323 ( 9) SS BOND : bond 0.00419 ( 43) SS BOND : angle 2.49208 ( 86) covalent geometry : bond 0.00370 (27619) covalent geometry : angle 0.72177 (37562) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 644 time to evaluate : 3.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.8606 (m) cc_final: 0.8203 (p) REVERT: A 80 ASP cc_start: 0.6789 (OUTLIER) cc_final: 0.6380 (m-30) REVERT: A 138 ASP cc_start: 0.8659 (t0) cc_final: 0.7993 (p0) REVERT: A 140 PHE cc_start: 0.8305 (p90) cc_final: 0.8094 (p90) REVERT: A 294 ASP cc_start: 0.8343 (p0) cc_final: 0.7862 (p0) REVERT: A 297 SER cc_start: 0.9235 (m) cc_final: 0.8726 (p) REVERT: A 320 VAL cc_start: 0.9135 (t) cc_final: 0.8706 (m) REVERT: A 340 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8139 (tm-30) REVERT: A 374 PHE cc_start: 0.7597 (m-80) cc_final: 0.7305 (m-80) REVERT: A 384 PRO cc_start: 0.8566 (Cg_endo) cc_final: 0.8236 (Cg_exo) REVERT: A 387 LEU cc_start: 0.9106 (mm) cc_final: 0.8872 (mp) REVERT: A 451 TYR cc_start: 0.7329 (m-80) cc_final: 0.6653 (m-80) REVERT: A 586 ASP cc_start: 0.8188 (m-30) cc_final: 0.7809 (m-30) REVERT: A 591 SER cc_start: 0.9071 (t) cc_final: 0.8653 (p) REVERT: A 619 GLU cc_start: 0.8205 (mp0) cc_final: 0.7850 (mp0) REVERT: A 697 MET cc_start: 0.8643 (ptm) cc_final: 0.8249 (ptm) REVERT: A 763 LEU cc_start: 0.9118 (mt) cc_final: 0.8883 (mp) REVERT: A 764 ASN cc_start: 0.8866 (m-40) cc_final: 0.8544 (m110) REVERT: A 780 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8513 (mm-30) REVERT: A 819 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8265 (mt-10) REVERT: A 957 GLN cc_start: 0.8774 (tt0) cc_final: 0.8569 (tt0) REVERT: A 968 SER cc_start: 0.9257 (m) cc_final: 0.8996 (t) REVERT: A 1029 MET cc_start: 0.8955 (tpp) cc_final: 0.8366 (tpp) REVERT: A 1037 SER cc_start: 0.9291 (t) cc_final: 0.8830 (p) REVERT: A 1101 HIS cc_start: 0.8023 (m170) cc_final: 0.7801 (m90) REVERT: A 1119 ASN cc_start: 0.8495 (m-40) cc_final: 0.8237 (p0) REVERT: A 1137 VAL cc_start: 0.9443 (t) cc_final: 0.9182 (p) REVERT: B 90 VAL cc_start: 0.8733 (OUTLIER) cc_final: 0.8470 (p) REVERT: B 96 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6811 (tt0) REVERT: B 102 ARG cc_start: 0.7595 (mmt-90) cc_final: 0.7354 (mmp80) REVERT: B 133 PHE cc_start: 0.7268 (m-80) cc_final: 0.6740 (m-80) REVERT: B 135 PHE cc_start: 0.8142 (m-80) cc_final: 0.7826 (m-80) REVERT: B 153 MET cc_start: 0.7689 (tmm) cc_final: 0.7466 (tmm) REVERT: B 154 GLU cc_start: 0.6665 (OUTLIER) cc_final: 0.5209 (mp0) REVERT: B 190 ARG cc_start: 0.8582 (tpt90) cc_final: 0.8200 (mmm-85) REVERT: B 271 GLN cc_start: 0.8765 (mt0) cc_final: 0.8556 (mt0) REVERT: B 290 ASP cc_start: 0.8036 (t0) cc_final: 0.7746 (t0) REVERT: B 304 LYS cc_start: 0.9330 (mmtp) cc_final: 0.9100 (mmmm) REVERT: B 319 ARG cc_start: 0.8831 (ttp-110) cc_final: 0.8527 (ttm-80) REVERT: B 357 ARG cc_start: 0.8665 (ttp80) cc_final: 0.8411 (tmm-80) REVERT: B 398 ASP cc_start: 0.7978 (m-30) cc_final: 0.7517 (m-30) REVERT: B 399 SER cc_start: 0.8941 (m) cc_final: 0.8717 (p) REVERT: B 607 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8486 (mt0) REVERT: B 695 TYR cc_start: 0.8822 (p90) cc_final: 0.8447 (p90) REVERT: B 697 MET cc_start: 0.8705 (ptm) cc_final: 0.8341 (ptm) REVERT: B 762 GLN cc_start: 0.8953 (mt0) cc_final: 0.8563 (mt0) REVERT: B 790 LYS cc_start: 0.8922 (tttt) cc_final: 0.8666 (ttpt) REVERT: B 808 ASP cc_start: 0.8192 (t0) cc_final: 0.7659 (t70) REVERT: B 824 ASN cc_start: 0.9125 (m-40) cc_final: 0.8745 (m-40) REVERT: B 918 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8645 (mt-10) REVERT: B 935 GLN cc_start: 0.8529 (tm-30) cc_final: 0.8199 (tm-30) REVERT: B 979 ASP cc_start: 0.8346 (m-30) cc_final: 0.8057 (m-30) REVERT: B 995 ARG cc_start: 0.8801 (mtt-85) cc_final: 0.8277 (mtt-85) REVERT: B 1111 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7584 (tm-30) REVERT: B 1113 GLN cc_start: 0.8727 (mt0) cc_final: 0.8414 (mt0) REVERT: C 41 LYS cc_start: 0.8758 (mttt) cc_final: 0.8228 (mttp) REVERT: C 99 ASN cc_start: 0.8258 (t0) cc_final: 0.7947 (t0) REVERT: C 102 ARG cc_start: 0.8116 (mmm160) cc_final: 0.7800 (mmm160) REVERT: C 173 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8142 (mm110) REVERT: C 206 LYS cc_start: 0.8785 (tppt) cc_final: 0.8352 (tptt) REVERT: C 238 PHE cc_start: 0.8548 (p90) cc_final: 0.7989 (p90) REVERT: C 271 GLN cc_start: 0.8992 (mt0) cc_final: 0.8624 (mt0) REVERT: C 273 ARG cc_start: 0.8593 (ttm-80) cc_final: 0.8359 (ttm-80) REVERT: C 278 LYS cc_start: 0.8752 (tttt) cc_final: 0.8395 (ttpt) REVERT: C 377 PHE cc_start: 0.8478 (t80) cc_final: 0.7713 (t80) REVERT: C 465 GLU cc_start: 0.8120 (tp30) cc_final: 0.7884 (tp30) REVERT: C 472 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7720 (tt) REVERT: C 473 TYR cc_start: 0.8585 (t80) cc_final: 0.8378 (t80) REVERT: C 516 GLU cc_start: 0.7690 (pt0) cc_final: 0.7416 (pt0) REVERT: C 604 THR cc_start: 0.9009 (m) cc_final: 0.8568 (t) REVERT: C 619 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7597 (tm-30) REVERT: C 654 GLU cc_start: 0.8536 (tp30) cc_final: 0.8240 (tp30) REVERT: C 711 SER cc_start: 0.9230 (t) cc_final: 0.8710 (p) REVERT: C 737 ASP cc_start: 0.8445 (t0) cc_final: 0.8237 (t0) REVERT: C 780 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8441 (mm-30) REVERT: C 790 LYS cc_start: 0.8942 (ttpt) cc_final: 0.8671 (ttmm) REVERT: C 804 GLN cc_start: 0.8841 (mm-40) cc_final: 0.8583 (mm-40) REVERT: C 994 ASP cc_start: 0.8639 (t70) cc_final: 0.8128 (t0) REVERT: C 1073 LYS cc_start: 0.9050 (mttt) cc_final: 0.8727 (mmtp) REVERT: C 1092 GLU cc_start: 0.8360 (mp0) cc_final: 0.8119 (mp0) REVERT: C 1119 ASN cc_start: 0.8540 (OUTLIER) cc_final: 0.8156 (p0) outliers start: 122 outliers final: 82 residues processed: 719 average time/residue: 0.3920 time to fit residues: 442.5243 Evaluate side-chains 693 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 604 time to evaluate : 3.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1146 ASP Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 39 optimal weight: 4.9990 chunk 156 optimal weight: 5.9990 chunk 305 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 325 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 254 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 230 optimal weight: 3.9990 chunk 275 optimal weight: 2.9990 chunk 218 optimal weight: 9.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN A 658 ASN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A 957 GLN A1011 GLN B 388 ASN B 474 GLN B 658 ASN B 784 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1088 HIS C 314 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.093685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.073860 restraints weight = 70217.977| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 3.84 r_work: 0.2988 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 27758 Z= 0.325 Angle : 0.864 18.298 37936 Z= 0.419 Chirality : 0.050 0.338 4518 Planarity : 0.005 0.060 4731 Dihedral : 10.398 106.422 5537 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.21 % Favored : 93.70 % Rotamer: Outliers : 5.24 % Allowed : 17.14 % Favored : 77.63 % 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: -1.07 (0.14), residues: 3254 helix: 1.17 (0.19), residues: 777 sheet: -0.26 (0.18), residues: 665 loop : -1.82 (0.13), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 436 HIS 0.008 0.001 HIS A1083 PHE 0.043 0.002 PHE A1148 TYR 0.044 0.002 TYR A 421 ARG 0.006 0.001 ARG A 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00543 ( 54) link_NAG-ASN : angle 3.42838 ( 162) link_ALPHA1-4 : bond 0.01757 ( 10) link_ALPHA1-4 : angle 3.80881 ( 30) link_BETA1-4 : bond 0.00352 ( 29) link_BETA1-4 : angle 1.63579 ( 87) hydrogen bonds : bond 0.04822 ( 1083) hydrogen bonds : angle 6.14814 ( 2973) link_BETA1-6 : bond 0.01532 ( 3) link_BETA1-6 : angle 2.46119 ( 9) SS BOND : bond 0.00554 ( 43) SS BOND : angle 2.46172 ( 86) covalent geometry : bond 0.00721 (27619) covalent geometry : angle 0.81885 (37562) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 627 time to evaluate : 2.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 GLN cc_start: 0.8723 (mt0) cc_final: 0.8343 (mt0) REVERT: A 320 VAL cc_start: 0.9186 (t) cc_final: 0.8787 (m) REVERT: A 340 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8314 (tm-30) REVERT: A 362 VAL cc_start: 0.7194 (OUTLIER) cc_final: 0.6773 (p) REVERT: A 374 PHE cc_start: 0.7684 (m-80) cc_final: 0.7405 (m-80) REVERT: A 451 TYR cc_start: 0.7329 (m-80) cc_final: 0.6648 (m-80) REVERT: A 464 PHE cc_start: 0.6832 (OUTLIER) cc_final: 0.6616 (p90) REVERT: A 586 ASP cc_start: 0.8262 (m-30) cc_final: 0.7871 (m-30) REVERT: A 591 SER cc_start: 0.9165 (t) cc_final: 0.8844 (p) REVERT: A 619 GLU cc_start: 0.8224 (mp0) cc_final: 0.7705 (mp0) REVERT: A 661 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7694 (tm-30) REVERT: A 697 MET cc_start: 0.8622 (ptm) cc_final: 0.8224 (ptm) REVERT: A 763 LEU cc_start: 0.9176 (mt) cc_final: 0.8959 (mp) REVERT: A 764 ASN cc_start: 0.8917 (m-40) cc_final: 0.8565 (m110) REVERT: A 808 ASP cc_start: 0.8249 (t0) cc_final: 0.8043 (t0) REVERT: A 823 PHE cc_start: 0.8536 (m-80) cc_final: 0.8153 (m-80) REVERT: A 929 SER cc_start: 0.9310 (m) cc_final: 0.8938 (p) REVERT: A 957 GLN cc_start: 0.8754 (tt0) cc_final: 0.8509 (tt0) REVERT: A 1037 SER cc_start: 0.9342 (t) cc_final: 0.8971 (p) REVERT: A 1138 TYR cc_start: 0.8409 (t80) cc_final: 0.8052 (t80) REVERT: B 96 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.6566 (tt0) REVERT: B 102 ARG cc_start: 0.7673 (mmt-90) cc_final: 0.7382 (mmp80) REVERT: B 133 PHE cc_start: 0.7384 (m-80) cc_final: 0.6682 (m-80) REVERT: B 140 PHE cc_start: 0.8345 (p90) cc_final: 0.8034 (p90) REVERT: B 154 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.5626 (mp0) REVERT: B 239 GLN cc_start: 0.8277 (tp40) cc_final: 0.8070 (tp40) REVERT: B 304 LYS cc_start: 0.9343 (mmtp) cc_final: 0.9130 (mmmm) REVERT: B 319 ARG cc_start: 0.8807 (ttp-110) cc_final: 0.8529 (ttm-80) REVERT: B 353 TRP cc_start: 0.8414 (p-90) cc_final: 0.7442 (p-90) REVERT: B 374 PHE cc_start: 0.8143 (m-10) cc_final: 0.7922 (m-10) REVERT: B 398 ASP cc_start: 0.8085 (m-30) cc_final: 0.6189 (m-30) REVERT: B 399 SER cc_start: 0.8921 (m) cc_final: 0.8493 (t) REVERT: B 544 ASN cc_start: 0.9009 (m-40) cc_final: 0.8709 (m110) REVERT: B 697 MET cc_start: 0.8819 (ptm) cc_final: 0.8413 (ptm) REVERT: B 758 SER cc_start: 0.8519 (m) cc_final: 0.8173 (p) REVERT: B 790 LYS cc_start: 0.8935 (tttt) cc_final: 0.8575 (ttpt) REVERT: B 808 ASP cc_start: 0.8170 (t0) cc_final: 0.7771 (t0) REVERT: B 819 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8177 (mm-30) REVERT: B 824 ASN cc_start: 0.9171 (m-40) cc_final: 0.8812 (m-40) REVERT: B 868 GLU cc_start: 0.8576 (mp0) cc_final: 0.8270 (mp0) REVERT: B 918 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8635 (mt-10) REVERT: B 935 GLN cc_start: 0.8550 (tm-30) cc_final: 0.8207 (tm-30) REVERT: B 979 ASP cc_start: 0.8474 (m-30) cc_final: 0.8238 (m-30) REVERT: B 986 LYS cc_start: 0.8344 (mmmm) cc_final: 0.7933 (tppt) REVERT: B 1040 VAL cc_start: 0.9443 (m) cc_final: 0.9191 (p) REVERT: B 1072 GLU cc_start: 0.8779 (pm20) cc_final: 0.8570 (pm20) REVERT: B 1111 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7588 (tm-30) REVERT: B 1113 GLN cc_start: 0.8718 (mt0) cc_final: 0.8408 (mt0) REVERT: C 41 LYS cc_start: 0.8799 (mttt) cc_final: 0.8486 (mttp) REVERT: C 102 ARG cc_start: 0.8215 (mmm160) cc_final: 0.7861 (mmm160) REVERT: C 154 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.6011 (mm-30) REVERT: C 271 GLN cc_start: 0.8974 (mt0) cc_final: 0.8606 (mt0) REVERT: C 273 ARG cc_start: 0.8626 (ttm-80) cc_final: 0.8335 (ttm-80) REVERT: C 278 LYS cc_start: 0.8802 (tttt) cc_final: 0.8524 (ttpt) REVERT: C 287 ASP cc_start: 0.8591 (t0) cc_final: 0.8374 (t0) REVERT: C 321 GLN cc_start: 0.9370 (mm-40) cc_final: 0.9061 (mm110) REVERT: C 472 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.7774 (tt) REVERT: C 516 GLU cc_start: 0.7646 (pt0) cc_final: 0.7344 (pt0) REVERT: C 583 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7818 (tm-30) REVERT: C 654 GLU cc_start: 0.8594 (tp30) cc_final: 0.8325 (tp30) REVERT: C 711 SER cc_start: 0.9233 (t) cc_final: 0.8732 (p) REVERT: C 737 ASP cc_start: 0.8471 (t0) cc_final: 0.8243 (t0) REVERT: C 780 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8506 (mm-30) REVERT: C 790 LYS cc_start: 0.8943 (ttpt) cc_final: 0.8684 (ttmm) REVERT: C 804 GLN cc_start: 0.8975 (mm110) cc_final: 0.8709 (mm110) REVERT: C 819 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8193 (mm-30) REVERT: C 904 TYR cc_start: 0.8642 (m-80) cc_final: 0.8039 (m-10) REVERT: C 1017 GLU cc_start: 0.8604 (tt0) cc_final: 0.8237 (tt0) REVERT: C 1073 LYS cc_start: 0.9068 (mttt) cc_final: 0.8711 (mmtp) REVERT: C 1119 ASN cc_start: 0.8656 (OUTLIER) cc_final: 0.8191 (p0) REVERT: C 1129 VAL cc_start: 0.9341 (t) cc_final: 0.8971 (p) outliers start: 150 outliers final: 103 residues processed: 726 average time/residue: 0.3851 time to fit residues: 439.7739 Evaluate side-chains 707 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 597 time to evaluate : 2.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1146 ASP Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.4649 > 50: distance: 24 - 27: 35.728 distance: 27 - 28: 40.739 distance: 27 - 179: 32.831 distance: 28 - 31: 39.994 distance: 30 - 176: 34.691 distance: 37 - 39: 4.608 distance: 38 - 40: 17.617 distance: 39 - 40: 15.445 distance: 42 - 43: 39.624 distance: 42 - 45: 56.774 distance: 43 - 49: 56.149 distance: 45 - 46: 40.253 distance: 52 - 79: 54.944 distance: 55 - 56: 4.577 distance: 56 - 57: 66.039 distance: 56 - 59: 6.576 distance: 57 - 63: 41.145 distance: 58 - 87: 66.324 distance: 60 - 61: 40.234 distance: 60 - 62: 39.457 distance: 63 - 64: 38.750 distance: 64 - 65: 40.766 distance: 65 - 66: 54.467 distance: 65 - 71: 56.305 distance: 71 - 72: 38.680 distance: 72 - 75: 41.235 distance: 73 - 79: 40.687 distance: 75 - 76: 45.231 distance: 76 - 77: 24.023 distance: 79 - 80: 40.132 distance: 81 - 82: 37.206 distance: 81 - 87: 37.120 distance: 83 - 84: 40.532 distance: 84 - 85: 56.681 distance: 88 - 89: 40.211 distance: 88 - 91: 38.856 distance: 89 - 93: 39.543 distance: 91 - 92: 57.074 distance: 93 - 94: 40.403 distance: 94 - 97: 39.826 distance: 95 - 102: 38.976 distance: 97 - 98: 11.515 distance: 98 - 99: 9.843 distance: 99 - 100: 57.398 distance: 100 - 101: 7.030 distance: 103 - 104: 40.524 distance: 103 - 106: 40.533 distance: 104 - 109: 34.286